Contacts of the helix formed by residues 93 - 99 (chain B) in PDB entry 1OHV
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 ASN 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B LEU* 2.8 43.9 + - - +
88B VAL 5.4 0.9 - - - +
90B GLN* 3.0 20.8 + - - +
92B GLN* 1.3 87.1 + - - +
94B VAL* 1.3 63.5 + - - +
95B SER 3.4 1.3 - - - -
96B THR* 3.3 18.1 + - - -
97B PHE* 3.1 21.8 - - + -
362B LEU* 3.6 32.8 - - + +
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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
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85A VAL* 4.1 26.9 - - + -
88A VAL* 4.2 27.8 - - + -
89A GLN* 4.8 15.7 - - + +
88B VAL 5.6 1.1 - - - +
90B GLN 3.9 2.9 + - - +
91B PRO* 3.2 28.8 + - + +
93B ASN* 1.3 76.6 - - - +
95B SER* 1.3 65.1 + - - +
97B PHE* 3.0 15.8 + - - +
98B ILE* 3.3 29.6 + - + +
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Residues in contact with SER 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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49A TYR* 3.2 22.8 - - - +
50A GLU* 3.7 32.7 + - - -
80A SER* 4.9 2.2 - - - -
92B GLN 4.5 1.5 + - - -
93B ASN 3.4 0.4 - - - -
94B VAL* 1.3 79.0 - - - +
96B THR* 1.3 56.3 + - - +
98B ILE* 4.0 5.4 - - - -
99B ASN* 2.8 60.8 + - - +
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Residues in contact with THR 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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50A GLU* 4.2 11.3 + - - -
92B GLN 5.0 0.3 + - - -
93B ASN* 3.3 18.9 + - - -
94B VAL 3.2 0.8 - - - -
95B SER* 1.3 78.7 - - - +
97B PHE* 1.3 59.5 + - - +
99B ASN 4.4 9.9 + - - +
100B ARG* 5.1 1.6 + - - +
110B ASN* 5.1 6.5 + - - +
357B ASP* 4.4 4.3 - - - +
358B PRO* 3.6 19.3 - - + +
359B SER* 3.5 38.4 + - - +
362B LEU* 4.2 18.5 - - + +
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Residues in contact with PHE 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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88A VAL* 4.1 27.1 - - + -
97A PHE* 3.5 41.9 - + + -
360A LYS* 4.6 9.4 + - - +
363A LEU* 3.4 21.7 - - - +
88B VAL* 3.9 37.5 - - + -
93B ASN* 3.1 28.5 - - + -
94B VAL 3.0 7.1 + - - +
96B THR* 1.3 80.2 - - - +
98B ILE* 1.3 58.7 + - - +
99B ASN 5.4 0.2 - - - -
100B ARG* 6.1 0.6 - - - +
359B SER* 3.6 27.6 - - - -
360B LYS* 6.4 0.2 - - - -
362B LEU* 4.1 22.9 - - + -
363B LEU* 4.5 11.2 - - + -
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Residues in contact with ILE 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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75A ILE* 5.1 3.6 - - - +
78A GLY 5.4 2.3 - - - +
80A SER* 3.7 22.0 - - - -
81A HIS 4.2 2.0 - - - +
84A LEU* 3.8 32.7 - - + +
85A VAL* 3.7 34.8 - - + +
88A VAL* 3.5 31.6 - - + -
332A MET* 5.0 7.7 - - - +
363A LEU* 4.2 11.2 - - + -
94B VAL* 3.5 17.5 - - + +
95B SER* 3.9 7.9 - - - +
97B PHE* 1.3 78.4 - - - +
99B ASN* 1.3 72.7 + - - +
100B ARG* 3.7 3.6 + - - -
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Residues in contact with ASN 99 (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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49A TYR* 3.5 29.5 + - + +
75A ILE* 4.6 6.5 - - - +
78A GLY 4.5 1.0 - - - +
79A TYR* 3.4 18.9 - - + +
80A SER* 2.8 45.2 + - - +
95B SER* 2.8 41.6 + - - +
96B THR* 4.4 6.5 - - - +
97B PHE 3.7 0.2 - - - -
98B ILE* 1.3 83.8 - - - +
100B ARG* 1.3 62.8 + - - +
101B PRO* 3.3 11.4 - - - +
358B PRO* 5.6 0.2 - - - +
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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