Contacts of the helix formed by residues 82 - 92 (chain B) in PDB entry 1OVM
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 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLU* 3.8 20.0 - - + +
53B LEU* 4.5 0.2 - - - +
56B SER* 3.9 8.3 - - - -
71B LEU* 3.9 24.9 - - + -
73B THR* 4.5 1.1 - - + -
78B GLY 3.4 8.0 + - - +
79B GLU 3.1 9.9 + - - +
80B LEU 3.0 0.8 - - - -
81B SER* 1.3 78.8 - - - +
83B MET* 1.3 63.8 + - - +
84B ASN 3.3 2.9 - - - -
85B GLY* 2.9 13.9 + - - -
86B ILE* 3.1 14.1 + - + +
98B HIS* 4.3 6.5 - - + -
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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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80A LEU* 4.0 17.5 - - + +
83A MET* 4.4 12.8 - - + +
129A MET* 3.7 25.6 - - - -
79B GLU* 3.3 10.5 + - + +
80B LEU* 3.2 46.3 + - + +
81B SER 3.5 0.2 - - - -
82B ALA* 1.3 76.7 - - - +
84B ASN* 1.3 63.4 + - - +
85B GLY 3.1 0.2 + - - -
86B ILE* 3.2 5.5 + - + +
87B ALA* 2.9 24.8 + - - +
98B HIS* 5.9 3.4 - - + +
126B PHE 4.9 2.2 - - - +
129B MET* 4.2 5.2 - - - +
130B SER* 3.3 38.1 - - - +
133B ILE* 3.7 17.5 - - + +
164B TYR* 5.9 0.7 - - + -
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Residues in contact with ASN 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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77A VAL* 3.4 14.8 + - - +
80A LEU* 3.9 10.2 + - + +
81A SER* 3.1 35.5 + - - +
53B LEU* 4.2 8.5 - - + -
57B TYR* 3.0 12.5 + - - -
81B SER 5.0 0.8 + - - +
82B ALA 3.3 1.2 - - - -
83B MET* 1.3 78.5 - - - +
85B GLY* 1.3 61.1 + - - +
87B ALA* 3.7 2.4 + - - +
88B GLY* 3.1 16.1 + - - -
407B TRP* 2.8 43.8 + - - +
409B SER* 2.9 23.8 + - - -
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Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.0 2.8 - - - +
56B SER* 3.3 27.9 + - - +
57B TYR* 4.2 17.2 - - - -
60B ASP* 4.6 2.1 - - - +
82B ALA 2.9 5.3 + - - -
84B ASN* 1.3 77.4 - - - +
86B ILE* 1.3 65.7 + - - +
88B GLY* 3.0 4.2 + - - -
89B SER* 3.0 23.6 + - - -
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Residues in contact with ILE 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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56B SER* 4.8 2.9 - - - -
71B LEU* 4.0 22.0 - - + -
82B ALA 3.1 14.6 + - - +
83B MET* 3.8 6.7 - - + +
85B GLY* 1.3 75.0 - - - +
87B ALA* 1.3 57.9 + - - +
89B SER* 3.0 6.6 + - - +
90B TYR* 2.8 28.1 + - - +
96B VAL* 4.2 22.7 - - + +
98B HIS* 3.9 31.4 - - + +
130B SER* 5.1 2.9 - - - +
133B ILE* 3.5 33.4 - - + +
134B THR* 4.3 7.9 - - + -
162B PRO* 3.7 12.8 - - + -
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Residues in contact with ALA 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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80A LEU* 3.4 26.7 - - + -
118A LEU* 4.2 4.7 - - + +
83B MET 2.9 16.8 + - - +
84B ASN 3.7 1.3 - - - +
86B ILE* 1.3 77.5 - - - +
88B GLY* 1.3 57.5 + - - +
90B TYR* 3.2 2.5 + - - +
91B ALA* 2.8 30.5 + - - +
133B ILE* 3.9 23.5 - - + +
407B TRP* 3.6 18.6 - - + -
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Residues in contact with GLY 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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60B ASP* 4.3 3.7 - - - +
84B ASN 3.1 5.4 + - - -
85B GLY 3.0 7.1 + - - -
87B ALA* 1.3 79.0 - - - +
89B SER* 1.3 57.2 + - - +
91B ALA 3.3 0.5 + - - -
92B GLU* 3.0 35.9 + - - +
404B GLN* 4.1 8.1 - - - -
407B TRP* 3.3 32.3 - - - +
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Residues in contact with SER 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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56B SER 5.0 1.2 + - - -
60B ASP* 2.7 28.8 + - - +
85B GLY 3.0 12.9 + - - -
86B ILE* 3.0 11.3 + - - +
88B GLY* 1.3 75.3 - - - +
90B TYR* 1.3 57.7 + - - +
92B GLU 3.4 0.3 + - - -
93B HIS 3.0 9.7 + - - -
94B VAL* 2.7 39.7 + - - +
96B VAL* 3.7 14.9 - - - +
162B PRO* 3.4 17.2 - - - +
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Residues in contact with TYR 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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118A LEU* 3.6 32.8 - - + -
120A ASP* 5.5 5.0 + - + -
86B ILE 2.8 10.7 + - - +
87B ALA 3.6 3.8 - - - +
89B SER* 1.3 77.7 - - - +
91B ALA* 1.3 61.8 + - - +
92B GLU 3.3 0.3 + - - -
93B HIS 3.4 4.2 + - - -
132B PRO 3.9 11.0 + - - -
133B ILE* 3.3 35.4 - - + +
134B THR* 3.6 26.7 + - - -
135B VAL* 3.9 5.4 - - + +
161B ARG* 2.8 73.3 + - + -
162B PRO* 3.4 13.4 - - + +
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR 3.7 22.7 - - - +
118A LEU* 4.0 17.5 - - - +
87B ALA 2.8 21.1 + - - +
88B GLY 3.3 4.7 + - - +
90B TYR* 1.3 77.2 - - - +
92B GLU* 1.3 60.0 + - + +
93B HIS* 3.7 9.0 + - - -
161B ARG* 4.4 0.9 + - - -
218B PHE* 4.8 2.1 - - - -
406B LEU* 3.4 21.8 - - + +
407B TRP* 4.0 20.4 - - + -
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Residues in contact with GLU 92 (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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64B ARG* 2.9 29.8 + - - +
88B GLY 3.0 17.7 + - - +
91B ALA* 1.3 82.0 - - + +
93B HIS* 1.3 58.1 + - - +
94B VAL* 3.5 4.0 + - + -
218B PHE* 3.7 10.2 - - - -
222B ARG* 2.7 37.6 + - - +
245B MET* 3.5 18.1 - - + +
403B VAL 3.5 3.5 - - - +
404B GLN* 3.2 29.3 - - + +
406B LEU* 2.8 32.5 + - + +
407B TRP* 3.0 9.9 + - + +
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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