Contacts of the helix formed by residues 71 - 88 (chain B) in PDB entry 2OKC
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 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ALA 4.4 2.6 + - - +
70B PHE* 1.3 78.5 - - - +
72B GLY* 1.3 68.4 + - - +
74B ASP* 3.5 11.6 + - - +
75B LEU* 3.1 17.2 + - - -
111B LYS* 3.5 31.1 + - - +
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Residues in contact with GLY 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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71B ASP* 1.3 77.6 + - - +
73B LEU* 1.3 61.7 + - - -
75B LEU* 3.3 15.1 + - - +
76B VAL 3.4 3.5 + - - -
107B PRO* 3.2 37.1 + - - +
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Residues in contact with LEU 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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71B ASP 3.6 0.2 + - - -
72B GLY* 1.3 70.7 - - - -
74B ASP* 1.3 67.6 - - - +
76B VAL* 3.2 7.5 + - + +
77B LYS* 3.0 24.5 + - - +
107B PRO* 4.4 9.2 - - + -
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 3.9 24.1 - - + -
71B ASP 3.5 9.8 + - - +
73B LEU* 1.3 79.0 - - - +
75B LEU* 1.3 54.5 - - - +
77B LYS* 3.4 24.7 + - - +
78B GLN* 2.9 28.8 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.2 42.4 - - + +
70B PHE* 3.5 21.9 - - + +
71B ASP* 3.1 22.5 + - - -
72B GLY 3.4 10.8 - - - +
73B LEU 3.2 0.4 - - - -
74B ASP* 1.3 73.1 - - - +
76B VAL* 1.3 61.7 + - - +
78B GLN* 3.4 0.5 + - - +
79B TYR* 2.9 30.5 + - - +
107B PRO 4.1 9.4 - - - +
110B LEU* 4.0 10.5 - - + -
111B LYS* 4.0 34.1 - - + +
114B ILE* 3.8 16.8 - - + -
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLY 3.4 12.5 + - - +
73B LEU* 3.2 9.2 + - - +
75B LEU* 1.3 75.3 - - - +
77B LYS* 1.3 59.1 + - - +
79B TYR* 3.5 1.0 + - - +
80B GLU* 2.9 60.3 + - - +
102B ASN* 3.8 9.6 - - - +
104B ILE 4.3 7.4 - - - +
105B ASP* 4.4 10.3 - - + +
107B PRO* 3.8 26.5 - - + -
110B LEU* 4.0 21.1 - - + -
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU 3.0 11.7 + - - +
74B ASP* 3.6 28.1 + - - +
76B VAL* 1.3 75.5 - - - +
78B GLN* 1.3 64.6 + - - +
80B GLU* 3.3 7.4 + - - +
81B GLU* 2.9 29.3 + - + +
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Residues in contact with GLN 78 (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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61B GLY 2.9 27.5 + - - -
62B TYR* 3.8 25.8 - - - +
66B ASP* 4.0 12.7 - - - +
67B LEU* 4.1 16.0 - - + +
70B PHE* 3.6 39.3 - - + -
74B ASP 2.9 20.5 + - - +
75B LEU 3.8 4.3 - - - +
76B VAL 3.4 0.2 - - - -
77B LYS* 1.3 73.3 - - - +
79B TYR* 1.3 57.9 + - - +
81B GLU* 3.4 3.1 + - - +
82B THR* 2.9 38.9 + - - +
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Residues in contact with TYR 79 (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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35B GLN* 2.6 37.9 + - - +
38B TYR* 3.5 14.2 - - + +
39B LEU* 3.5 30.6 - - + +
42B LEU* 5.9 2.0 - - + -
67B LEU* 3.8 19.5 - - + +
75B LEU 2.9 19.2 + - - +
76B VAL 3.6 3.8 - - - +
78B GLN* 1.3 76.9 - - - +
80B GLU* 1.3 56.8 + - - +
82B THR* 3.2 8.1 + - + -
83B LEU* 2.9 52.2 + - + +
102B ASN* 3.1 42.6 - - + -
110B LEU* 3.7 27.8 - - + -
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 2.9 35.0 + - - +
77B LYS* 3.3 6.1 + - - +
79B TYR* 1.3 75.8 - - - +
81B GLU* 1.3 58.6 + - - +
83B LEU* 3.4 9.3 + - - +
84B LYS* 3.1 27.4 + - - +
102B ASN* 3.0 42.4 + - + +
