Contacts of the helix formed by residues 71 - 85 (chain B) in PDB entry 2H8C
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 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP 5.6 1.0 + - - -
94A VAL* 3.1 28.2 + - + +
95A VAL* 3.7 21.3 - - - +
96A ASP 4.0 2.2 - - - +
97A TYR* 3.9 13.7 - - + -
61B CYS* 3.6 33.9 - - + -
63B MET* 4.6 6.5 - - + -
69B ARG 3.6 4.4 + - - +
70B ASN* 1.3 68.1 - - - +
72B ASP* 1.3 61.0 + - - +
73B ASN 3.0 2.5 - - - -
74B LEU* 2.8 31.7 + - + +
75B GLN* 3.1 8.3 + - - +
99B VAL* 3.7 22.2 - - + +
101B LYS* 4.1 18.8 - - + +
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN* 3.4 39.1 + - - +
76A LYS* 5.0 8.8 - - - +
79A PHE* 5.3 3.3 - - + -
91A ASP* 5.6 2.9 - - - +
97A TYR* 3.4 17.7 + - + +
70B ASN* 3.1 26.5 + - - +
71B LEU* 1.3 74.9 - - - +
73B ASN* 1.3 80.3 + - - -
75B GLN* 3.2 8.5 + - - +
76B LYS* 2.9 28.1 + - - +
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Residues in contact with ASN 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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11B PRO* 5.4 0.2 - - - +
14B ASN* 3.5 43.3 + - + +
70B ASN* 3.8 14.8 - - - +
71B LEU 3.0 1.0 - - - -
72B ASP* 1.3 91.3 + - - +
74B LEU* 1.3 67.8 + - + +
76B LYS* 4.0 4.0 - - - +
77B ALA* 3.4 22.0 + - - +
12W T 3.1 35.4 + - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TRP* 3.4 37.5 - - + +
11B PRO* 4.1 19.7 - - + -
59B ILE* 5.3 2.4 - - + +
61B CYS* 3.1 44.0 - - + -
63B MET* 4.1 9.9 - - + -
69B ARG* 5.2 4.3 - - - -
70B ASN 4.2 7.9 - - - +
71B LEU* 2.8 15.3 + - + +
73B ASN* 1.3 77.8 - - + +
75B GLN* 1.3 68.7 + - - +
77B ALA* 3.5 4.1 + - - +
78B ALA* 3.1 23.2 + - - +
110B LEU* 4.4 11.8 - - + +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 3.0 39.7 + - - +
75A GLN* 4.4 3.1 - - - +
97A TYR* 3.9 8.1 + - - +
59B ILE* 4.0 17.9 - - + -
71B LEU 3.1 4.6 + - - -
72B ASP* 3.2 12.6 + - - +
74B LEU* 1.3 77.6 - - - +
76B LYS* 1.3 72.9 + - - +
78B ALA* 3.7 1.0 - - - +
79B PHE* 3.0 49.6 + - + +
97B TYR* 3.6 31.8 + - + -
99B VAL* 3.8 16.9 - - + +
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Residues in contact with LYS 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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72A ASP* 5.2 7.2 - - - +
14B ASN* 4.2 13.5 - - - +
18B TYR* 3.9 17.0 - - + +
72B ASP 2.9 16.2 + - - +
73B ASN* 4.0 7.0 - - - +
74B LEU 3.4 0.2 - - - -
75B GLN* 1.3 87.8 - - - +
77B ALA* 1.3 57.0 + - - +
79B PHE* 3.6 2.6 + - - +
80B ASP* 2.9 28.9 + - + +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 3.9 28.9 - - + -
12B PRO 5.5 1.1 - - - +
14B ASN* 5.4 3.6 - - + +
17B TYR* 3.8 27.2 + - + -
18B TYR* 4.8 1.6 - - - +
34B TYR* 4.5 4.5 - - + -
73B ASN 3.4 14.4 + - - +
74B LEU 4.0 3.1 - - - +
75B GLN 3.2 1.0 - - - -
76B LYS* 1.3 76.9 - - - +
78B ALA* 1.3 67.3 + - - +
80B ASP* 3.2 20.0 + - - +
81B ALA* 3.2 8.1 + - - +
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Residues in contact with ALA 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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8B LEU* 4.9 14.8 - - + +
34B TYR* 5.3 5.6 - - - -
59B ILE* 4.8 13.5 - - + -
74B LEU 3.1 18.3 + - - +
75B GLN* 3.7 2.9 - - - +
77B ALA* 1.3 73.4 - - - +
79B PHE* 1.3 72.3 + - + +
81B ALA* 3.0 16.1 + - - +
82B LEU* 3.1 18.2 + - - +
110B LEU* 4.4 17.0 - - + +
112B LEU* 5.1 7.0 - - + -
