Contacts of the helix formed by residues 77 - 91 (chain B) in PDB entry 2O5F
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 THR 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ARG* 5.9 0.9 - - - +
72B VAL* 4.1 2.5 - - - -
75B GLY 4.1 0.4 + - - -
76B GLU* 1.3 76.4 - - - +
78B TYR* 1.3 72.9 + - - +
79B GLU* 3.6 10.1 + - + +
80B GLU* 3.0 49.3 + - + +
81B ALA* 3.0 22.3 + - - +
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Residues in contact with TYR 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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16B ASP* 3.1 20.6 + - - -
35B ARG* 2.8 50.5 - - + +
36B VAL 3.7 15.0 - - - -
37B VAL* 3.4 20.6 - - + +
72B VAL* 4.0 5.6 - - + +
77B THR* 1.3 80.2 + - - +
79B GLU* 1.3 62.8 + - - +
81B ALA* 3.1 6.8 + - - +
82B PHE* 2.9 19.6 + - - +
115B PHE* 3.7 9.9 - - - +
116B MET* 4.0 13.3 + - - -
117B CYS* 3.8 19.7 - - + -
119B TYR* 3.3 15.5 - - - +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR* 3.3 9.8 + - + +
78B TYR* 1.3 78.1 - - - +
80B GLU* 1.3 63.6 + - + +
82B PHE* 3.1 8.7 + - + +
83B ARG* 2.9 51.5 + - - +
94B ILE* 5.2 0.4 - - + -
99B TRP* 3.7 33.8 - - + -
119B TYR* 3.2 12.4 + - + +
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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
----------------------------------------------------------
75B GLY 4.3 3.8 - - - +
76B GLU* 3.6 22.3 - - + +
77B THR* 3.0 35.8 + - + +
79B GLU* 1.3 76.8 - - + +
81B ALA* 1.3 62.9 + - - +
83B ARG* 3.4 14.4 + - - +
84B ARG* 3.0 23.9 + - - +
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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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37B VAL* 3.9 10.9 - - + +
72B VAL* 3.8 23.8 - - + -
76B GLU* 3.3 25.3 - - - +
77B THR 3.0 11.7 + - - +
78B TYR 3.1 8.5 + - - +
80B GLU* 1.3 78.2 - - - +
82B PHE* 1.3 56.4 + - - +
84B ARG* 3.4 12.4 + - - +
85B GLU* 2.9 32.4 + - - +
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Residues in contact with PHE 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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37B VAL* 4.1 10.9 - - + +
38B ASN 5.7 0.2 - - - -
39B ALA* 3.4 27.1 - - + -
68B VAL* 4.4 10.5 - - + -
78B TYR 2.9 5.9 + - - +
79B GLU* 3.1 8.5 + - + +
81B ALA* 1.3 78.4 - - - +
83B ARG* 1.3 63.2 + - - +
85B GLU* 3.9 1.2 - - - +
86B ALA* 3.0 25.5 + - + +
94B ILE* 3.7 33.9 - - + -
99B TRP* 3.8 31.0 - + + -
119B TYR* 3.6 53.4 - + + -
121B LEU* 4.5 17.5 - - + -
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Residues in contact with ARG 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 GLU* 2.9 39.0 + - - +
80B GLU* 3.8 14.0 - - - +
82B PHE* 1.3 77.2 - - - +
84B ARG* 1.3 62.4 + - - +
86B ALA* 4.0 1.6 - - - +
87B ARG* 3.2 48.4 + - + +
92B VAL 4.8 1.2 - - - +
93B GLU* 5.2 2.9 - - - +
94B ILE* 3.5 42.4 - - + +
95B ASP* 3.4 34.7 + - - -
99B TRP* 4.6 4.6 - - - -
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Residues in contact with ARG 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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37B VAL* 5.9 0.2 - - - +
