Contacts of the helix formed by residues 527 - 554 (chain A) in PDB entry 3L7A
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 ASP 527 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ARG* 5.5 2.1 + - - -
523A SER 5.1 1.7 + - - +
524A TYR* 2.9 48.5 + - + +
526A ASP* 1.3 75.7 - - - +
528A GLU* 1.3 58.9 + - - +
529A ALA* 3.1 23.0 + - - +
530A PHE* 3.2 11.7 + - + +
531A ILE* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ASP 3.4 10.2 + - - +
527A ASP* 1.3 73.7 + - - +
529A ALA* 1.3 62.9 + - - +
531A ILE* 3.7 9.0 + - - +
532A ARG* 3.2 41.7 + - - +
795A ARG* 2.8 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ARG* 4.0 12.6 - - - +
527A ASP* 3.1 10.8 + - - +
528A GLU* 1.3 78.5 - - - +
530A PHE* 1.3 57.2 + - - +
532A ARG* 3.3 18.3 + - - +
533A ASP* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A LEU* 6.0 0.4 - - + -
502A ILE* 3.9 29.6 - - + -
503A ILE* 4.7 5.6 - - + -
506A ARG* 3.6 36.0 - - + +
521A LEU* 3.8 32.1 - - + -
524A TYR* 3.7 20.9 - - + +
527A ASP* 3.2 23.4 + - + +
529A ALA* 1.3 76.1 - - - +
531A ILE* 1.3 60.0 + - - +
533A ASP* 3.0 1.6 + - - +
534A VAL* 2.8 56.0 + - + +
802A ILE* 3.9 31.9 - - + -
805A ILE* 6.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A VAL 3.4 22.7 - - - +
526A ASP 4.2 3.4 - - - -
527A ASP 3.0 26.4 + - - +
528A GLU* 3.9 10.5 - - - +
530A PHE* 1.3 75.1 - - - +
532A ARG* 1.3 63.0 + - - +
534A VAL 3.6 0.2 + - - -
535A ALA* 3.2 21.5 + - + +
795A ARG* 3.6 42.8 - - + +
798A THR* 3.6 23.7 - - + +
799A ARG* 3.8 11.7 - - + -
802A ILE* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A GLU* 3.2 41.6 + - - +
529A ALA* 3.5 16.2 + - - +
531A ILE* 1.3 77.1 - - - +
533A ASP* 1.3 62.7 + - - +
535A ALA* 3.4 5.9 + - - +
536A LYS* 2.9 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ILE* 3.7 23.6 - - + +
505A GLU* 4.7 3.3 - - - +
506A ARG* 2.8 30.4 + - - +
529A ALA* 3.0 14.8 + - - +
530A PHE* 3.0 7.2 + - + +
532A ARG* 1.3 79.7 + - - +
534A VAL* 1.3 65.3 + - - +
536A LYS* 3.3 20.3 + - - +
537A VAL* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A LEU* 4.9 8.7 - - + +
502A ILE* 3.8 13.9 - - + -
530A PHE* 2.8 56.4 + - + +
531A ILE 4.0 3.8 - - - +
533A ASP* 1.3 71.6 - - - +
535A ALA* 1.3 62.7 - - - +
537A VAL* 3.5 3.3 + - - +
538A LYS* 3.3 22.2 + - + +
685A GLY* 6.1 0.2 - - - -
798A THR* 3.9 17.9 - - + -
801A VAL* 4.2 22.2 - - + -
802A ILE* 4.0 8.7 - - + -
805A ILE* 4.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A ILE* 3.2 18.6 + - + +
532A ARG* 3.8 5.4 - - - +
534A VAL* 1.3 74.4 - - - +
536A LYS* 1.3 65.0 + - - +
538A LYS* 3.4 7.1 + - - +
539A GLN* 3.1 22.5 + - - +
798A THR* 3.9 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ILE* 4.6 5.5 - - - +
532A ARG* 2.9 21.7 + - + +
