Contacts of the helix formed by residues 66 - 76 (chain B) in PDB entry 2WJZ
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 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.2 20.9 - - + -
8B VAL* 4.1 13.2 - - + -
35B VAL* 4.3 4.7 - - + -
36B GLU* 4.1 14.1 - - - -
37B SER* 3.4 27.6 - - - +
61B LEU* 3.0 19.1 + - - +
64B ASN* 3.4 26.5 - - + +
65B ASP* 1.3 76.8 - - - +
67B ILE* 1.3 67.7 + - - +
68B ASP 3.0 2.2 - - - -
69B PHE* 2.8 41.5 + - + +
70B VAL* 2.8 22.2 + - + +
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Residues in contact with ILE 67 (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 MET* 5.0 11.9 - - + +
61B LEU* 3.6 16.3 + - - +
62B ARG* 4.3 13.7 - - - +
65B ASP* 3.7 0.6 - - - -
66B LEU* 1.3 78.0 - - - +
68B ASP* 1.3 58.6 + - - +
70B VAL* 3.6 5.7 + - - +
71B ARG* 3.1 22.5 + - - -
103B LEU* 4.5 26.2 - - + +
14C ASP* 3.7 45.8 - - + +
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Residues in contact with ASP 68 (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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65B ASP* 4.2 7.9 - - - +
66B LEU* 3.0 1.0 - - - +
67B ILE* 1.3 77.4 - - - +
69B PHE* 1.3 60.1 + - - +
70B VAL 3.1 1.6 - - - -
71B ARG* 4.3 1.8 - - - +
72B LYS* 2.8 29.1 + - - -
13C LYS* 2.2 36.9 + - - +
14C ASP* 2.7 19.8 + - - +
53C THR* 5.9 0.2 - - - -
54C ALA* 4.0 23.6 + - - +
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Residues in contact with PHE 69 (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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6B ILE* 5.7 0.7 - - + -
35B VAL* 4.1 7.2 - - + -
37B SER 3.7 7.4 - - - -
38B PRO* 3.2 21.3 - - + +
39B ARG* 3.0 39.5 - - - -
43B TYR* 3.7 26.7 - + - -
46B LEU* 4.4 8.3 - - + -
65B ASP 4.2 5.6 + - - +
66B LEU* 2.8 40.1 + - + +
68B ASP* 1.3 79.4 - - - +
70B VAL* 1.3 56.1 + - + +
72B LYS* 3.8 1.4 + - - +
73B HIS* 2.6 60.1 + + - -
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Residues in contact with VAL 70 (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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6B ILE* 4.1 15.7 - - + -
46B LEU* 3.8 18.8 - - + -
48B ILE* 4.2 10.3 - - + -
66B LEU* 2.8 20.0 + - + +
67B ILE* 3.9 5.6 - - - +
69B PHE* 1.3 75.9 - - + +
71B ARG* 1.3 60.6 + - - +
72B LYS 3.1 1.6 - - - -
73B HIS* 2.9 24.0 + - - +
74B VAL* 3.0 12.5 + - + +
80B VAL* 4.1 17.5 - - + -
103B LEU* 4.9 10.1 - - + -
105B LEU* 3.8 27.4 - - + -
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Residues in contact with ARG 71 (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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67B ILE 3.1 13.4 + - - -
68B ASP* 3.3 4.7 + - - +
70B VAL* 1.3 81.2 - - - +
72B LYS* 1.3 55.6 + - - +
74B VAL* 3.6 7.4 + - - +
75B GLU* 3.0 32.3 + - - +
105B LEU* 5.2 4.9 - - - -
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Residues in contact with LYS 72 (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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68B ASP 2.8 16.1 + - - -
69B PHE 4.2 2.2 - - - -
70B VAL 3.1 0.2 - - - -
71B ARG* 1.3 73.9 - - - +
73B HIS* 1.3 63.5 + - - +
75B GLU* 3.8 7.1 - - - +
76B ASP* 3.1 25.8 + - - +
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Residues in contact with HIS 73 (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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43B TYR* 3.0 46.8 + + - +
46B LEU* 3.7 23.1 - - + +
69B PHE* 2.6 62.4 + + - -
70B VAL* 2.9 9.3 + - - +
72B LYS* 1.3 74.7 - - - +
74B VAL* 1.3 66.5 + - - +
76B ASP 3.1 6.1 + - - -
78B ARG* 3.0 41.4 + - + +
79B TYR 5.2 0.9 - - - -
80B VAL* 3.7 16.4 - - + -
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Residues in contact with VAL 74 (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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70B VAL* 3.0 15.5 + - + +
71B ARG 3.8 4.3 - - - +
73B HIS* 1.3 75.3 - - - +
75B GLU* 1.3 65.9 + - - +
77B GLU* 3.1 15.2 + - - -
78B ARG 4.4 3.5 - - - +
80B VAL* 3.8 19.5 - - + +
105B LEU* 3.4 37.5 - - + -
172B ILE* 3.4 31.9 - - + -
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Residues in contact with GLU 75 (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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71B ARG 3.0 20.2 + - - +
72B LYS* 3.8 9.4 - - - +
74B VAL* 1.3 77.9 - - - +
76B ASP* 1.3 58.1 + - + +
77B GLU 3.3 2.7 + - - -
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Residues in contact with ASP 76 (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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72B LYS 3.1 16.1 + - - +
73B HIS 3.1 2.8 + - - -
75B GLU* 1.3 77.2 - - + +
77B GLU* 1.3 60.3 + - - +
78B ARG* 2.9 45.4 + - + +
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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