Contacts of the helix formed by residues 76 - 90 (chain B) in PDB entry 2I2X
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 ALA 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ILE* 3.9 12.9 - - + +
43B ILE* 3.8 37.8 - - + +
44B ALA* 4.5 6.9 + - - +
47B ILE* 5.4 0.5 - - - +
59B LEU* 4.7 1.8 - - + -
72B LEU* 2.7 40.9 + - + +
75B ASP* 1.3 77.1 - - - +
77B LEU* 1.3 60.7 + - - +
78B MET 3.8 0.2 - - - -
79B VAL* 4.3 2.6 - - - +
80B GLY* 3.7 15.1 + - - -
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.8 24.9 - - + -
47B ILE* 3.9 22.0 - - + +
55B VAL* 4.1 10.1 - - + -
59B LEU* 4.3 9.0 - - + -
72B LEU 3.0 12.0 + - - +
73B ILE* 3.4 15.0 - - + +
76B ALA* 1.3 75.9 - - - +
78B MET* 1.3 60.7 + - + +
79B VAL 3.3 1.8 - - - -
80B GLY* 3.7 0.5 + - - -
81B MET* 3.1 28.9 + - - +
105B MET* 3.7 22.4 - - + +
108B GLY* 3.5 8.7 - - - +
109B ILE* 3.4 41.5 - - + +
112B CYS* 4.6 6.1 - - - -
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Residues in contact with MET 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 2.8 27.6 + - + +
74B ASP* 3.7 30.2 - - + +
77B LEU* 1.3 70.8 - - + +
79B VAL* 1.3 61.0 + - + +
81B MET* 4.0 6.8 - - - +
82B GLY* 3.1 21.7 + - - -
105B MET* 5.4 5.8 - - - +
109B ILE* 6.3 2.7 - - + -
123B LYS* 5.9 1.6 - - - -
148B ARG 4.7 5.4 - - - +
149B ALA* 3.8 16.5 - - - +
150B ASN* 4.0 4.5 - - - +
151B GLY* 3.5 38.1 - - - +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU 5.8 0.2 - - - +
35B PRO* 3.8 33.4 - - + -
40B ILE* 5.4 0.2 - - + -
44B ALA* 5.2 0.2 - - - -
74B ASP 3.5 18.2 - - - +
75B ASP* 3.4 27.1 - - - +
76B ALA 4.8 1.1 - - - +
77B LEU 3.3 1.0 - - - +
78B MET* 1.3 76.8 - - - +
80B GLY* 1.3 63.0 + - - +
82B GLY* 3.3 2.9 + - - -
83B VAL* 3.3 24.1 + - + +
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA* 4.0 28.6 - - - +
47B ILE* 3.4 16.9 - - - +
48B PHE* 5.4 0.2 - - - +
76B ALA 3.7 8.4 + - - -
77B LEU 3.7 3.7 + - - -
79B VAL* 1.3 75.7 - - - +
81B MET* 1.3 64.0 + - - +
83B VAL* 3.1 19.0 + - - +
84B VAL* 3.2 14.0 + - - +
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Residues in contact with MET 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.5 6.9 - - + +
77B LEU 3.1 19.3 + - - +
78B MET* 4.1 6.3 - - - +
80B GLY* 1.3 75.5 - - - +
82B GLY* 1.3 56.0 + - - +
84B VAL* 3.1 9.6 + - + +
85B ILE* 2.9 44.8 + - + +
98B VAL* 4.1 19.5 - - + +
101B SER* 4.2 25.8 - - - +
102B ALA* 3.8 29.8 - - + +
105B MET* 3.9 23.8 - - + +
145B ALA 5.3 0.9 - - - +
149B ALA* 3.6 30.5 - - + +
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B MET 3.1 19.6 + - - -
79B VAL* 3.3 3.6 + - - -
80B GLY 3.2 0.8 - - - -
81B MET* 1.3 72.9 - - - +
83B VAL* 1.3 63.1 + - - +
85B ILE* 4.0 12.1 - - - +
86B ARG* 3.3 22.9 + - - +
149B ALA 5.7 0.2 - - - -
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 4.1 15.0 - - + +
33B LEU* 3.8 43.7 - - + +
34B TYR* 4.5 15.3 - - + +
35B PRO* 4.9 2.9 - - + -
48B PHE* 5.1 3.6 - - + -
79B VAL* 3.3 17.4 + - + +
80B GLY* 3.1 12.7 + - - +
82B GLY* 1.3 77.1 - - - +
84B VAL* 1.3 64.2 + - + +
86B ARG* 3.2 6.1 + - - +
87B LEU* 3.0 42.1 + - + +
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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
