Contacts of the helix formed by residues 664 - 677 (chain A) in PDB entry 3KG2
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 ILE 664 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658A PHE* 5.1 6.5 - - + -
662A SER* 3.3 11.2 - - - +
663A LYS* 1.3 81.1 - - - +
665A ALA* 1.3 72.7 + - + +
666A VAL* 3.5 7.8 + - + +
667A PHE* 3.5 42.8 - - + -
668A ASP* 2.9 24.5 + - - +
727A LEU 5.6 1.3 - - - +
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Residues in contact with ALA 665 (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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663A LYS 3.8 2.2 + - - -
664A ILE* 1.3 79.7 - - + +
666A VAL* 1.3 70.4 + - + +
668A ASP* 3.2 15.0 + - - +
669A LYS* 3.4 6.9 + - - +
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Residues in contact with VAL 666 (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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636A ALA* 4.1 9.4 - - + +
637A GLU* 3.8 40.8 - - + +
640A SER* 3.8 11.2 - - - +
664A ILE* 3.5 4.9 - - + +
665A ALA* 1.3 78.6 - - + +
667A PHE* 1.3 73.0 + - + +
668A ASP 3.1 1.4 + - - -
669A LYS* 3.2 15.7 + - - +
670A MET* 3.2 23.3 + - - +
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Residues in contact with PHE 667 (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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636A ALA* 4.4 7.4 - - + -
658A PHE* 4.1 9.2 - + - -
659A PHE* 3.6 32.0 - + + +
662A SER* 3.5 19.5 - - - +
664A ILE* 3.5 45.7 + - + +
665A ALA 3.4 0.2 - - - -
666A VAL* 1.3 80.3 - - + +
668A ASP* 1.3 61.0 + - - +
670A MET* 3.6 12.7 - - - +
671A TRP* 3.1 23.7 + - - +
727A LEU* 3.4 61.9 - - + -
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Residues in contact with ASP 668 (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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659A PHE 5.2 0.7 - - - -
662A SER 4.6 14.5 + - - +
663A LYS* 5.2 5.2 - - - +
664A ILE 2.9 20.9 + - - +
665A ALA* 3.2 8.5 - - - +
667A PHE* 1.3 76.7 - - - +
669A LYS* 1.3 64.2 + - - +
671A TRP* 3.1 10.6 + - - +
672A THR* 3.0 29.5 + - - -
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Residues in contact with LYS 669 (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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640A SER* 4.6 14.6 - - - +
647A TYR* 5.1 0.2 - - - -
665A ALA 3.4 5.2 + - - +
666A VAL* 3.2 10.1 + - - +
668A ASP* 1.3 81.1 + - - +
670A MET* 1.3 63.0 + - - +
672A THR* 3.1 9.8 + - - -
673A TYR* 3.0 22.3 + - - +
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Residues in contact with MET 670 (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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636A ALA* 4.0 21.1 - - + +
639A LEU* 4.1 18.2 - - + -
640A SER* 4.1 12.6 - - - -
647A TYR* 3.6 36.6 - - + +
659A PHE* 4.0 19.5 - - + -
666A VAL* 3.3 18.2 - - - +
667A PHE* 3.6 20.9 - - - +
668A ASP 3.2 0.4 - - - -
669A LYS* 1.3 77.5 - - - +
671A TRP* 1.3 62.1 + - - +
673A TYR* 3.2 4.7 + - - +
674A MET* 3.0 29.7 + - + +
703A LEU* 3.9 24.9 - - + -
727A LEU* 5.2 0.9 - - + -
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Residues in contact with TRP 671 (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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656A LYS* 4.2 16.4 - - + -
659A PHE* 3.5 34.8 - - + +
660A ARG* 3.6 38.0 + - + +
667A PHE 3.1 6.4 + - - +
668A ASP* 3.1 9.4 + - - +
670A MET* 1.3 76.3 - - - +
672A THR* 1.3 61.3 + - - +
674A MET* 3.8 13.9 - - + +
675A ARG* 2.7 57.2 + - + +
682A PHE* 3.9 29.4 - + - -
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Residues in contact with THR 672 (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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668A ASP* 3.0 25.0 + - - -
669A LYS* 3.4 12.4 - - - -
671A TRP* 1.3 81.8 - - - +
673A TYR* 1.3 62.9 + - - +
675A ARG* 3.6 9.7 + - - +
676A SER* 3.4 17.8 + - - +
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Residues in contact with TYR 673 (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 THR* 4.8 17.8 + - - -
646A ALA* 3.2 32.9 - - - +
647A TYR* 3.4 59.1 + + - +
669A LYS 3.0 11.1 + - - +
670A MET 3.5 5.2 - - - +
672A THR* 1.3 76.9 - - - +
674A MET* 1.3 76.2 + - + +
675A ARG 3.2 0.3 + - - -
676A SER* 3.3 4.5 + - - -
677A ALA* 2.9 47.9 + - + +
681A VAL* 3.9 5.4 - - - +
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Residues in contact with MET 674 (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* 3.5 29.8 - - + +
648A GLY* 3.7 22.7 - - - -
649A THR* 4.2 13.2 - - + +
659A PHE* 3.9 30.3 - - + -
670A MET* 3.0 22.7 + - + +
671A TRP* 3.8 23.1 - - + +
673A TYR* 1.3 84.6 - - + +
675A ARG* 1.3 60.7 + - - +
676A SER 3.3 0.5 + - - -
677A ALA* 3.6 7.3 + - - +
681A VAL* 3.8 11.6 - - + +
682A PHE* 3.1 35.9 - - + -
703A LEU* 4.4 2.2 - - + -
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Residues in contact with ARG 675 (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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671A TRP* 2.7 48.4 + - + +
672A THR* 3.8 8.3 - - - +
673A TYR 3.1 0.4 - - - -
674A MET* 1.3 74.5 - - - +
676A SER* 1.3 58.7 + - - +
682A PHE* 4.7 7.7 - - - -
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Residues in contact with SER 676 (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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672A THR* 3.4 14.5 + - - +
673A TYR* 3.3 3.3 + - - -
675A ARG* 1.3 78.4 - - - +
677A ALA* 1.3 65.3 + - - +
678A GLU* 3.5 6.2 + - - +
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Residues in contact with ALA 677 (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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673A TYR* 2.9 37.5 + - + +
674A MET* 3.6 10.7 + - - +
676A SER* 1.3 78.9 - - - +
678A GLU* 1.3 59.4 + - - +
679A PRO 3.0 12.6 - - - +
680A SER* 3.9 6.4 + - - -
681A VAL* 3.6 28.1 + - + -
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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