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Residues in contact with PHE 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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72A ASP* 4.8 5.6 - - + -
57B ILE* 3.5 32.5 - - + -
59B ILE* 3.7 22.0 - - + -
75B GLN* 3.0 36.7 + - - +
76B LYS* 3.7 4.9 - - - +
78B ALA* 1.3 78.7 - - + +
80B ASP* 1.3 55.7 + - - +
82B LEU* 3.3 2.9 + - + +
83B THR* 2.5 35.6 + - - -
88B TRP* 3.8 15.5 - + + -
91B ASP* 4.3 20.2 - - + +
94B VAL* 3.7 30.3 - - + -
97B TYR* 3.9 22.7 - + + -
112B LEU* 6.6 0.4 - - + -
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Residues in contact with ASP 80 (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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17B TYR* 2.5 28.9 + - - +
18B TYR* 4.4 11.0 + - - +
27B VAL* 4.7 1.9 - - - +
35B ARG* 2.6 44.0 + - - +
76B LYS* 2.9 16.5 + - + +
77B ALA* 3.2 12.6 - - - +
78B ALA 3.0 0.4 + - - -
79B PHE* 1.3 77.7 - - - +
81B ALA* 1.3 58.0 + - - +
83B THR* 3.6 5.3 + - - -
84B LYS* 3.0 35.1 + - - +
91B ASP* 5.5 0.2 - - - -
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Residues in contact with ALA 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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8B LEU* 6.3 0.7 - - + -
34B TYR* 4.4 8.5 - - + -
35B ARG* 4.4 10.7 - - - +
38B VAL* 3.7 34.1 - - + -
77B ALA 3.2 6.7 + - - +
78B ALA* 3.0 7.8 + - - +
80B ASP* 1.3 84.3 - - - +
82B LEU* 1.3 55.3 + - + +
84B LYS* 4.4 5.2 - - - -
85B ALA* 2.4 43.5 + - - +
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Residues in contact with LEU 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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6B ILE* 4.6 4.0 - - + -
8B LEU* 4.3 18.2 - - + -
38B VAL* 5.0 4.9 - - + -
42B ILE* 4.7 10.8 - - + -
57B ILE* 5.6 0.9 - - + -
78B ALA 3.1 17.4 + - - +
79B PHE* 3.3 3.6 + - + +
81B ALA* 1.3 80.3 - - - +
83B THR* 1.3 61.7 + - - +
85B ALA* 4.0 7.9 - - + -
86B GLY 3.4 1.7 + - - -
87B PHE* 3.0 61.0 + - + +
88B TRP* 3.4 37.5 + - + -
112B LEU* 3.8 24.9 - - + -
114B ILE* 5.2 2.0 - - + -
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Residues in contact with THR 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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79B PHE 2.5 25.7 + - - -
80B ASP* 3.6 6.7 + - - -
82B LEU* 1.3 77.4 - - - +
84B LYS* 1.3 72.4 + - - +
86B GLY* 3.5 8.7 + - - -
88B TRP* 3.2 20.3 + - + +
89B LEU 3.2 25.7 - - - +
90B ASP* 4.6 1.1 - - - -
91B ASP* 3.3 26.1 + - - +
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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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35B ARG* 3.0 51.1 - - + +
39B ALA* 4.8 4.1 - - - +
80B ASP* 3.0 21.0 + - - +
81B ALA 4.1 2.2 - - - +
83B THR* 1.3 82.9 - - - +
85B ALA* 1.3 58.5 + - - +
86B GLY* 3.0 10.4 + - - -
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Residues in contact with ALA 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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38B VAL* 4.8 1.3 - - + -
39B ALA* 3.7 35.6 - - + +
42B ILE* 3.1 36.6 - - + +
48B ASP* 4.3 3.6 - - - +
81B ALA 2.4 33.1 + - - +
82B LEU* 3.6 7.4 + - + +
83B THR 3.3 0.4 - - - -
84B LYS* 1.3 72.5 - - - +
86B GLY* 1.3 64.3 + - - +
87B PHE 3.4 0.2 - - - -
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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