Contacts of the helix formed by residues 1146 - 1157 (chain A) in PDB entry 2OVP
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 THR1146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1144A ASP 3.9 0.6 + - - +
1145A PHE* 1.3 78.2 - - - +
1147A GLU* 1.3 69.5 + - - +
1148A GLU* 4.0 7.9 + - - +
1149A GLU* 2.9 31.5 + - - +
1150A GLU* 3.0 13.9 + - - +
2309B ARG* 3.4 25.4 - - - +
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Residues in contact with GLU1147 (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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1146A THR* 1.3 78.8 - - - +
1148A GLU* 1.3 75.4 + - + +
1150A GLU* 4.0 3.0 - - - +
1151A ALA* 3.4 15.3 + - - +
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Residues in contact with GLU1148 (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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1146A THR* 4.4 6.2 + - - +
1147A GLU* 1.3 87.1 + - + +
1149A GLU* 1.3 67.3 + - - +
1151A ALA* 3.1 10.0 + - - +
1152A GLN* 2.9 20.1 + - - +
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Residues in contact with GLU1149 (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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1145A PHE* 3.5 14.1 - - + -
1146A THR* 2.9 35.0 + - + +
1147A GLU 3.3 0.2 - - - -
1148A GLU* 1.3 76.4 - - - +
1150A GLU* 1.3 67.6 + - - +
1152A GLN* 2.7 21.5 + - - +
1153A VAL* 2.8 16.4 + - + +
2309B ARG* 2.8 52.8 + - - -
2312B ARG* 5.7 7.2 - - - +
2344B PRO* 4.2 17.4 - - + +
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Residues in contact with GLU1150 (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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1133A GLU* 4.9 4.7 - - - +
1136A ARG* 3.3 10.2 + - - -
1143A ASN* 2.5 35.5 + - - +
1145A PHE* 3.4 25.6 - - + +
1146A THR 3.0 13.4 + - - +
1147A GLU 4.0 2.9 - - - +
1149A GLU* 1.3 75.7 - - - +
1151A ALA* 1.3 64.8 + - - +
1153A VAL* 3.1 5.2 + - - +
1154A ARG* 2.8 48.6 + - + +
2306B GLN* 4.8 1.7 - - + +
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Residues in contact with ALA1151 (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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1147A GLU 3.4 9.5 + - - +
1148A GLU* 3.1 13.2 + - - +
1149A GLU 2.9 1.0 + - - -
1150A GLU* 1.3 78.0 - - - +
1152A GLN* 1.3 50.3 + - - +
1154A ARG* 2.8 16.6 + - - +
1155A LYS* 2.7 36.4 + - - +
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Residues in contact with GLN1152 (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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1148A GLU 2.9 11.9 + - - +
1149A GLU* 2.7 16.6 + - - +
1151A ALA* 1.3 72.3 - - - +
1153A VAL* 1.3 55.8 + - + +
1155A LYS* 4.0 17.2 - - - +
1156A GLU* 2.8 58.2 + - - +
2312B ARG* 4.5 7.6 - - - +
2342B ILE* 5.3 11.5 - - + +
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Residues in contact with VAL1153 (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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1145A PHE* 3.7 23.8 - - + -
1149A GLU 2.8 25.3 + - - +
1150A GLU* 3.4 7.2 - - + +
1152A GLN* 1.3 72.7 - - - +
1154A ARG* 1.3 58.0 - - - +
1156A GLU* 3.5 3.1 + - - -
1157A ASN* 2.8 46.1 + - - +
2305B ALA 3.3 26.9 - - - +
2306B GLN* 3.4 18.4 - - + -
2312B ARG* 3.7 31.6 - - - +
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Residues in contact with ARG1154 (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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1132A PRO* 4.4 4.8 - - - +
1133A GLU* 4.0 18.6 + - - -
1150A GLU* 2.8 47.7 + - + +
1151A ALA* 2.8 10.9 + - - +
1153A VAL* 1.3 75.4 - - - +
1155A LYS* 1.3 59.4 + - - +
1157A ASN 3.4 1.2 - - - +
1158A GLN* 3.0 36.1 + - - +
2306B GLN* 2.8 43.1 + - + +
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Residues in contact with LYS1155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1151A ALA 2.7 19.2 + - - +
1152A GLN* 3.6 17.3 - - - +
1154A ARG* 1.3 72.5 - - - +
1156A GLU* 1.3 59.0 + - - +
1158A GLN* 3.4 19.5 - - - +
2360B ARG* 2.9 20.8 + - - +
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Residues in contact with GLU1156 (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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1152A GLN* 2.8 44.4 + - - +
1153A VAL* 3.8 4.5 - - - +
1155A LYS* 1.3 79.4 - - + +
1157A ASN* 1.3 64.4 + - - +
1158A GLN 3.3 1.4 + - - -
2312B ARG* 2.8 27.2 + - - -
2316B GLU* 4.5 3.3 - - - +
2348B HIS* 2.7 35.8 + - - -
2352B LYS* 4.4 9.8 + - - -
2356B ILE* 2.9 30.6 - - + +
2360B ARG* 3.5 10.8 + - - +
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Residues in contact with ASN1157 (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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1153A VAL* 2.8 44.2 + - - +
1154A ARG 3.4 4.3 - - - -
1156A GLU* 1.3 80.9 + - - +
1158A GLN* 1.3 68.1 + - - +
1159A TRP* 4.4 2.3 - - - +
2302B LEU* 3.2 58.3 + - + +
2303B GLN* 4.4 1.6 - - - +
2305B ALA* 3.6 16.6 - - - +
2306B GLN* 3.3 15.5 + - - +
2312B ARG* 5.0 4.2 - - - +
2316B GLU* 4.8 1.2 + - - +
2352B LYS* 3.7 18.9 - - - +
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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