Contacts of the helix formed by residues 78 - 99 (chain B) in PDB entry 2O3B
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 GLU 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ASP 5.5 1.0 - - - +
76B TRP 4.2 8.2 - - - +
77B TYR* 1.3 80.8 - - - +
79B ASP* 1.3 73.6 + - - +
80B GLU* 3.3 3.3 + - + +
81B GLU* 3.1 14.2 + - - +
82B ASN* 2.9 31.7 + - - +
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Residues in contact with ASP 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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78B GLU* 1.3 81.5 - - - +
80B GLU* 1.3 63.4 + - - +
82B ASN* 3.3 7.6 + - - +
83B ALA* 3.0 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
----------------------------------------------------------
113A SER* 3.3 36.7 + - - +
116A SER* 5.5 3.1 - - - -
191A LYS* 5.7 4.4 - - - -
78B GLU* 3.3 2.1 - - + +
79B ASP* 1.3 78.5 - - - +
81B GLU* 1.3 72.4 + - + +
83B ALA* 3.6 4.5 + - - +
84B VAL* 3.4 26.3 + - + +
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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
----------------------------------------------------------
111A THR* 4.2 5.7 + - - +
112A PRO* 6.4 0.4 - - + -
113A SER* 3.4 26.6 + - - +
76B TRP* 3.8 21.4 - - + -
77B TYR* 3.4 41.3 - - + -
78B GLU* 3.1 27.2 + - - +
80B GLU* 1.3 80.3 - - + +
82B ASN* 1.3 66.6 + - - +
84B VAL* 3.4 6.9 + - - +
85B VAL* 3.0 28.8 + - - +
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Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PRO* 4.9 9.0 - - - +
77B TYR* 3.6 24.6 + - - +
78B GLU* 2.9 32.5 + - - +
79B ASP* 3.8 8.1 + - - +
81B GLU* 1.3 72.7 - - - +
83B ALA* 1.3 65.7 + - - +
85B VAL* 3.3 7.0 + - - +
86B ALA* 3.0 24.1 + - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASP 3.0 16.7 + - - +
80B GLU* 3.9 5.6 - - - +
82B ASN* 1.3 76.0 - - - +
84B VAL* 1.3 63.9 + - + +
86B ALA* 3.3 8.4 + - - +
87B LYS* 3.1 40.1 + - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.4 7.0 - - + -
20B LEU 5.5 1.6 - - - +
70B ALA 5.4 0.7 - - - +
80B GLU* 3.4 17.6 + - + +
81B GLU* 3.4 10.4 + - - +
82B ASN 3.3 0.6 - - - -
83B ALA* 1.3 76.2 - - + +
85B VAL* 1.3 67.1 + - + +
87B LYS* 3.4 13.1 + - + +
88B PHE* 3.1 47.4 + - + -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ARG 5.5 0.2 - - - +
70B ALA 3.7 15.0 - - - +
71B THR 3.8 24.9 - - - +
72B THR 4.7 1.8 - - - +
73B PRO* 4.5 14.1 - - + -
77B TYR* 3.5 31.4 - - + +
81B GLU 3.0 19.9 + - - +
82B ASN* 3.6 9.9 - - - +
83B ALA 3.3 0.2 - - - -
84B VAL* 1.3 75.7 - - + +
86B ALA* 1.3 65.2 + - - +
88B PHE* 3.1 3.1 + - - +
89B GLN* 2.9 40.4 + - - +
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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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82B ASN 3.0 13.6 + - - +
83B ALA* 3.6 10.8 - - - +
85B VAL* 1.3 77.1 - - - +
87B LYS* 1.3 57.6 + - + +
89B GLN* 3.3 14.7 + - - +
90B LYS* 3.0 31.4 + - - +
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Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA 4.3 7.2 - - - +
17B ASP 6.0 1.8 - - - +
18B GLY 5.7 4.9 + - - +
19B LEU* 4.2 22.7 - - + +
83B ALA* 3.1 29.3 + - - +
84B VAL* 3.7 12.1 - - + +
85B VAL 3.2 0.2 - - - -
86B ALA* 1.3 77.2 - - + +
88B PHE* 1.3 57.2 + - - +
90B LYS* 3.6 15.8 + - - +
91B LEU* 3.0 26.3 + - - +
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.3 44.4 - - + -
20B LEU 3.7 17.9 - - - -
21B PHE* 4.2 13.0 - + - -
22B MET 5.4 0.4 - - - -
29B PHE* 3.8 22.2 - + - -
67B PHE* 4.2 12.9 - + - -
70B ALA* 3.5 42.8 - - + +
71B THR* 3.8 8.4 - - + +
84B VAL* 3.1 39.5 + - + +
85B VAL 3.1 1.3 + - - +
87B LYS* 1.3 73.4 - - - +
89B GLN* 1.3 61.9 + - - +
90B LYS 3.1 1.6 - - - -
91B LEU* 3.6 7.0 - - + +
92B LEU* 2.8 30.5 + - - +
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 3.1 40.3 + - - +
73B PRO* 4.7 5.3 - - - +
85B VAL* 2.9 31.6 + - - +
86B ALA* 3.3 13.4 + - - +
88B PHE* 1.3 76.9 - - - +
90B LYS* 1.3 61.6 + - - +
92B LEU* 3.8 5.2 - - - +
93B GLU* 3.1 22.5 + - - +
