Contacts of the strand formed by residues 536 - 551 (chain D) in PDB entry 2C10
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 GLU 536 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532D VAL 4.4 1.4 - - - +
534D GLY* 3.4 2.0 - - - +
535D LEU* 1.3 94.6 - - - +
537D ASN* 1.3 71.9 + - - +
538D TRP* 3.7 21.5 - - + -
591D SER* 4.1 6.6 + - - -
592D ASN* 4.3 2.1 + - + +
671D GLY 3.5 24.7 - - - +
672D LYS* 3.9 6.3 - - - +
673D ASP 4.9 1.4 + - - +
1O NAG 5.3 5.8 - - - -
2O NAG 5.9 1.9 - - - +
5O FUC 4.7 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 537 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530D LEU 3.8 7.6 - - - +
531D ASP* 3.7 6.9 - - - -
532D VAL* 3.0 52.0 + - - +
534D GLY 3.9 1.6 + - - -
535D LEU 3.8 5.9 - - - +
536D GLU* 1.3 92.7 + - - +
538D TRP* 1.3 67.4 + - - +
589D LEU* 4.5 6.0 - - + +
590D ALA 3.2 18.1 + - - +
591D SER* 3.9 0.2 - - - +
669D ILE 3.6 0.3 - - - +
671D GLY 3.1 18.5 + - - -
672D LYS 3.0 21.7 + - - +
674D LEU* 3.5 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536D GLU* 3.7 20.6 - - + -
537D ASN* 1.3 78.2 - - - +
539D VAL* 1.3 65.5 + - - +
540D TRP* 4.1 13.7 - + - +
568D LEU* 3.9 27.1 - - + +
588D TYR 3.7 0.2 - - - +
589D LEU* 3.2 6.6 - - - +
590D ALA 2.8 35.2 + - - +
591D SER 4.0 2.0 - - - +
592D ASN* 3.4 57.9 - - + -
669D ILE 3.9 4.3 - - - -
670D ALA* 3.5 29.1 - - + +
671D GLY* 3.4 24.1 - - - +
1O NAG 4.6 1.6 - - - -
5O FUC 4.4 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538D TRP* 1.3 79.6 - - - +
540D TRP* 1.3 63.9 + - - +
568D LEU* 3.4 10.1 - - - +
569D LEU* 3.0 56.2 + - + +
575D ALA* 4.7 5.8 - - + -
587D LEU* 4.2 15.3 - - + -
588D TYR 3.5 7.2 - - - +
589D LEU* 3.7 18.4 - - + -
634D VAL* 3.8 7.6 - - + -
669D ILE* 3.7 22.0 + - + +
674D LEU* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 540 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538D TRP* 4.3 13.3 - + + +
539D VAL* 1.3 78.6 - - - +
541D ALA* 1.3 61.2 + - - +
542D GLU* 4.1 1.1 - - + -
566D ARG* 3.6 36.6 - - + -
567D LYS 3.8 12.6 - - - -
568D LEU* 3.9 38.4 - - + -
586D TYR 3.7 0.9 - - - +
587D LEU* 3.5 7.8 - - - +
588D TYR* 2.8 78.7 + + + +
590D ALA* 3.6 20.2 - - + +
591D SER 5.2 1.0 + - - -
600D PRO* 4.2 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 541 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539D VAL 4.2 0.2 + - - -
540D TRP* 1.3 72.6 - - - +
542D GLU* 1.3 63.3 + - - +
543D ASP 4.4 0.2 + - - -
565D THR 3.8 0.5 - - - +
566D ARG* 3.3 3.8 - - - -
567D LYS* 2.8 49.5 + - + +
569D LEU* 4.1 23.3 - - + +
584D PRO* 3.8 26.5 - - + -
586D TYR 3.5 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 542 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C ASN* 5.0 0.7 - - - +
685C ILE* 3.8 15.0 - - + +
540D TRP* 4.1 0.4 - - + -
541D ALA* 1.3 80.2 - - - +
543D ASP* 1.3 64.4 + - - +
564D VAL* 4.3 1.2 - - - +
565D THR 3.1 10.3 - - - +
566D ARG* 2.6 46.3 + - + +
584D PRO* 4.0 1.7 - - - +
585D ARG 3.7 1.7 + - - -
586D TYR* 2.8 49.7 + - + +
588D TYR* 2.9 31.1 + - + +
708D TYR* 2.7 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 543 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683C LEU* 4.3 8.5 - - - -
