Contacts of the helix formed by residues 634 - 652 (chain A) in PDB entry 3C4C
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 634 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573A ILE* 4.1 21.3 - - - +
623A GLU* 5.5 0.2 + - - -
631A ASN* 4.0 15.8 + - - -
632A PRO 3.2 9.5 + - - -
633A TYR* 1.3 75.7 - - - +
635A PHE* 1.3 66.2 + - - +
636A GLN* 2.9 38.4 + - - +
637A SER* 2.9 17.2 + - - -
638A ASP* 3.2 11.3 + - - +
701A ARG* 4.6 1.9 + - - -
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Residues in contact with PHE 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A HIS* 3.2 54.4 - + + +
571A SER* 4.0 35.0 - - - -
573A ILE* 3.8 21.5 - - + -
634A SER* 1.3 73.9 - - - +
636A GLN* 1.3 68.7 + - + +
638A ASP* 3.3 6.1 - - - +
639A VAL* 3.1 27.3 + - + +
706A SER* 5.9 9.6 - - - -
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Residues in contact with GLN 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A GLU* 4.9 0.4 - - - +
631A ASN* 5.3 1.0 - - - +
634A SER* 2.9 26.8 + - - +
635A PHE* 1.3 82.9 - - + +
637A SER* 1.3 58.9 + - - +
638A ASP 3.1 0.4 - - - -
639A VAL* 2.8 34.2 + - + +
640A TYR 3.1 1.4 + - - -
701A ARG* 3.2 49.2 + - + +
702A ASP* 2.6 27.3 - - - +
704A ARG* 3.0 23.4 + - + +
706A SER* 6.4 1.6 - - - -
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Residues in contact with SER 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A ILE* 5.9 0.2 - - - -
619A TRP 4.9 1.4 - - - +
621A ALA* 4.5 5.1 + - - +
623A GLU* 3.6 8.4 + - - -
624A VAL* 3.3 31.0 - - - +
632A PRO 3.3 17.3 + - - -
633A TYR* 4.3 7.9 - - - -
634A SER* 2.9 16.7 + - - -
636A GLN* 1.3 77.3 - - - +
638A ASP* 1.3 63.2 - - - +
640A TYR* 3.5 3.3 + - - +
641A ALA* 3.2 20.6 + - - +
704A ARG* 3.8 8.7 - - - +
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Residues in contact with ASP 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A MET* 3.3 17.6 - - + +
568A HIS* 3.6 20.5 + - + +
572A ILE 4.3 0.2 - - - +
573A ILE* 3.7 10.4 - - - +
574A HIS* 2.9 34.6 + - - +
575A ARG* 3.2 26.0 + - - -
576A ASP 4.9 0.2 + - - -
577A LEU* 4.5 6.0 + - - +
634A SER 3.2 2.8 + - - +
635A PHE 3.3 12.8 - - - +
637A SER* 1.3 79.2 - - - +
639A VAL* 1.3 56.9 + - - +
641A ALA* 3.1 9.8 - - - +
642A PHE* 2.9 25.6 + - - +
707A PHE* 4.4 3.6 - - + -
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Residues in contact with VAL 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A HIS* 5.1 0.2 - - + -
635A PHE* 3.1 17.4 + - + +
636A GLN* 2.8 18.6 + - + +
638A ASP* 1.3 74.9 - - - +
640A TYR* 1.3 61.1 + - - +
642A PHE* 3.2 5.3 + - - +
643A GLY 3.1 16.3 + - - -
696A CYS* 3.6 29.9 - - + +
704A ARG* 4.1 6.1 - - - -
705A PRO* 3.2 35.9 - - + +
706A SER* 4.4 5.4 - - - -
707A PHE* 3.8 25.4 - - + -
710A ILE* 3.8 3.6 - - + -
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Residues in contact with TYR 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A LEU 4.8 2.1 + - - -
619A TRP 3.7 5.2 - - - -
620A MET 3.7 16.7 + - - -
621A ALA* 3.5 21.5 - - + -
