Contacts of the helix formed by residues 56 - 64 (chain B) in PDB entry 2CUK
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 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B LYS* 2.9 33.7 + - - -
54B ARG* 3.3 28.3 + - - +
55B ILE* 1.3 76.1 - - - +
57B ALA* 1.3 64.4 + - - +
58B GLU* 3.2 20.6 + - - +
59B VAL* 3.2 24.7 + - - +
60B MET* 3.3 17.7 + - - +
80B ASP* 4.3 7.2 - - + +
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Residues in contact with ALA 57 (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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56B ASP* 1.3 75.5 - - - +
58B GLU* 1.3 56.5 + - - +
60B MET* 3.3 8.9 + - - +
61B ASP* 2.9 35.7 + - - +
80B ASP* 4.7 3.6 + - - +
83B ALA* 4.1 19.9 - - + +
87B ARG* 3.7 23.8 - - - +
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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
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34B LYS* 3.9 22.2 - - - +
38B LEU* 3.8 30.9 - - + +
56B ASP* 3.2 11.2 + - - +
57B ALA* 1.3 79.5 - - - +
59B VAL* 1.3 57.5 + - - +
61B ASP* 3.4 5.9 + - - +
62B ARG* 2.9 45.3 + - + +
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Residues in contact with VAL 59 (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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34B LYS* 5.4 4.9 - - + +
37B LEU* 3.9 24.9 - - + -
38B LEU* 3.7 18.2 - - + -
41B VAL* 3.8 24.4 - - + +
47B LEU* 4.7 4.3 - - + -
54B ARG 3.7 19.7 - - - +
55B ILE* 4.2 18.4 - - + -
56B ASP* 3.2 23.9 + - - +
58B GLU* 1.3 76.6 - - - +
60B MET* 1.3 59.4 + - - +
62B ARG* 3.4 1.7 + - - +
63B ALA* 2.9 27.7 + - - +
66B LEU* 5.5 1.8 - - + -
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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
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55B ILE* 3.6 31.4 - - + +
56B ASP 3.3 9.6 + - - +
57B ALA* 3.3 7.6 + - - +
58B GLU 3.3 0.2 - - - -
59B VAL* 1.3 80.1 - - - +
61B ASP* 1.3 64.4 + - - +
63B ALA* 3.2 21.1 - - - +
64B LYS 3.8 2.4 + - - -
65B GLY 5.4 0.2 + - - -
66B LEU* 4.8 5.6 + - + +
69B ILE* 4.4 13.2 - - + -
79B VAL* 4.6 1.3 - - + -
80B ASP* 3.4 25.1 - - + +
83B ALA* 3.7 16.2 - - + +
84B ALA* 3.4 35.2 - - + +
87B ARG* 3.8 14.6 - - - -
89B ILE* 3.8 20.6 - - + +
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Residues in contact with ASP 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 ALA* 2.9 20.9 + - - +
58B GLU* 3.8 6.1 - - - +
60B MET* 1.3 75.1 - - - +
62B ARG* 1.3 67.1 + - + +
63B ALA 3.4 0.3 + - - -
64B LYS* 3.4 12.6 + - - +
87B ARG* 2.8 39.5 + - - +
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Residues in contact with ARG 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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38B LEU* 3.8 51.7 + - + +
39B LYS* 5.3 2.2 - - - +
41B VAL* 4.4 7.6 - - + -
42B GLU* 3.8 30.9 + - - +
58B GLU* 2.9 31.1 + - + +
59B VAL 3.8 3.8 - - - +
61B ASP* 1.3 76.8 - - + +
63B ALA* 1.3 68.3 + - - +
64B LYS* 3.0 9.7 + - - +
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Residues in contact with ALA 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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41B VAL* 3.5 24.5 - - + +
43B GLY* 2.7 28.2 + - - -
44B ALA 4.1 2.5 + - - +
59B VAL 2.9 13.8 + - - +
60B MET 3.2 13.2 - - - +
61B ASP 3.2 0.2 - - - -
62B ARG* 1.3 76.0 - - - +
64B LYS* 1.3 64.6 + - - +
65B GLY* 3.4 0.6 + - - -
66B LEU* 3.4 35.0 - - + +
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Residues in contact with LYS 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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42B GLU* 4.1 25.8 + - + -
43B GLY* 4.5 11.3 - - - +
60B MET 3.8 2.8 + - - -
61B ASP 3.4 10.4 + - - +
62B ARG 3.0 11.4 + - - +
63B ALA* 1.3 82.6 - - - +
65B GLY* 1.4 56.6 + - - +
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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