71B ALA 3.2 23.0 + - - -
73B GLN* 3.0 28.7 + - - +
76B GLU* 2.7 41.3 + - - +
80B GLU 3.0 15.7 + - - +
81B ALA* 3.7 12.7 + - - +
83B ARG* 1.3 78.0 - - - +
85B GLU* 1.3 79.9 + - - +
87B ARG* 3.2 9.6 + - - +
88B GLU* 2.9 64.6 + - + +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 4.8 5.8 - - + +
68B VAL* 3.6 10.1 - - + -
69B GLY 3.2 29.8 - - - +
70B GLY* 3.5 15.6 - - - +
71B ALA 4.6 0.7 - - - +
81B ALA 2.9 17.4 + - - +
82B PHE* 4.0 4.3 - - - +
84B ARG* 1.3 97.4 + - - +
86B ALA* 1.3 58.3 + - - +
88B GLU* 4.2 9.4 - - - +
89B GLU* 2.8 67.7 + - - +
133B ASP* 5.0 2.1 - - - +
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Residues in contact with ALA 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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68B VAL* 3.8 13.4 - - + +
82B PHE* 3.0 27.4 + - + +
83B ARG 4.0 1.3 - - - +
85B GLU* 1.3 77.1 - - - +
87B ARG* 1.3 58.1 + - - +
90B LEU* 3.1 23.6 + - + +
91B ASN 3.2 6.1 + - - -
92B VAL* 3.3 27.0 + - + +
94B ILE* 3.9 20.9 - - + -
121B LEU* 5.3 2.5 - - + -
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Residues in contact with ARG 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 ARG* 3.2 41.6 + - - +
84B ARG* 3.5 9.6 - - - +
85B GLU 3.2 0.2 - - - -
86B ALA* 1.3 80.1 - - - +
88B GLU* 1.3 63.9 + - + +
91B ASN* 3.1 31.3 + - - +
92B VAL 3.3 10.7 + - - +
93B GLU* 3.4 34.3 + - - +
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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 ARG* 2.9 57.7 + - + +
85B GLU* 4.1 11.5 - - - +
87B ARG* 1.3 84.2 - - + +
89B GLU* 1.3 58.1 + - + +
91B ASN* 4.6 3.8 - - - +
130B ASN* 3.3 29.6 + - - +
133B ASP* 5.1 0.9 - - - +
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Residues in contact with GLU 89 (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 LYS* 4.8 3.5 + - - -
67B SER 5.5 0.4 - - - -
68B VAL* 3.1 16.2 - - + +
69B GLY 3.0 37.2 + - - +
85B GLU* 2.8 39.5 + - - +
88B GLU* 1.3 76.6 - - + +
90B LEU* 1.3 68.4 + - + +
91B ASN 3.6 0.2 - - - -
129B PHE* 3.3 4.5 - - - +
130B ASN* 2.8 31.2 + - - -
133B ASP* 3.5 34.0 - - + +
134B ILE* 4.3 10.4 - - + +
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Residues in contact with LEU 90 (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 LEU* 4.5 11.9 - - + -
49B TRP* 3.8 22.4 - - + -
67B SER* 3.7 30.5 - - - +
68B VAL* 4.2 21.3 - - + -
86B ALA* 3.1 12.3 + - + +
89B GLU* 1.3 86.0 - - + +
91B ASN* 1.3 72.7 + - - +
92B VAL* 3.2 23.7 - - + +
121B LEU* 5.0 6.7 - - + -
127B PRO* 4.1 23.1 - - + +
128B ILE* 3.7 15.6 + - - +
129B PHE* 4.3 5.6 - - + +
134B ILE* 3.9 6.7 - - + -
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Residues in contact with ASN 91 (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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86B ALA 3.2 0.4 + - - -
87B ARG* 3.1 22.0 + - - +
88B GLU* 4.8 4.0 - - - +
90B LEU* 1.3 78.3 - - - +
92B VAL* 1.3 62.0 + - - +
93B GLU* 5.2 1.3 - - - -
128B ILE* 2.7 35.5 + - + +
129B PHE 4.3 7.5 + - - -
130B ASN* 4.4 10.9 + - - +
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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