Contacts of the helix formed by residues 529 - 559 (chain D) in PDB entry 3A98
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 529 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 4.0 1.5 - - - -
530D SER* 1.3 62.8 + - - +
531D GLY 3.3 0.7 - - - -
532D PRO* 3.1 19.5 - - - +
533D ILE* 2.8 31.8 - - - +
706D ILE* 3.0 40.9 + - - +
707D PRO 3.4 15.8 + - - -
708D ASP* 4.5 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 530 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529D SER* 1.3 69.4 - - - +
531D GLY* 1.3 58.0 + - - +
533D ILE* 3.1 8.3 + - - -
534D LEU* 2.6 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 531 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 4.4 7.8 + - - -
18C ASN* 4.6 1.1 - - - -
529D SER* 3.3 1.2 - - - -
530D SER* 1.3 82.6 + - - +
532D PRO* 1.3 69.5 - - - +
534D LEU* 3.2 9.2 + - - +
535D GLU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 532 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 3.5 41.3 - - + +
18C ASN* 3.6 20.3 - - - +
31C ILE* 3.7 38.2 + - + +
529D SER* 3.1 29.6 - - - +
531D GLY* 1.3 85.1 - - - +
533D ILE* 1.3 56.9 + - - +
535D GLU* 3.1 3.6 + - - +
536D LEU* 2.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 533 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE* 4.5 14.4 - - + -
529D SER 2.8 33.9 - - - +
530D SER* 3.1 9.3 + - - +
532D PRO* 1.3 83.9 - - + +
534D LEU* 1.3 56.1 - - - +
536D LEU* 3.2 8.1 + - + +
537D LYS* 2.8 51.9 + - + +
694D ILE* 3.9 27.6 - - + -
698D LEU* 4.8 12.8 - - + -
706D ILE* 5.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 534 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530D SER* 2.6 24.9 + - - +
531D GLY* 3.4 8.5 - - - +
533D ILE* 1.3 73.3 - - - +
535D GLU* 1.3 71.4 + - - +
537D LYS* 3.4 17.6 + - + +
538D GLU* 3.1 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 535 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ASN* 3.2 33.0 - - + +
20C GLN* 3.3 25.8 + - - +
30C GLN* 4.8 5.6 - - - +
531D GLY* 2.9 22.1 + - - +
532D PRO 3.4 6.1 - - - +
534D LEU* 1.3 86.1 - - - +
536D LEU* 1.3 65.4 + - - +
538D GLU* 3.3 6.8 + - - +
539D LYS* 3.0 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 536 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLN* 3.6 36.9 + - + +
31C ILE* 3.9 23.6 - - + +
532D PRO 2.8 15.7 + - - +
533D ILE* 3.5 7.4 - - - +
535D GLU* 1.3 77.8 - - - +
537D LYS* 1.3 62.4 + - - +
539D LYS* 3.3 4.8 + - - +
540D ILE* 3.0 41.1 + - + +
694D ILE* 4.7 22.9 - - + +
697D ARG* 3.7 42.6 - - + +
698D LEU* 4.9 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 537 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533D ILE* 2.8 34.9 + - + +
534D LEU* 3.6 18.3 - - + +
536D LEU* 1.3 70.1 - - - +
538D GLU* 1.3 57.5 + - - +
541D GLN* 2.6 43.1 + - - +
690D LEU* 4.2 24.9 - - + +
691D SER* 6.2 0.2 - - - -
694D ILE* 3.4 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D LEU* 3.1 10.7 + - + +
535D GLU* 3.3 10.5 + - - +
537D LYS* 1.3 78.7 - - - +
539D LYS* 1.3 60.3 + - + +
541D GLN* 4.6 12.0 + - - +
542D PRO* 3.1 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER* 6.4 0.2 - - - -
30C GLN* 3.1 37.0 - - - +
535D GLU* 3.0 19.6 + - + +
536D LEU 3.5 4.3 - - - +
538D GLU* 1.3 80.7 - - + +
540D ILE* 1.3 62.1 + - + +
542D PRO* 4.0 6.7 - - - +
543D GLU* 5.0 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 540 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLN* 5.8 0.2 - - - +
536D LEU* 3.0 34.9 + - + +
539D LYS* 1.3 81.9 - - + +
541D GLN* 1.3 65.6 + - - +