105B ASP* 5.6 1.7 - - - +
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Residues in contact with GLU 81 (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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62B TYR* 3.6 28.4 + - + +
77B LYS* 2.9 19.8 + - + +
78B GLN* 3.8 5.4 - - - +
80B GLU* 1.3 74.9 - - - +
82B THR* 1.3 60.4 + - - +
84B LYS* 3.9 27.7 + - - +
85B LEU* 3.0 40.4 + - + +
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Residues in contact with THR 82 (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 LEU* 4.1 16.8 - - + -
62B TYR* 3.6 44.7 + - + +
67B LEU* 4.9 5.1 - - + +
78B GLN* 2.9 28.9 + - - +
79B TYR* 3.2 11.2 + - + -
81B GLU* 1.3 76.8 - - - +
83B LEU* 1.3 65.1 + - + +
85B LEU* 3.3 3.0 + - - +
86B LEU* 3.0 47.1 + - + +
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Residues in contact with LEU 83 (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 TYR* 3.7 31.9 - - + -
79B TYR* 2.9 50.6 + - + +
80B GLU* 3.6 8.7 - - - +
81B GLU 3.4 0.2 - - - -
82B THR* 1.3 77.7 - - + +
84B LYS* 1.3 58.4 + - - +
86B LEU* 3.6 4.8 + - - +
87B SER* 3.1 28.6 + - - -
97B TYR* 4.0 16.8 - - + -
100B ALA* 3.7 18.9 - - + +
101B GLN* 4.0 6.3 - - - +
102B ASN* 3.6 32.1 - - + +
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Residues in contact with LYS 84 (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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80B GLU 3.1 16.4 + - - +
81B GLU* 3.8 29.1 + - - +
82B THR 3.3 0.2 - - - -
83B LEU* 1.3 73.8 - - - +
85B LEU* 1.3 69.8 + - - +
87B SER* 2.7 24.6 + - - +
88B GLU* 2.3 49.9 + - - +
100B ALA 5.3 2.4 + - - -
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Residues in contact with LEU 85 (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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59B PRO* 3.8 23.8 - - + -
62B TYR* 3.4 46.0 - - + -
81B GLU* 3.0 25.8 + - - +
82B THR* 3.7 4.0 - - - +
84B LYS* 1.3 79.8 - - - +
86B LEU* 1.3 63.2 + - + +
88B GLU* 3.1 31.7 + - - +
89B LEU* 3.7 10.6 + - + +
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Residues in contact with LEU 86 (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 LEU* 4.1 13.5 - - + -
58B ILE* 4.0 28.5 - - + -
59B PRO* 4.3 7.4 - - + -
62B TYR* 5.3 1.6 - - + +
82B THR* 3.0 39.7 + - + +
83B LEU 4.0 1.8 - - - +
85B LEU* 1.3 76.4 - - + +
87B SER* 1.3 62.3 + - - +
89B LEU* 3.2 39.8 + - + +
93B ILE* 3.7 10.4 - - + +
94B GLY* 4.0 5.2 - - - -
97B TYR* 3.6 50.4 - - + +
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Residues in contact with SER 87 (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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83B LEU 3.1 13.0 + - - -
84B LYS* 2.7 26.0 + - - +
86B LEU* 1.3 76.7 - - - +
88B GLU* 1.3 62.8 + - - +
89B LEU 3.4 6.4 + - - +
94B GLY* 4.4 7.4 - - - +
97B TYR* 3.1 30.5 - - - -
98B THR* 5.6 0.3 - - - -
99B LYS* 4.5 7.1 + - - -
100B ALA 4.1 8.7 - - - -
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Residues in contact with GLU 88 (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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84B LYS* 2.3 51.4 + - - +
85B LEU* 3.1 21.9 + - + +
86B LEU 3.1 0.8 - - - -
87B SER* 1.3 80.4 + - - +
89B LEU* 1.3 65.0 + - - +
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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