622A PRO* 3.9 16.6 - - + -
636A GLN 3.1 6.5 + - - -
637A SER 3.5 1.5 + - - +
639A VAL* 1.3 70.6 - - - +
641A ALA* 1.3 69.4 + - - +
643A GLY* 2.9 12.0 + - - -
644A ILE* 3.1 43.2 + - + +
656A TYR* 3.7 19.6 + - - -
669A VAL* 4.0 13.7 - - - +
674A LEU 5.5 0.3 + - - -
675A SER* 5.5 1.0 - - - -
676A PRO* 4.5 6.1 - - + +
696A CYS 3.5 10.0 + - - -
697A LEU* 3.8 36.0 - - + +
698A LYS 4.2 1.1 - - - -
699A LYS* 5.5 2.0 - - + -
704A ARG* 3.6 33.0 - - - +
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Residues in contact with ALA 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A ARG 6.5 0.4 - - - -
577A LEU* 4.0 33.2 - - + +
619A TRP* 3.6 21.5 + - - +
637A SER 3.2 11.9 + - - +
638A ASP* 3.1 15.5 - - - +
640A TYR* 1.3 79.9 - - - +
642A PHE* 1.3 62.5 + - - +
644A ILE* 3.1 12.0 + - - +
645A VAL* 3.3 15.1 + - - +
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Residues in contact with PHE 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ALA* 3.9 10.5 - - + -
560A THR* 3.7 32.5 - - + -
561A ALA* 3.8 12.8 - - + -
564A MET* 5.0 0.4 - - + -
577A LEU* 3.8 11.8 - - + +
638A ASP 2.9 14.9 + - - +
639A VAL* 3.5 6.7 - - - +
640A TYR 3.2 0.6 - - - -
641A ALA* 1.3 76.3 - - - +
643A GLY* 1.3 57.6 + - - +
645A VAL* 3.4 11.0 - - + +
646A LEU* 3.0 60.1 + - + -
692A LEU* 4.9 0.4 - - + -
696A CYS* 4.2 13.9 - - - -
707A PHE* 3.8 24.9 - + + -
710A ILE* 4.2 16.2 - - + -
714A ILE* 3.9 21.3 - - + -
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Residues in contact with GLY 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A VAL 3.1 7.7 + - - -
640A TYR 2.9 5.2 + - - -
642A PHE* 1.3 74.4 - - - +
644A ILE* 1.3 58.9 + - - +
646A LEU* 2.8 12.9 + - - +
647A TYR* 2.8 26.3 + - - +
693A MET* 4.0 1.8 - - - +
696A CYS* 3.9 15.0 - - - +
697A LEU* 3.3 25.7 - - - +
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Residues in contact with ILE 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A LEU 3.3 24.2 - - - +
619A TRP* 3.4 28.5 - - + +
640A TYR* 3.1 46.1 + - + +
641A ALA 3.1 5.8 + - - +
643A GLY* 1.3 75.0 - - - +
645A VAL* 1.3 58.1 + - - +
647A TYR* 3.3 6.1 + - + +
648A GLU* 3.0 28.9 + - + +
655A PRO* 4.4 19.1 - - + -
656A TYR* 5.1 0.7 - - - +
676A PRO* 4.1 15.5 - - + -
697A LEU* 3.3 24.2 - - + -
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Residues in contact with VAL 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A LEU* 4.5 9.6 - - + -
560A THR* 4.5 13.5 - - + +
577A LEU* 4.0 18.8 - - + -
578A LYS* 4.2 4.0 - - - -
579A SER* 4.3 3.1 - - - +
582A ILE* 4.2 23.6 - - + -
619A TRP* 3.9 17.9 - - + +
641A ALA 3.3 11.9 + - - +
642A PHE* 3.4 12.3 - - + +
644A ILE* 1.3 78.1 - - - +
646A LEU* 1.3 57.1 + - - +
648A GLU* 3.4 9.9 + - - +
649A LEU* 2.8 45.5 + - + +
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Residues in contact with LEU 646 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557A ALA* 4.2 6.3 - - + -
642A PHE* 3.0 48.4 + - + +
643A GLY* 2.8 17.5 + - - +
645A VAL* 1.3 77.6 - - - +