----------------------------------------------------------
47B ILE* 3.9 7.9 - - + -
48B PHE* 3.8 36.6 - - + -
80B GLY 3.4 14.1 - - - +
81B MET* 3.1 15.0 + - + +
83B VAL* 1.3 77.0 - - + +
85B ILE* 1.3 56.2 + - - +
87B LEU* 4.9 1.1 - - - -
88B TYR* 2.9 25.1 + - - +
93B ILE* 3.4 24.7 - - + +
98B VAL* 4.0 20.9 - - + -
101B SER* 3.8 24.5 - - - +
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Residues in contact with ILE 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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81B MET* 2.9 31.6 + - + +
82B GLY* 4.0 9.0 - - - +
84B VAL* 1.3 75.4 - - + +
86B ARG* 1.3 60.2 + - - +
88B TYR* 3.7 6.9 - - + +
89B ASP* 2.9 42.5 + - - +
98B VAL* 5.4 4.0 - - + -
146B LEU* 4.4 21.1 - - + -
149B ALA* 3.4 47.8 - - + +
150B ASN* 5.2 11.4 - - - +
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Residues in contact with ARG 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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33B LEU* 3.5 43.5 - - + +
82B GLY 3.3 16.5 + - - +
83B VAL* 3.2 7.2 + - - +
85B ILE* 1.3 76.9 - - - +
87B LEU* 1.3 59.3 + - - +
89B ASP* 3.2 9.7 + - - +
90B GLU* 2.8 58.2 + - - +
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Residues in contact with LEU 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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26B PRO 4.6 0.7 - - - +
29B ALA* 4.1 13.2 - - + +
30B ALA* 3.8 34.8 - - + +
33B LEU* 3.8 20.4 - - + -
48B PHE* 4.0 16.2 - - + -
83B VAL* 3.0 20.7 + - + +
84B VAL* 3.9 1.3 - - - +
86B ARG* 1.3 73.4 - - - +
88B TYR* 1.3 63.0 + - - +
90B GLU* 3.4 16.9 + - - +
91B GLY 2.9 4.2 + - - -
92B VAL* 2.8 50.7 + - + -
93B ILE* 3.8 15.7 - - + -
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Residues in contact with TYR 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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236A LYS* 3.2 45.1 + - + +
237A ASN* 2.8 22.1 + - - -
84B VAL 2.9 17.8 + - - +
85B ILE* 3.7 7.4 - - + +
87B LEU* 1.3 75.2 - - - +
89B ASP* 1.3 67.2 + - - +
91B GLY* 2.9 18.4 + - - -
93B ILE* 3.5 20.9 - - + +
94B PHE 3.9 1.3 - - - -
95B LEU* 3.5 30.0 - - + +
98B VAL* 3.6 26.5 - - + -
142B ILE* 5.0 6.8 - - + +
146B LEU* 4.5 30.5 - - + -
230B GLU* 5.2 4.7 + - - -
232B ALA* 6.2 3.4 - - + -
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Residues in contact with ASP 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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236A LYS* 3.3 17.3 + - - +
85B ILE* 2.9 35.8 + - - +
86B ARG* 3.4 7.8 - - - +
88B TYR* 1.3 80.7 - - - +
90B GLU* 1.3 61.9 + - + +
91B GLY 3.2 0.9 + - - -
146B LEU* 5.7 2.3 - - - +
232B ALA* 4.8 13.2 - - - +
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Residues in contact with GLU 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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22B LYS* 3.6 37.0 + - - +
33B LEU* 5.4 0.9 - - - +
86B ARG* 2.8 58.3 + - + +
87B LEU* 3.9 12.1 - - - +
89B ASP* 1.3 72.9 - - + +
91B GLY* 1.3 60.5 + - - +
92B VAL* 3.3 14.8 + - + +
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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