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Residues in contact with LYS 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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14B GLN 6.1 0.2 - - - +
15B ALA* 5.3 11.0 - - + +
86B ALA 3.0 17.3 + - - +
87B LYS* 3.7 15.4 - - - +
89B GLN* 1.3 75.7 - - - +
91B LEU* 1.3 65.8 + - - +
93B GLU* 3.1 16.6 + - - +
94B VAL* 3.0 37.1 + - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.4 8.7 - - + +
15B ALA* 3.6 37.0 - - + +
16B SER* 4.2 10.8 - - - +
19B LEU* 3.6 24.0 - - + -
29B PHE* 4.1 12.1 - - + -
67B PHE* 4.9 5.6 - - + -
87B LYS 3.0 18.7 + - - +
88B PHE* 3.2 11.9 + - + +
90B LYS* 1.3 77.3 - - - +
92B LEU* 1.3 62.5 + - - +
94B VAL* 3.2 2.4 + - - +
95B ILE* 3.0 37.1 + - + +
128B ILE* 4.0 26.0 - - + -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.5 26.0 - - + +
64B ASP* 4.3 16.4 - - - +
67B PHE* 3.5 36.6 - - + -
71B THR* 4.4 22.0 - - + +
88B PHE 2.8 17.0 + - - +
89B GLN* 3.8 5.8 - - - +
91B LEU* 1.3 76.5 - - - +
93B GLU* 1.3 62.6 + - - +
95B ILE* 3.2 9.2 + - - +
96B LYS* 3.0 40.4 + - + +
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Residues in contact with GLU 93 (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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89B GLN 3.1 11.8 + - - +
90B LYS* 3.1 20.7 + - - +
92B LEU* 1.3 75.8 - - - +
94B VAL* 1.3 69.2 + - + +
95B ILE 3.0 0.3 + - - -
96B LYS* 3.1 7.4 + - - +
97B SER* 2.9 36.7 + - - +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 3.7 39.3 - - + +
12B LEU* 4.3 10.6 - - + +
15B ALA* 3.9 17.9 - - + -
90B LYS* 3.0 23.6 + - + +
91B LEU 3.6 6.1 - - - +
93B GLU* 1.3 79.1 - - + +
95B ILE* 1.3 61.6 + - - +
97B SER* 4.0 3.8 - - - -
98B ASN* 3.0 45.8 + - - +
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Residues in contact with ILE 95 (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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12B LEU* 4.1 22.7 - - + -
63B ILE* 3.5 22.0 - - + -
67B PHE* 4.2 15.5 - - + -
91B LEU* 3.0 23.1 + - + +
92B LEU* 3.3 9.6 - - - +
93B GLU 3.0 0.8 - - - -
94B VAL* 1.3 74.7 - - - +
96B LYS* 1.3 61.9 + - - +
99B LEU* 2.8 48.6 + - + +
102B PRO* 4.2 10.1 - - + -
116B VAL* 4.0 15.9 - - + -
128B ILE* 3.7 28.5 - - + -
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Residues in contact with LYS 96 (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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63B ILE* 4.0 23.1 - - + -
64B ASP* 2.6 34.5 + - - -
92B LEU* 3.0 37.6 + - + +
93B GLU* 3.1 5.8 + - - +
95B ILE* 1.3 77.6 - - + +
97B SER* 1.3 61.5 + - - +
98B ASN 3.5 0.2 - - - -
99B LEU 3.6 12.9 - - - +
102B PRO* 4.6 9.6 - - + -
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Residues in contact with SER 97 (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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1B SER* 4.1 19.6 + - - -
93B GLU* 2.9 31.2 + - - +
94B VAL* 4.0 5.6 - - - -
96B LYS* 1.3 80.8 - - - +
98B ASN* 1.3 68.5 + - - +
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Residues in contact with ASN 98 (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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1B SER* 4.5 13.5 - - - -
3B LYS* 4.1 13.2 - - - +
8B ILE* 4.0 32.2 - - + +
11B GLN* 3.4 38.8 + - - +
12B LEU* 5.8 0.8 - - + +
94B VAL* 3.0 31.0 + - - +
97B SER* 1.3 86.6 - - - +
99B LEU* 1.3 62.9 + - + +
100B LYS* 4.0 0.3 + - - +
119B GLU 3.7 8.1 - - - +
121B PRO* 3.9 17.2 - - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.2 13.2 - - + -
12B LEU* 4.6 11.7 - - + -
95B ILE* 2.8 42.0 + - + +
96B LYS 3.6 10.7 - - - +
97B SER 5.4 0.2 - - - -
98B ASN* 1.3 77.4 - - + +
100B LYS* 1.3 59.9 + - - +
102B PRO* 3.3 20.5 - - + +
116B VAL* 4.9 4.5 - - + +
118B GLY* 3.9 23.3 - - - +
119B GLU 3.5 1.1 - - - +
120B THR* 4.1 24.2 - - + -
126B ALA 3.8 28.7 - - - +
127B GLY* 3.9 14.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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