542D PRO* 3.1 3.6 - - - -
543D GLU* 3.0 40.5 - - + +
544D ILE* 3.4 8.7 - - + +
690D LEU* 3.8 18.2 - - + -
693D GLU* 3.6 37.2 - - + -
694D ILE* 5.3 1.1 - - + +
697D ARG* 4.0 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 541 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D LYS* 2.6 26.9 + - - +
538D GLU* 4.3 13.2 + - - +
540D ILE* 1.3 71.5 - - - +
542D PRO* 1.3 67.7 - - + +
544D ILE* 3.2 10.6 + - - +
545D LEU* 3.1 40.5 + - + +
686D LEU* 4.0 28.4 - - + +
690D LEU* 4.2 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 542 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538D GLU* 3.1 24.5 - - - +
539D LYS 4.0 6.3 - - - +
540D ILE 3.2 5.6 - - - +
541D GLN* 1.3 92.7 - - + +
543D GLU* 1.3 63.3 + - - +
544D ILE 3.3 0.2 + - - -
545D LEU* 3.3 11.0 + - + +
546D GLU* 3.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 543 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LYS* 3.9 19.9 + - - -
539D LYS 5.0 2.8 + - - +
540D ILE* 3.0 44.1 - - + +
542D PRO* 1.3 76.6 - - - +
544D ILE* 1.3 61.5 + - + +
546D GLU* 3.3 8.5 + - - +
547D LEU* 3.0 32.1 + - + +
693D GLU* 4.8 2.9 - - - +
697D ARG* 5.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 544 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LYS* 5.2 2.9 - - - -
540D ILE* 3.4 33.0 - - + +
541D GLN* 3.5 8.5 - - - +
542D PRO 3.2 0.6 - - - -
543D GLU* 1.3 82.9 - - + +
545D LEU* 1.3 60.3 + - - +
547D LEU* 2.9 18.2 + - + +
548D ILE* 2.8 41.4 + - + +
686D LEU* 3.8 22.7 - - + -
689D LEU* 3.7 43.3 - - + +
690D LEU* 4.4 10.5 - - + +
693D GLU* 4.8 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 545 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D GLN* 3.1 35.9 + - + +
542D PRO* 3.3 11.9 + - + +
544D ILE* 1.3 75.3 - - - +
546D GLU* 1.3 52.6 + - - +
548D ILE* 3.2 14.6 + - + +
549D LYS* 2.7 33.5 + - - +
677D MSE 4.8 3.7 - - - +
682D THR* 4.8 10.8 - - + -
686D LEU* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D PRO 3.3 8.8 + - - +
543D GLU* 3.3 10.9 + - - +
544D ILE 3.2 0.4 - - - -
545D LEU* 1.3 75.9 - - - +
547D LEU* 1.3 60.3 + - - +
549D LYS* 3.1 36.0 + - - +
550D GLN* 2.8 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 547 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LYS* 3.8 42.8 - - + -
106C TYR* 3.8 5.1 - - + -
107C VAL* 3.7 27.9 - - + +
543D GLU* 3.0 15.4 + - + +
544D ILE* 2.9 24.6 + - + +
546D GLU* 1.3 78.2 - - - +
548D ILE* 1.3 59.0 + - - +
550D GLN* 3.4 17.1 + - - +
551D GLN* 3.1 21.8 + - - +
689D LEU* 4.4 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 548 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 3.4 31.9 - - + +
544D ILE* 2.8 26.2 + - + +
545D LEU* 3.4 17.3 - - + +
547D LEU* 1.3 75.0 - - - +
549D LYS* 1.3 66.1 + - - +
551D GLN* 3.1 3.3 + - - +
552D ARG* 3.0 52.7 + - + +
677D MSE 4.3 6.7 - - - -
682D THR* 4.0 15.5 - - + +
685D ASP* 4.1 2.0 - - + +
686D LEU* 3.7 38.8 - - + +
689D LEU* 4.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 549 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545D LEU 2.7 18.1 + - - +
546D GLU* 3.3 37.1 + - - +
548D ILE* 1.3 73.7 - - - +
550D GLN* 1.3 63.6 + - - +
552D ARG* 3.2 2.6 + - - +
553D LEU* 3.0 43.1 + - + +
671D ALA* 4.1 34.7 + - + -
677D MSE 4.0 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 550 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C VAL* 3.8 19.6 - - + +
546D GLU* 2.8 47.3 + - - +
547D LEU* 3.6 19.2 - - - +
549D LYS* 1.3 78.0 - - - +
551D GLN* 1.3 57.8 + - - +
553D LEU* 3.3 8.0 + - + +
