Contacts of the helix formed by residues 56 - 64 (chain B) in PDB entry 2K8M
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 LEU 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B VAL* 4.5 11.4 - - + +
38B PHE* 3.7 34.1 - - + -
39B LYS* 3.8 49.8 - - + +
42B VAL* 3.8 24.5 - - + -
52B ASP* 4.1 10.3 + - - +
53B VAL* 4.8 2.0 - - - +
54B GLY 3.7 3.0 + - - +
55B SER* 1.3 71.2 - - - +
57B ASP* 1.3 63.1 + - - +
58B GLU 3.0 1.8 - - - -
59B LYS* 2.9 29.5 + - + +
60B MET* 3.2 13.1 + - + -
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Residues in contact with ASP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY 4.7 1.6 - - - +
55B SER* 3.9 14.6 - - - -
56B LEU* 1.3 80.0 + - - +
58B GLU* 1.3 61.9 + - - +
59B LYS 3.1 0.2 - - - -
60B MET* 3.7 13.2 - - - +
61B LYS* 2.6 68.6 + - - +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 5.2 6.6 - - - +
94A ARG* 2.7 34.0 + - - -
55B SER* 3.2 19.7 - - - +
56B LEU 3.0 0.2 - - - -
57B ASP* 1.3 86.4 + - - +
59B LYS* 1.3 78.7 + - - +
61B LYS* 4.4 4.4 - - - +
62B SER* 2.7 31.0 + - - +
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.0 2.2 - - - +
38B PHE* 4.6 3.8 - - + -
50B LEU* 5.2 17.9 - - + -
52B ASP* 2.6 39.2 + - + -
55B SER 2.7 22.1 + - - +
56B LEU* 2.9 24.7 + - + +
58B GLU* 1.3 104.7 + - - +
60B MET* 1.3 66.0 + - - +
62B SER* 2.9 14.3 + - - -
63B LEU* 2.9 32.2 + - + +
79B LEU* 5.2 6.5 - - + -
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Residues in contact with MET 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 6.0 9.4 - - + -
38B PHE* 4.6 14.5 - - + -
56B LEU* 3.2 11.8 + - + +
57B ASP* 3.3 14.1 + - - +
59B LYS* 1.3 78.6 - - - +
61B LYS* 1.3 84.3 + - + +
62B SER 3.1 0.9 + - - -
63B LEU* 4.7 2.9 - - - -
64B ASP* 2.8 43.9 + - + +
67B GLN* 4.3 20.2 - - + -
69B SER* 4.0 35.2 - - - +
71B LEU* 4.2 24.5 - - + -
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ASP* 2.6 52.1 + - - +
58B GLU* 4.6 4.9 - - - +
60B MET* 1.3 94.3 - - + +
62B SER* 1.3 59.8 + - - +
64B ASP* 4.2 10.8 - - - +
67B GLN* 3.7 25.9 - - - +
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLU* 2.7 24.8 + - - +
59B LYS* 2.9 8.3 + - - -
61B LYS* 1.3 80.4 + - - +
63B LEU* 1.3 66.9 + - - +
64B ASP 4.9 0.9 - - - -
78B ARG* 3.7 13.6 + - - -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PHE* 3.8 29.8 - - + -
59B LYS* 2.9 22.0 + - + +
60B MET 4.0 1.6 - - - +
62B SER* 1.3 87.1 - - - +
64B ASP* 1.3 64.4 + - - +
65B VAL* 3.4 3.5 + - - +
71B LEU* 4.6 7.4 - - + -
75B GLU* 3.9 15.3 - - - +
78B ARG* 2.9 61.0 + - + +
79B LEU* 3.9 26.2 - - + +
82B GLU* 4.9 11.0 - - + -
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B MET* 2.8 24.4 + - + +
61B LYS* 4.2 12.3 - - - +
62B SER 4.9 0.7 - - - -
63B LEU* 1.3 77.2 + - - +
65B VAL* 1.3 62.2 + - - +
66B ASN* 2.7 35.4 + - - +
67B GLN* 3.0 19.8 + - - +
68B ASP* 3.0 26.9 + - - +
69B SER 3.6 6.4 + - - -
70B GLU 4.2 5.1 + - - -
71B LEU* 3.5 21.4 - - + +
75B GLU* 4.2 8.2 - - - +
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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