533A ASP* 3.3 34.0 + - - +
535A ALA* 1.3 73.9 - - - +
537A VAL* 1.3 76.8 + - - +
539A GLN* 3.3 7.2 + - + +
540A GLU* 3.0 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ASN* 3.9 2.5 - - - +
498A GLY* 3.8 26.0 - - - +
499A LEU* 3.6 29.4 - - + +
502A ILE* 3.9 12.8 - - + -
533A ASP 3.1 19.5 + - - +
534A VAL 3.8 4.7 - - - +
535A ALA 3.4 0.2 - - - -
536A LYS* 1.3 88.9 - - - +
538A LYS* 1.3 58.7 + - - +
540A GLU* 3.4 13.8 + - - +
541A ASN* 3.0 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 3.3 12.1 + - + +
535A ALA* 3.7 10.3 - - - +
536A LYS 3.3 0.2 - - - -
537A VAL* 1.3 79.4 - - - +
539A GLN* 1.3 57.7 + - - +
541A ASN* 3.2 7.1 + - - +
542A LYS* 2.9 39.0 + - + +
657A ILE 4.1 1.4 + - - -
658A PRO 2.7 29.5 + - - +
659A ALA 4.1 8.5 - - - +
660A ALA 2.8 29.7 + - - +
661A ASP* 3.7 18.2 - - - +
684A ASN 2.9 22.7 + - - -
685A GLY* 3.5 19.5 + - - -
686A ALA 4.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ALA 3.1 15.3 + - - +
536A LYS* 3.7 9.6 - - - +
538A LYS* 1.3 77.0 - - - +
540A GLU* 1.3 57.2 + - + +
542A LYS* 3.3 17.1 + - - +
543A LEU* 2.9 48.2 + - + +
559A PRO* 3.1 29.3 + - - +
560A ASN* 4.2 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A GLY* 5.7 3.1 - - - -
536A LYS* 3.0 46.3 + - + +
537A VAL* 3.6 14.6 - - - +
539A GLN* 1.3 75.6 - - + +
541A ASN* 1.3 60.8 + - - +
543A LEU* 3.3 11.7 + - + +
544A LYS* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A CYS 5.5 1.0 - - - +
496A ASN* 3.1 33.6 + - - +
498A GLY* 5.9 0.7 + - - -
537A VAL* 3.0 30.9 + - - +
538A LYS* 3.6 5.9 - - - +
540A GLU* 1.3 77.4 - - - +
542A LYS* 1.3 58.5 + - - +
544A LYS* 3.5 10.8 + - - +
545A PHE* 3.0 29.5 + - - +
655A LYS 5.3 0.3 - - - +
658A PRO* 3.2 40.2 + - + +
659A ALA* 3.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A LYS* 2.9 34.1 + - + +
539A GLN* 3.6 18.7 + - - +
540A GLU 3.2 0.2 - - - -
541A ASN* 1.3 73.2 - - - +
543A LEU* 1.3 60.2 + - - +
545A PHE* 3.8 1.2 - - - +
546A ALA* 2.8 31.8 + - - +
559A PRO* 3.5 19.6 + - - +
560A ASN 4.7 1.0 - - - -
561A SER 2.9 20.0 + - - -
563A PHE* 3.8 27.0 - - + -
659A ALA* 3.2 25.8 - - - +
661A ASP* 2.7 30.0 + - - +
791A TYR* 3.1 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A GLN* 2.9 40.1 + - + +
540A GLU* 3.3 12.1 + - + +
542A LYS* 1.3 74.3 - - - +
544A LYS* 1.3 66.3 + - - +
546A ALA* 3.4 4.8 + - + +
547A ALA* 3.0 24.3 + - - +
559A PRO* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 4.0 28.5 + - - -
497A PRO* 6.3 1.4 - - - +
540A GLU 2.9 17.4 + - - +
541A ASN* 3.7 11.7 - - - +
543A LEU* 1.3 74.4 - - - +
545A PHE* 1.3 59.6 + - - +
547A ALA* 3.3 7.7 + - - +
548A TYR* 2.9 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ASN 3.0 17.8 + - - +
542A LYS 4.0 2.5 - - - +