685C ILE* 4.2 4.2 - - - +
542D GLU* 1.3 71.6 - - - +
544D MET* 1.3 72.0 + - - +
564D VAL* 3.4 11.4 - - - +
565D THR* 2.9 36.4 + - - +
583D THR 4.3 1.2 - - - +
584D PRO* 3.3 12.6 - - + +
585D ARG* 2.9 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 544 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C VAL* 5.7 1.1 - - + -
521C THR* 3.8 14.8 - - + -
612C GLY* 4.1 3.8 - - - -
613C GLU* 3.4 57.6 - - + +
683C LEU* 3.9 30.3 - - + -
543D ASP* 1.3 92.7 - - - +
545D VAL* 1.3 66.1 + - - +
546D PHE* 3.6 12.8 - - + -
562D LEU* 3.5 25.8 - - + -
563D GLN 3.2 10.5 - - - +
564D VAL* 5.3 0.4 - - - -
565D THR* 3.5 6.1 + - - +
585D ARG* 4.1 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 545 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C GLU* 4.4 11.0 - - - +
544D MET* 1.3 77.0 - - - +
546D PHE* 1.3 78.1 + - - +
547D VAL* 4.3 11.0 - - + -
561D ARG 3.6 0.2 - - - +
562D LEU* 3.5 5.0 - - - +
563D GLN* 2.8 58.7 + - + +
565D THR* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C ILE* 4.2 13.9 - - + -
383C ARG* 4.9 0.2 - - - -
521C THR* 5.9 1.1 - - + -
613C GLU* 3.4 46.1 + - - +
614C PRO 3.7 8.5 - - - -
615C LEU* 3.6 27.4 - - + -
616C PRO* 3.7 28.3 - - + -
544D MET* 3.6 11.2 - - + -
545D VAL* 1.3 82.0 - - - +
547D VAL* 1.3 65.2 + - - +
548D PRO* 3.6 8.6 - - - +
560D GLN* 3.8 28.3 - - + +
561D ARG 3.4 1.3 - - - -
562D LEU* 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 547 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545D VAL* 4.3 13.0 - - + -
546D PHE* 1.3 76.3 - - - +
548D PRO* 1.4 74.7 - - + +
549D MET* 3.4 24.2 + - + +
560D GLN* 4.6 0.4 - - - -
561D ARG* 2.8 41.2 + - - +
563D GLN* 3.6 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 548 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D PHE 3.6 9.6 - - - +
547D VAL* 1.4 90.3 - - + +
549D MET* 1.3 60.0 + - - +
558D GLN* 3.8 17.7 + - - +
559D LEU 3.5 8.5 - - - +
560D GLN* 4.0 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 549 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C MET* 6.3 0.9 - - + -
507C TYR* 5.4 0.2 - - - +
547D VAL* 3.4 29.1 + - + +
548D PRO* 1.3 74.1 - - - +
550D ALA* 1.3 70.8 - - - +
552D PRO* 6.3 1.3 - - - -
558D GLN* 3.6 10.6 - - - +
559D LEU* 3.0 38.9 + - + +
561D ARG* 3.3 45.5 - - + +
563D GLN* 4.5 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 550 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D MET* 1.3 85.7 - - - +
551D VAL* 1.3 64.1 + - - +
552D PRO* 3.2 11.6 - - - +
555D PRO* 3.9 25.8 - - + +
557D HIS 3.7 7.0 - - - -
558D GLN* 4.0 8.7 + - - +
559D LEU* 4.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 551 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C LEU* 4.1 13.9 - - + -
381C THR* 5.8 0.2 - - + -
549D MET 3.8 0.2 + - - -
550D ALA* 1.3 70.6 - - - +
552D PRO* 1.4 69.9 - - + +
553D TRP* 3.3 51.6 - - + +
554D SER* 2.9 35.1 + - - +
555D PRO* 3.1 4.3 - - - +
557D HIS* 3.2 32.8 + - + +
558D GLN 4.0 9.6 - - - +
559D LEU* 3.8 19.3 - - + -
----------------------------------------------------------
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