Contacts of the helix formed by residues 73 - 87 (chain B) in PDB entry 2OHW
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 GLN 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B GLU 3.9 3.6 + - - +
72B LEU* 1.3 74.3 - - - +
74B TYR* 1.3 66.7 + - - +
75B GLN* 3.3 9.5 + - + +
76B SER* 2.9 29.7 + - - +
77B TYR* 3.4 5.9 - - - -
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Residues in contact with TYR 74 (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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72B LEU 4.0 0.2 + - - -
73B GLN* 1.3 72.0 - - - +
75B GLN* 1.3 68.9 + - + +
76B SER 3.0 0.7 + - - -
77B TYR* 3.0 33.6 + + - +
78B SER* 2.9 45.2 + - - -
81B ILE* 4.1 24.6 - - + +
82B GLN* 5.2 5.5 + - - -
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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
----------------------------------------------------------
73B GLN* 3.2 8.6 + - + +
74B TYR* 1.3 82.9 - - + +
76B SER* 1.3 62.6 + - - +
78B SER* 3.4 16.5 + - - +
79B SER* 5.1 1.2 + - - -
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.4 25.1 - - - +
46B LEU* 3.2 33.0 - - - +
47B ARG 5.5 0.3 - - - +
72B LEU* 4.5 11.3 - - - +
73B GLN* 2.9 25.7 + - - +
75B GLN* 1.3 80.8 - - - +
77B TYR* 1.3 59.4 + - - +
79B SER* 5.1 2.1 + - - -
80B TYR* 4.6 3.6 - - - -
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Residues in contact with TYR 77 (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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45B VAL* 4.2 15.3 - - + -
68B ILE* 3.5 30.7 - - + +
69B ASN 4.7 0.9 - - - -
70B GLY* 5.6 0.4 - - - -
72B LEU* 3.4 34.4 + - + -
73B GLN 3.4 19.5 - - - -
74B TYR* 3.0 28.4 + + - +
76B SER* 1.3 75.9 - - - +
78B SER* 1.3 66.7 + - - +
79B SER 3.2 3.8 - - - -
80B TYR* 3.0 20.2 + - - +
81B ILE* 3.4 34.4 + - + +
93B ILE* 3.8 29.6 - - + +
105B ILE* 4.6 7.6 - - + -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 2.9 46.4 + - - -
75B GLN* 3.4 16.8 + - - +
76B SER 3.6 1.0 - - - -
77B TYR* 1.3 82.1 - - - +
79B SER* 1.3 65.2 + - - +
81B ILE* 3.3 8.2 + - - +
82B GLN* 3.2 26.2 + - - +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER 5.1 2.9 + - - -
50B PRO* 3.9 33.9 - - - +
75B GLN 5.1 1.5 + - - -
76B SER 5.1 1.5 + - - -
77B TYR 3.1 1.4 + - - -
78B SER* 1.3 82.3 + - - +
80B TYR* 1.3 63.2 + - - +
82B GLN* 3.3 10.8 + - - +
83B MET* 3.1 30.6 + - - +
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Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.6 13.2 - - + +
44B GLN 4.3 4.5 + - - -
45B VAL* 4.1 21.6 + - + -
47B ARG 5.4 0.6 + - - -
49B LYS 4.6 0.3 + - - -
50B PRO* 3.4 16.9 - - + +
51B TYR* 3.0 41.6 + - - -
54B ALA* 3.9 26.7 - - + -
58B LEU* 4.3 4.4 - - + +
66B LEU* 3.5 15.6 - - + +
76B SER 4.6 2.2 - - - -
77B TYR* 3.0 18.7 + - + +
79B SER* 1.3 78.9 - - - +
81B ILE* 1.3 59.5 + - - +
83B MET* 3.4 17.6 + - - +
84B ALA* 2.9 29.8 + - - +
105B ILE* 3.3 34.1 - - + -
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Residues in contact with ILE 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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66B LEU* 4.4 3.8 - - - -
68B ILE* 3.8 19.7 - - + -
74B TYR* 4.1 21.8 - - + +
77B TYR* 3.4 34.0 + - + +
78B SER* 3.3 9.3 + - - +
80B TYR* 1.3 74.9 - - - +
82B GLN* 1.3 69.7 + - + +
84B ALA* 3.3 3.7 + - - +
85B SER* 2.9 27.7 + - - +
91B PHE* 3.6 45.8 - - + -
93B ILE* 4.8 0.4 - - + -
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Residues in contact with GLN 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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74B TYR* 5.2 5.5 + - - -
78B SER* 3.2 16.3 + - - +
79B SER* 3.4 11.7 - - - +
80B TYR 3.3 0.2 - - - -
81B ILE* 1.3 81.3 - - + +
83B MET* 1.3 62.8 + - + +
85B SER* 3.4 5.0 + - - -
86B ARG* 3.0 23.7 + - - +
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Residues in contact with MET 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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50B PRO* 3.5 33.7 - - + -
51B TYR 4.1 8.3 - - - +
52B LYS* 5.2 2.9 - - + +
55B GLU* 3.7 53.6 - - + +
58B LEU* 3.6 13.0 - - + -
79B SER 3.1 16.1 + - - +
80B TYR* 3.5 31.6 - - - +
82B GLN* 1.3 76.1 - - + +
84B ALA* 1.3 63.9 + - - +
86B ARG* 3.2 13.7 + - - +
87B TYR* 3.2 24.0 - - - -
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Residues in contact with ALA 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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58B LEU* 3.8 9.1 - - + +
66B LEU* 3.9 20.0 - - + -
80B TYR 2.9 17.4 + - - +
81B ILE* 3.7 4.7 - - - +
83B MET* 1.3 76.5 - - - +
85B SER* 1.3 62.7 + - - +
87B TYR* 3.0 9.2 + - - -
89B VAL* 2.9 56.8 + - + +
91B PHE* 5.0 4.9 - - + -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 2.9 25.9 + - - +
82B GLN* 3.9 4.7 - - - -
84B ALA* 1.3 75.8 - - - +
86B ARG* 1.3 62.8 + - - +
88B GLY* 3.1 13.0 + - - +
89B VAL 4.5 4.2 + - - +
91B PHE* 4.4 11.3 - - - -
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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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55B GLU* 3.3 19.1 + - - -
82B GLN 3.0 13.8 + - - +
83B MET* 3.3 13.5 - - - +
84B ALA 3.2 0.2 - - - -
85B SER* 1.3 76.2 - - - +
87B TYR* 1.3 91.1 + - + +
88B GLY 3.9 0.3 + - - -
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Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU* 2.7 44.1 + - + -
58B LEU* 3.6 23.2 - - + +
59B LYS* 3.8 54.3 - - + +
83B MET* 3.2 21.3 + - - -
84B ALA 3.0 6.5 + - - +
86B ARG* 1.3 110.6 + - + +
88B GLY* 1.3 63.3 + - - +
89B VAL* 3.3 8.1 + - + +
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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
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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