544A LYS* 1.3 75.3 - - - +
546A ALA* 1.3 64.4 + - - +
548A TYR* 3.2 22.0 + + + +
549A LEU* 3.1 42.3 + - + +
557A ILE* 4.9 0.2 - - + -
563A PHE* 4.6 7.9 - + - -
604A MET* 3.8 28.0 - - + -
645A LEU* 4.2 15.5 - - + -
652A LEU* 4.3 9.6 - - + -
655A LYS* 3.7 30.3 - - + +
656A VAL* 3.8 31.6 - - + -
659A ALA* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LYS 2.8 19.4 + - - +
543A LEU* 3.7 5.4 - - + +
545A PHE* 1.3 76.8 - - - +
547A ALA* 1.3 60.5 + - - +
549A LEU* 3.6 4.0 + - - +
550A GLU* 3.4 26.8 + - - +
555A VAL 4.5 0.7 - - - +
557A ILE* 3.8 36.2 + - + +
559A PRO* 4.2 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LEU 3.0 13.5 + - - +
544A LYS* 3.5 10.5 - - - +
545A PHE 3.2 0.2 - - - -
546A ALA* 1.3 76.4 - - - +
548A TYR* 1.3 65.2 + - - +
549A LEU 3.2 0.2 - - - -
550A GLU* 3.3 6.8 + - - +
551A ARG* 3.0 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU* 5.1 4.7 - - - -
544A LYS* 2.9 14.7 + - + +
545A PHE* 3.5 28.3 - + + +
547A ALA* 1.3 76.8 - - - +
549A LEU* 1.3 65.4 + - + +
551A ARG* 3.7 19.2 - - - +
552A GLU* 2.9 53.6 + - + +
553A TYR* 3.8 32.9 + + - -
649A ARG* 4.5 12.6 + - - -
652A LEU* 4.1 23.6 - - + +
655A LYS* 3.7 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A PHE* 3.1 37.2 + - + +
546A ALA 3.7 5.4 - - - +
547A ALA 3.2 0.2 - - - -
548A TYR* 1.3 86.1 - - + +
550A GLU* 1.3 56.9 + - - +
553A TYR* 2.8 43.2 + - + +
554A LYS 3.1 4.9 + - - -
555A VAL* 3.5 27.8 - - + +
557A ILE* 3.7 37.0 - - + -
604A MET* 5.0 3.6 - - - -
643A ILE* 5.0 7.6 - - + -
645A LEU* 4.1 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A ALA 3.4 12.0 + - - +
547A ALA* 3.3 10.1 + - - +
549A LEU* 1.3 77.0 - - - +
551A ARG* 1.3 62.4 + - + +
554A LYS* 3.0 34.2 + - - +
555A VAL 3.2 27.4 - - - +
556A HIS* 3.7 35.8 + - + +
557A ILE 4.6 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ALA* 3.0 27.3 + - - +
548A TYR* 3.7 29.6 - - - +
550A GLU* 1.3 79.4 - - + +
552A GLU* 1.3 77.4 + - + +
554A LYS* 4.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A TYR* 2.9 42.4 + - + +
551A ARG* 1.3 97.0 + - + +
553A TYR* 1.3 86.6 + - + +
554A LYS* 5.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A TYR* 3.8 34.2 + + - -
549A LEU* 2.8 22.8 + - + +
552A GLU* 1.3 93.5 - - + +
554A LYS* 1.3 74.3 + - - +
555A VAL* 3.2 22.9 + - + +
646A GLU* 4.0 50.1 + - + +
647A ASN* 5.0 3.5 - - - +
649A ARG* 4.9 8.1 + - - -
652A LEU* 5.7 2.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A LEU 3.1 0.2 + - - -
550A GLU* 3.0 31.2 + - - +
551A ARG* 4.0 15.0 + - - +
552A GLU 5.6 0.4 - - - -
553A TYR* 1.3 81.1 - - - +
555A VAL* 1.3 59.8 + - - +
556A HIS* 4.0 14.5 - - - +
----------------------------------------------------------
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