Contacts of the helix formed by residues 110 - 118 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A THR* 5.1 6.8 + - - +
108A PRO* 3.6 22.6 - - - +
109A GLU* 1.3 78.6 - - + +
111A PHE* 1.3 60.7 + - - +
112A VAL 3.4 1.6 - - - -
113A GLU* 3.9 12.6 - - + -
114A LYS* 2.9 50.7 + - + +
358A PRO* 5.7 3.2 - - - +
50B GLU* 5.8 0.6 - - - +
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Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.8 36.6 - - + -
107A PRO* 4.0 19.5 - - + -
108A PRO* 2.9 26.7 + - + +
109A GLU 3.2 1.6 + - - -
110A ASN* 1.3 82.5 - - - +
112A VAL* 1.3 63.2 + - + +
114A LYS* 4.0 2.7 - - + +
115A LEU* 3.2 49.4 + - + +
132A THR* 4.1 17.9 - - + -
358A PRO* 5.4 2.5 - - + -
361A ASN* 3.8 25.4 - - - -
34B LEU* 4.1 26.9 - - + -
38B GLN* 4.3 11.7 - - - -
46B PHE* 4.3 4.0 - - + -
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU 4.6 1.8 + - - +
110A ASN 3.4 0.2 - - - -
111A PHE* 1.3 77.4 - - + +
113A GLU* 1.3 57.7 + - - +
115A LEU* 3.2 9.6 + - + +
116A ARG* 2.9 62.0 + - + +
120A LEU* 5.3 0.4 - - + -
30B LEU* 4.3 10.8 - - + +
33B GLN* 4.2 10.8 - - + +
34B LEU* 3.9 39.5 - - + +
37B ILE* 4.3 20.0 - - + -
46B PHE* 4.4 11.4 - - + -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU 5.3 0.8 + - - +
110A ASN* 3.4 16.1 + - + +
112A VAL* 1.3 78.4 - - - +
114A LYS* 1.3 59.1 + - - +
116A ARG* 3.1 21.6 + - - +
117A GLU* 3.0 35.1 + - - +
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Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASN* 2.9 38.8 + - - +
111A PHE* 4.0 3.1 - - + +
113A GLU* 1.3 76.4 - - - +
115A LEU* 1.3 52.6 + - - +
117A GLU* 2.9 30.5 + - + +
118A SER* 2.7 34.4 + - - -
358A PRO 5.2 0.9 - - - +
361A ASN* 3.8 31.9 - - + +
362A LEU* 3.8 30.6 - - - +
365A ALA* 3.7 20.6 - - + +
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A PHE* 3.2 47.9 + - + +
112A VAL* 3.4 11.0 - - + +
114A LYS* 1.3 72.1 - - - +
116A ARG* 1.3 64.4 + - - +
118A SER* 3.1 11.8 + - - +
119A LEU* 3.2 16.7 + - + -
120A LEU* 3.0 41.0 + - + -
130A LEU* 4.1 25.6 - - + -
132A THR* 4.2 7.9 - - + -
361A ASN* 4.0 21.1 - - - +
34B LEU* 4.9 7.9 - - + -
37B ILE* 5.1 6.7 - - + -
38B GLN* 5.6 2.9 - - - +
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 2.9 43.9 + - + +
113A GLU* 3.1 25.1 + - - +
115A LEU* 1.3 78.3 - - - +
117A GLU* 1.3 59.0 + - - +
118A SER 3.5 0.3 + - - -
120A LEU* 4.0 20.5 - - + +
121A SER* 3.7 19.4 + - - -
33B GLN* 3.3 38.4 + - - +
37B ILE* 5.3 4.4 - - - +
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLU* 3.0 20.9 + - - +
114A LYS* 2.9 44.4 + - - +
115A LEU 3.2 0.2 - - - -
116A ARG* 1.3 75.5 - - - +
118A SER* 1.3 57.9 + - - +
121A SER* 3.9 8.6 + - - -
365A ALA* 3.7 28.5 - - + +
368A ILE* 4.3 6.6 - - - +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LYS 2.7 20.7 + - - -
115A LEU* 3.1 12.1 + - - +
117A GLU* 1.3 78.4 - - - +
119A LEU* 1.3 75.6 + - - +
120A LEU 3.3 1.6 - - - -
121A SER* 2.7 25.6 + - - -
122A VAL 3.8 0.9 + - - -
361A ASN* 4.4 8.0 + - - +
364A LEU* 4.0 15.1 - - - +
365A ALA* 3.8 24.5 - - - +
368A ILE* 3.5 16.3 - - - +
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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