Contacts of the helix formed by residues 1160 - 1171 (chain A) in PDB entry 3F2B
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 THR1160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1157A GLU 3.6 11.8 + - - -
1158A PHE 3.3 0.6 - - - -
1159A GLY* 1.3 77.4 - - - +
1161A ARG* 1.3 62.2 + - - +
1162A PHE* 3.1 14.6 - - + +
1163A VAL* 3.1 15.3 - - + +
1164A ARG* 2.9 32.7 + - - +
6T G 2.6 45.9 + - - +
7T G 4.3 6.6 + - - -
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Residues in contact with ARG1161 (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 MET* 5.2 3.6 + - - +
1159A GLY 3.9 0.2 + - - -
1160A THR* 1.3 74.3 + - - +
1162A PHE* 1.3 62.3 + - - +
1164A ARG* 3.8 23.8 - - - +
1165A GLN* 3.3 21.5 + - - +
1325A ILE* 4.7 2.6 - - - +
1329A ASN* 3.0 41.6 + - - +
1343A LEU* 3.8 22.0 - - - +
1347A GLU* 2.8 31.1 + - - +
4T A 3.6 25.1 - - + +
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Residues in contact with PHE1162 (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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1160A THR* 3.1 1.6 - - + +
1161A ARG* 1.3 77.0 - - - +
1163A VAL* 1.3 65.3 + - + +
1165A GLN* 3.3 6.4 + - + +
1166A MET* 3.1 46.0 + - + +
1184A LEU 5.0 1.1 - - - -
1185A SER* 4.2 10.3 - - - -
1191A TRP* 3.8 19.1 - + + -
1192A LEU* 3.5 37.7 - - + -
4T A 3.4 48.0 + + + +
5T C 3.6 40.4 - - - -
6T G 3.5 12.6 - - - +
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Residues in contact with VAL1163 (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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1157A GLU 3.3 22.2 - - - +
1158A PHE* 3.5 41.5 - - + +
1160A THR* 3.1 14.3 - - + +
1162A PHE* 1.3 76.2 - - + +
1164A ARG* 1.3 65.5 + - - +
1166A MET* 3.0 8.4 + - - +
1167A LEU* 2.8 22.8 + - + +
1181A ILE* 4.1 14.4 - - + -
1185A SER* 3.9 23.8 - - - +
6T G 4.0 13.9 - - - +
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Residues in contact with ARG1164 (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 MET 4.7 5.1 + - - -
1148A CYS* 3.2 36.6 - - - +
1150A VAL* 3.8 16.3 - - + +
1152A THR* 3.6 20.0 - - - +
1153A ILE* 3.9 17.2 - - - +
1158A PHE 3.9 2.4 + - - +
1159A GLY 2.8 24.4 + - - -
1160A THR* 2.9 16.2 + - - +
1161A ARG* 3.8 29.2 - - - +
1163A VAL* 1.3 77.7 - - - +
1165A GLN* 1.3 56.7 + - - +
1167A LEU* 3.2 6.7 + - - +
1168A GLU* 2.9 29.1 + - - +
1347A GLU* 2.6 42.6 + - - -
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Residues in contact with GLN1165 (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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1161A ARG 3.3 11.5 + - - +
1162A PHE* 3.6 9.4 - - + +
1163A VAL 3.2 1.2 - - - -
1164A ARG* 1.3 75.1 - - - +
1166A MET* 1.3 66.5 + - + +
1168A GLU* 3.0 41.5 + - - +
1169A GLU* 3.1 28.7 + - - +
4T A 4.0 22.8 + - - +
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Residues in contact with MET1166 (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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1162A PHE* 3.1 40.6 + - + +
1163A VAL* 3.0 10.6 + - - +
1165A GLN* 1.3 76.3 - - + +
1167A LEU* 1.3 54.0 + - - +
1169A GLU* 3.2 9.5 + - - +
1170A THR* 2.5 41.3 + - + +
1181A ILE* 4.1 13.2 - - + -
1184A LEU* 3.2 36.6 - - + -
1185A SER* 3.7 28.5 - - - +
1191A TRP* 3.7 37.9 - - + +
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Residues in contact with LEU1167 (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 PHE* 3.3 21.6 - - + +
1150A VAL* 4.3 8.3 - - + -
1152A THR* 3.7 38.1 - - + +
1158A PHE* 3.8 23.6 - - + +
1163A VAL* 2.8 14.6 + - + +
1164A ARG* 3.4 10.5 - - - +
1166A MET* 1.3 73.3 - - - +
1168A GLU* 1.3 62.9 + - - +
1170A THR* 3.6 3.4 - - - +
1171A ARG* 2.8 33.4 + - - +
1172A PRO* 3.9 14.4 - - + -
1181A ILE* 3.5 37.2 - - + -
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Residues in contact with GLU1168 (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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1149A ASN* 2.6 45.8 + - + +
1150A VAL* 4.2 9.3 - - + +
1164A ARG 2.9 13.6 + - - +
1165A GLN* 3.0 37.0 + - - +
1167A LEU* 1.3 77.0 - - - +
1169A GLU* 1.3 60.7 + - + +
1171A ARG* 3.4 40.8 + - - +
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Residues in contact with GLU1169 (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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1165A GLN* 3.1 29.2 + - - +
1166A MET* 3.2 7.7 + - - +
1167A LEU 3.1 0.6 - - - -
1168A GLU* 1.3 80.9 - - + +
1170A THR* 1.3 60.4 + - + +
1171A ARG* 4.7 2.3 - - - +
1191A TRP* 3.9 19.1 + - + -
1196A GLN* 3.1 32.7 - - - +
1200A GLN* 3.3 19.8 - - - +
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Residues in contact with THR1170 (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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1166A MET* 2.5 29.4 + - + +
1167A LEU* 3.6 4.3 - - - -
1169A GLU* 1.3 83.7 - - + +
1171A ARG* 1.3 73.3 + - - +
1172A PRO* 3.3 9.3 - - - +
1181A ILE* 3.9 19.2 - - + +
1191A TRP* 3.6 31.0 - - + -
1199A ILE* 5.8 0.2 - - + -
1206A LEU* 4.1 35.1 - - + +
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Residues in contact with ARG1171 (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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1134A SER* 2.7 49.3 + - - +
1149A ASN* 5.5 3.0 + - - +
1150A VAL* 4.7 2.6 - - - +
1167A LEU 2.8 16.5 + - - +
1168A GLU* 3.4 39.8 + - - +
1169A GLU 4.7 1.6 - - - -
1170A THR* 1.3 78.5 - - - +
1172A PRO* 1.3 72.2 - - - +
1173A LYS* 3.6 17.0 + - + +
1177A GLU* 4.4 2.3 - - - +
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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