Contacts of the helix formed by residues 82 - 92 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D GLU* 3.8 22.2 - - + +
53D LEU* 4.4 0.4 - - - +
56D SER* 3.9 4.9 + - - -
71D LEU* 3.9 24.2 - - + -
73D THR* 4.5 0.7 - - + -
78D GLY 3.4 8.0 + - - +
79D GLU 3.1 9.5 + - - +
80D LEU 3.0 0.8 - - - -
81D SER* 1.3 78.1 - - - +
83D MET* 1.3 64.2 + - - +
84D ASN 3.3 2.2 - - - -
85D GLY* 2.9 15.0 + - - -
86D ILE* 3.1 14.0 + - + +
98D HIS* 4.2 8.1 - - + -
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Residues in contact with MET 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 3.9 17.0 - - + +
83C MET* 4.3 14.1 - - + +
129C MET* 3.6 27.1 - - - -
79D GLU* 3.3 10.1 + - + +
80D LEU* 3.1 46.3 + - + +
81D SER 3.4 0.4 - - - -
82D ALA* 1.3 76.6 - - - +
84D ASN* 1.3 59.0 + - - +
86D ILE* 3.3 3.0 + - + +
87D ALA* 2.9 30.6 + - - +
98D HIS* 6.0 2.9 - - + -
126D PHE 4.9 1.6 - - - +
129D MET* 4.3 4.7 - - - +
130D SER* 3.4 38.1 - - - +
133D ILE* 3.6 20.0 - - + +
164D TYR* 5.8 1.1 - - + -
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Residues in contact with ASN 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C VAL* 3.4 13.2 - - - +
80C LEU* 3.9 10.1 + - - +
81C SER* 2.9 38.9 + - - +
53D LEU* 4.2 9.0 - - + -
57D TYR* 3.2 10.1 + - - -
81D SER 4.9 1.2 + - - -
82D ALA 3.3 1.0 - - - -
83D MET* 1.3 78.0 - - - +
85D GLY* 1.3 63.4 + - - +
87D ALA* 3.6 1.5 - - - +
88D GLY* 3.1 16.3 + - - -
407D TRP* 2.8 45.5 + - - +
409D SER* 2.9 23.2 + - - -
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Residues in contact with GLY 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 4.0 2.6 - - - +
56D SER* 3.3 27.6 + - - +
57D TYR* 4.3 17.7 - - - -
60D ASP* 4.7 1.6 - - - +
82D ALA 2.9 7.7 + - - -
84D ASN* 1.3 76.5 - - - +
86D ILE* 1.3 65.7 + - - -
88D GLY* 3.0 4.2 + - - -
89D SER* 3.0 24.3 + - - -
404D GLN* 5.7 0.3 + - - -
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Residues in contact with ILE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D SER* 4.5 2.9 - - - -
71D LEU* 4.0 14.6 - - + -
82D ALA 3.1 13.0 + - - +
83D MET* 3.9 7.4 - - + +
85D GLY* 1.3 75.1 - - - +
87D ALA* 1.3 52.2 + - - +
89D SER* 3.0 6.5 + - - +
90D TYR* 2.8 33.3 + - - +
96D VAL* 4.2 23.3 - - + +
98D HIS* 3.7 40.4 - - + +
130D SER* 5.1 2.2 - - - +
133D ILE* 3.6 33.4 - - + +
134D THR* 4.3 7.0 - - + -
162D PRO* 3.7 12.3 - - + -
164D TYR* 6.6 0.2 - - + -
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Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 3.4 25.8 - - + -
118C LEU* 4.2 4.5 - - + +
83D MET 2.9 18.6 + - - +
84D ASN 3.6 1.1 - - - +
86D ILE* 1.3 76.5 - - - +
88D GLY* 1.3 57.8 + - - +
90D TYR* 3.2 3.1 + - - +
91D ALA* 2.8 29.8 + - - +
133D ILE* 3.8 22.6 - - + +
407D TRP* 3.6 18.6 - - + -
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Residues in contact with GLY 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ASP* 4.3 3.8 - - - +
84D ASN 3.1 7.7 + - - -
85D GLY 3.0 7.3 + - - -
87D ALA* 1.3 75.6 - - - +
89D SER* 1.3 62.9 + - - +
91D ALA* 3.2 0.7 + - - +
92D GLU* 2.9 31.2 + - - +
404D GLN* 4.1 7.4 - - - -
407D TRP* 3.3 32.9 - - - +
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Residues in contact with SER 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D SER 4.9 1.2 + - - -
60D ASP* 2.7 28.3 + - - +
85D GLY 3.0 12.9 + - - -
86D ILE* 3.0 10.7 + - - +
88D GLY* 1.3 75.6 - - - +
90D TYR* 1.3 58.5 + - - +
92D GLU 3.4 0.2 + - - -
93D HIS 2.9 10.9 + - - -
94D VAL* 2.8 46.0 + - - +
96D VAL* 3.6 18.3 - - - +
162D PRO* 3.5 10.1 - - - -
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Residues in contact with TYR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 3.6 32.1 - - + -
120C ASP* 5.4 5.3 + - + -
125C HIS* 6.3 0.2 - + - -
86D ILE 2.8 11.6 + - - +
87D ALA 3.5 7.0 - - - +
89D SER* 1.3 73.8 - - - +
91D ALA* 1.3 63.7 + - - +
92D GLU 3.4 0.5 + - - -
93D HIS 3.4 4.3 + - - -
132D PRO 3.8 11.5 + - - -
133D ILE* 3.2 37.0 - - + +
134D THR* 3.6 26.5 - - - -
135D VAL* 3.9 5.0 - - + +
161D ARG* 2.9 72.1 + - - -
162D PRO* 3.4 14.3 - - + +
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Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C THR 3.7 22.7 - - - +
118C LEU* 4.0 17.5 - - - +
87D ALA 2.8 20.4 + - - +
88D GLY 3.6 4.5 - - - +
90D TYR* 1.3 77.5 - - - +
92D GLU* 1.3 59.6 + - + +
93D HIS* 3.7 10.4 + - - -
218D PHE* 4.8 2.1 - - - -
406D LEU* 3.4 21.9 - - + +
407D TRP* 4.0 21.1 - - + -
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ARG* 3.0 25.7 + - - +
88D GLY 2.9 17.3 + - - +
89D SER 3.5 0.2 - - - -
91D ALA* 1.3 82.3 - - + +
93D HIS* 1.3 57.8 + - - +
94D VAL* 3.5 4.2 - - + +
218D PHE* 3.6 10.4 - - - -
222D ARG* 2.7 42.5 + - - +
245D MET* 3.5 17.5 - - + +
403D VAL 3.5 3.6 - - - +
404D GLN* 3.1 28.3 - - + -
406D LEU* 2.8 34.2 + - + +
407D 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