Contacts of the helix formed by residues 110 - 118 (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 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLU* 5.8 1.2 - - - +
96B THR* 5.1 6.1 + - - -
108B PRO* 3.6 22.8 - - - +
109B GLU* 1.3 78.6 - - + +
111B PHE* 1.3 62.1 + - - +
112B VAL 3.4 1.3 - - - -
113B GLU* 3.9 13.0 - - + -
114B LYS* 2.9 49.5 + - + +
358B PRO* 5.7 3.2 - - - +
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Residues in contact with PHE 111 (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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34A LEU* 4.0 27.8 - - + -
38A GLN* 4.2 12.3 - - - -
46A PHE* 4.2 3.8 - - + -
103B LEU* 3.7 37.2 - - + -
107B PRO* 4.0 19.5 - - + -
108B PRO* 2.9 27.3 + - + +
109B GLU 3.2 1.6 + - - -
110B ASN* 1.3 81.8 - - - +
112B VAL* 1.3 63.5 + - - +
114B LYS* 4.0 2.7 - - + +
115B LEU* 3.1 48.8 + - + +
132B THR* 4.2 17.5 - - + -
358B PRO* 5.4 2.9 - - + -
361B ASN* 3.8 25.4 - - - -
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Residues in contact with VAL 112 (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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30A LEU* 4.2 12.6 - - + +
33A GLN* 4.2 11.9 - - + +
34A LEU* 3.8 39.7 - - + +
37A ILE* 4.3 19.1 - - + -
46A PHE* 4.3 11.9 - - + -
109B GLU 4.7 1.8 + - - +
110B ASN 3.4 0.2 - - - -
111B PHE* 1.3 72.8 - - + +
113B GLU* 1.3 60.1 + - - +
115B LEU* 3.2 9.6 + - + +
116B ARG* 2.9 61.3 + - - +
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Residues in contact with GLU 113 (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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109B GLU 5.4 1.0 + - - +
110B ASN* 3.4 16.1 + - + +
112B VAL* 1.3 79.4 - - - +
114B LYS* 1.3 57.2 + - - +
116B ARG* 3.0 22.4 + - - +
117B GLU* 2.9 35.1 + - - +
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Residues in contact with LYS 114 (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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110B ASN* 2.9 38.5 + - - +
111B PHE* 4.0 4.3 - - + +
113B GLU* 1.3 77.2 - - - +
115B LEU* 1.3 52.8 + - - +
117B GLU* 2.9 31.3 + - + +
118B SER* 2.7 33.8 + - - -
358B PRO 5.3 0.9 - - - +
361B ASN* 3.8 30.5 - - + +
362B LEU* 3.8 30.0 - - + +
365B ALA* 3.7 19.9 - - + +
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Residues in contact with LEU 115 (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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34A LEU* 4.8 8.1 - - + -
37A ILE* 5.0 9.2 - - + -
38A GLN* 5.4 3.4 - - - +
111B PHE* 3.1 47.0 + - + +
112B VAL* 3.4 12.3 - - + +
114B LYS* 1.3 75.2 - - - +
116B ARG* 1.3 62.8 - - - +
118B SER* 3.2 9.5 + - - +
119B LEU* 3.3 16.2 + - + -
120B LEU* 3.0 38.9 + - + -
130B LEU* 4.1 25.4 - - + -
132B THR* 4.2 8.1 - - + -
361B ASN* 4.0 20.9 - - - +
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Residues in contact with ARG 116 (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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33A GLN* 3.3 40.6 + - - +
37A ILE* 5.3 4.8 - - - +
112B VAL* 2.9 44.0 + - - +
113B GLU* 3.0 24.4 + - - +
115B LEU* 1.3 76.7 - - - +
117B GLU* 1.3 60.3 + - - +
118B SER 3.4 0.7 + - - -
120B LEU* 4.0 20.3 - - + +
121B SER* 3.6 19.8 + - - -
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Residues in contact with GLU 117 (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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113B GLU* 2.9 21.3 + - - +
114B LYS* 2.9 45.3 + - - +
116B ARG* 1.3 77.7 - - - +
118B SER* 1.3 57.5 + - - +
121B SER* 3.8 9.6 + - - -
365B ALA* 3.7 28.2 - - + +
368B ILE* 4.3 6.6 - - - +
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Residues in contact with SER 118 (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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114B LYS 2.7 22.3 + - - -
115B LEU* 3.2 10.7 + - - +
117B GLU* 1.3 78.6 - - - +
119B LEU* 1.3 76.5 + - - +
120B LEU 3.3 1.8 - - - -
121B SER* 2.6 25.6 + - - -
122B VAL 3.8 0.7 + - - -
361B ASN* 4.4 8.7 + - - +
364B LEU* 4.1 14.8 - - - +
365B ALA* 3.8 23.6 - - - +
368B ILE* 3.5 15.2 - - - +
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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