647A TYR* 1.3 49.9 + - - -
649A LEU* 3.7 3.8 - - + +
650A MET* 2.7 43.6 + - + +
689A MET* 3.2 38.6 - - + +
692A LEU* 4.1 12.6 - - + +
693A MET* 3.6 39.3 - - + +
696A CYS* 4.9 1.1 - - - -
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Residues in contact with TYR 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643A GLY 2.8 14.5 + - - +
644A ILE* 3.5 11.9 - - - +
646A LEU* 1.3 70.0 - - - +
648A GLU* 1.3 58.2 + - - +
651A THR* 2.6 65.2 + - + +
653A GLN* 3.2 22.0 + - + -
654A LEU 4.1 1.9 + - - -
655A PRO* 3.7 33.6 - - + +
656A TYR 5.2 0.5 + - - -
657A SER* 5.1 1.0 + - - -
676A PRO* 3.5 30.7 - - + -
677A ASP* 2.9 35.4 + - - +
678A LEU* 4.0 11.0 - - + -
680A LYS* 3.7 20.8 + - - +
693A MET* 3.6 13.6 - - - -
697A LEU* 5.0 2.2 - - + -
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Residues in contact with GLU 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A LEU* 6.2 0.4 - - + -
541A LEU* 3.8 12.9 - - + +
542A HIS* 2.3 37.5 + - + +
579A SER* 2.6 32.6 + - - -
619A TRP* 3.0 22.4 + - + +
644A ILE* 3.0 14.7 + - + +
645A VAL* 3.5 10.1 - - - +
647A TYR* 1.3 76.4 - - - +
649A LEU* 1.3 54.7 + - - +
652A GLY* 2.6 35.7 + - - -
653A GLN 3.3 20.8 + - - +
654A LEU* 3.4 17.6 - - + +
655A PRO* 4.9 3.4 - - + -
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Residues in contact with LEU 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A LEU* 4.0 13.2 - - + -
541A LEU* 3.8 12.6 - - + +
553A LEU* 3.5 57.8 - - + +
556A ILE* 3.7 20.4 - - + -
557A ALA* 3.7 32.8 - - + +
560A THR* 5.6 0.7 - - - +
642A PHE* 6.0 0.7 - - + -
645A VAL* 2.8 40.7 + - + +
646A LEU* 3.7 7.0 - - + +
648A GLU* 1.3 75.2 - - - +
650A MET* 1.3 71.7 + - + +
651A THR 3.5 2.4 + - - -
652A GLY* 3.6 5.7 + - - -
682A ARG* 5.0 1.7 - - - -
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Residues in contact with MET 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A MET* 4.1 19.7 - - - +
553A LEU* 3.8 35.4 - - + +
554A ILE* 4.3 3.4 - - + +
646A LEU* 2.7 27.9 + - + +
649A LEU* 1.3 80.1 - - + +
651A THR* 1.3 59.6 + - + +
681A VAL* 3.2 24.8 - - + +
682A ARG* 3.5 8.9 + - - -
685A CYS* 3.5 24.7 - - - +
689A MET* 3.1 52.5 - - + +
690A LYS* 6.3 0.2 - - - -
693A MET* 4.8 10.1 - - + -
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Residues in contact with THR 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A TYR* 2.6 65.7 + - + +
650A MET* 1.3 78.9 - - - +
652A GLY* 1.3 62.4 + - - +
653A GLN* 3.3 18.0 + - - +
680A LYS* 3.4 23.0 - - - +
681A VAL* 3.4 28.7 - - + +
682A ARG* 4.4 13.8 - - - +
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Residues in contact with GLY 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A LEU* 3.7 26.8 - - - +
542A HIS* 4.3 1.6 + - - -
553A LEU* 6.3 0.4 - - - -
648A GLU 2.6 20.9 + - - -
649A LEU 3.6 6.6 + - - -
651A THR* 1.3 73.9 - - - +
653A GLN* 1.3 62.9 + - - +
682A ARG* 4.7 6.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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