554D ASN* 2.9 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 551 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 3.4 54.9 + - + +
107C VAL* 3.6 16.4 - - - +
109C SER* 3.6 12.7 + - - +
547D LEU 3.1 6.7 + - - +
548D ILE 3.1 6.9 + - - +
550D GLN* 1.3 76.4 - - - +
552D ARG* 1.3 108.1 + - - +
554D ASN* 3.5 2.3 + - - +
555D ARG* 3.0 54.1 + - - +
660D HIS* 6.0 1.0 + - - -
664D ILE* 4.3 1.8 - - - +
681D LEU* 5.7 0.8 - - - +
685D ASP* 4.7 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 552 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 3.7 1.6 + - - -
548D ILE* 3.0 24.0 + - - +
549D LYS 3.5 2.5 - - - +
551D GLN* 1.3 116.6 + - - +
553D LEU* 1.3 62.8 + - + +
555D ARG* 3.0 7.2 + - - +
556D LEU* 3.0 28.4 + - - +
664D ILE* 3.5 34.2 - - - +
667D ASP* 3.1 20.9 + - - +
668D GLY* 4.2 9.0 - - - -
677D MSE 3.2 26.5 - - + -
681D LEU* 3.6 13.6 - - - +
682D THR* 3.3 35.0 + - - +
685D ASP* 2.9 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 553 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D LYS* 3.0 42.0 + - + +
550D GLN* 3.8 7.0 - - + +
552D ARG* 1.3 77.7 - - - +
554D ASN* 1.3 63.5 + - - +
556D LEU* 2.9 8.1 + - + +
557D VAL* 2.8 27.8 + - - +
579D LEU* 4.2 7.1 - - + +
583D HIS* 3.7 35.7 - - + +
668D GLY* 4.1 25.8 - - - +
671D ALA* 4.8 5.2 - - + -
672D LEU* 4.1 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 554 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C VAL* 2.9 43.9 + - - +
108C ALA* 4.7 4.8 - - - +
550D GLN* 2.9 19.1 + - - +
551D GLN 3.7 4.5 - - - +
553D LEU* 1.3 76.5 - - - +
555D ARG* 1.3 59.0 + - + +
557D VAL* 3.4 8.4 + - - +
558D GLU* 2.9 29.1 + - - +
583D HIS* 5.1 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 555 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C SER* 2.9 38.0 + - - +
111C LYS* 3.9 31.3 - - - +
551D GLN* 3.0 35.4 + - - +
552D ARG 3.0 8.5 + - - +
554D ASN* 1.3 77.5 - - + +
556D LEU* 1.3 58.0 + - - +
558D GLU* 3.2 9.8 + - - +
559D GLY* 2.8 27.4 + - - +
560D THR* 4.6 5.7 - - + +
660D HIS* 4.1 15.9 + - - -
661D GLU* 3.8 20.2 + - - -
664D ILE* 3.5 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 556 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552D ARG 3.0 24.7 + - - +
553D LEU* 2.9 11.7 + - + +
555D ARG* 1.3 74.5 - - - +
557D VAL* 1.3 59.4 + - - +
559D GLY* 2.6 25.5 + - - -
578D ARG* 3.6 1.4 - - - -
579D LEU* 3.1 38.2 + - + -
586D LEU* 5.1 1.1 - - + -
664D ILE* 4.0 30.1 - - + +
665D TRP* 4.0 40.7 - - + -
668D GLY* 4.1 24.5 - - - -
669D LEU* 4.2 6.7 - - + +
672D LEU* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 557 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D LEU 2.8 19.7 + - - +
554D ASN* 3.7 11.2 - - - +
556D LEU* 1.3 72.1 - - - +
558D GLU* 1.3 63.4 + - - +
578D ARG* 3.0 22.9 + - - +
579D LEU* 3.1 24.9 - - + +
580D SER 3.8 3.8 - - - +
581D PRO* 4.3 19.5 - - + -
583D HIS* 3.7 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 558 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554D ASN 2.9 15.0 + - - +
555D ARG* 3.3 12.8 - - - +
557D VAL* 1.3 79.0 - - - +
559D GLY* 1.3 62.8 + - - +
576D TYR* 2.9 19.1 + - - -
578D ARG* 4.1 8.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 559 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D ARG 2.8 6.6 + - - +
556D LEU 2.6 25.2 + - - -
558D GLU* 1.3 78.6 - - - +
560D THR* 1.3 69.6 + - - +
576D TYR* 3.1 19.2 + - - -
577D CYS 3.3 13.2 - - - -
578D ARG* 4.1 2.7 - - - -
665D TRP* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il