Contacts of the helix formed by residues 1151 - 1168 (chain A) in PDB entry 1OBO
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 LEU1151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1124A GLY* 5.0 1.3 - - - +
1148A GLN* 3.0 29.3 + - + +
1150A ASP* 1.3 103.6 - - - +
1152A THR* 1.3 65.0 + - - +
1153A ASP 3.5 1.7 + - - -
1154A ASP* 3.6 7.5 + - - +
1155A ARG* 3.1 62.5 + - + +
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Residues in contact with THR1152 (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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1018A VAL* 4.2 9.2 - - + -
1021A ILE* 4.8 5.2 - - + -
1143A LEU* 4.0 28.5 - - + +
1144A ASP 4.6 2.6 + - - -
1145A GLU* 2.5 30.5 + - - +
1148A GLN 3.6 9.3 + - - -
1149A SER 3.5 7.2 + - - -
1151A LEU* 1.3 77.9 - - - +
1153A ASP* 1.3 69.6 + - - +
1155A ARG* 3.2 3.6 + - - +
1156A ILE* 2.9 43.9 + - + +
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Residues in contact with ASP1153 (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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1021A ILE* 3.4 32.2 - - + +
1025A GLU* 5.1 2.6 - - - +
1149A SER 4.8 5.1 + - - +
1150A ASP 5.3 2.4 + - - +
1151A LEU 3.5 0.8 - - - -
1152A THR* 1.3 79.4 - - - +
1154A ASP* 1.3 63.7 + - - +
1156A ILE* 3.3 7.7 + - - +
1157A LYS* 3.0 26.5 + - - +
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Residues in contact with ASP1154 (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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1151A LEU* 3.6 9.0 + - - +
1152A THR 3.4 0.2 - - - -
1153A ASP* 1.3 79.0 - - - +
1155A ARG* 1.3 65.0 + - - +
1157A LYS* 3.3 16.2 + - + +
1158A SER* 3.0 24.4 + - - -
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Residues in contact with ARG1155 (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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1120A TRP* 3.6 21.5 - - + +
1123A ASP 4.6 0.8 + - - -
1124A GLY* 3.4 19.8 + - - -
1125A TYR* 3.3 42.9 + - - -
1141A LEU* 4.1 12.3 - - + -
1142A ALA 3.9 8.5 + - - -
1143A LEU* 4.2 7.6 - - + +
1144A ASP 4.5 6.9 - - - +
1148A GLN* 2.9 41.2 + - - +
1151A LEU* 3.1 45.0 + - + +
1152A THR* 3.5 5.1 + - - +
1154A ASP* 1.3 77.4 - - + +
1156A ILE* 1.3 58.2 + - - +
1158A SER* 3.3 1.9 + - - -
1159A TRP* 2.9 30.9 + - - +
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Residues in contact with ILE1156 (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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1018A VAL* 3.8 19.3 - - + +
1021A ILE* 3.6 29.8 - - + -
1022A ILE* 3.7 26.2 - - + -
1025A GLU* 3.8 20.6 - - + -
1141A LEU* 4.0 21.8 - - + -
1143A LEU* 4.4 2.2 - - + -
1152A THR* 2.9 39.2 + - + +
1153A ASP 3.6 4.3 - - - +
1155A ARG* 1.3 77.0 - - - +
1157A LYS* 1.3 56.2 + - - +
1159A TRP* 5.6 0.2 - - + -
1160A VAL* 2.8 32.7 + - + +
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Residues in contact with LYS1157 (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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1025A GLU* 3.7 29.6 - - - +
1153A ASP 3.0 13.6 + - - +
1154A ASP* 3.5 20.4 - - - +
1155A ARG 3.3 0.2 - - - -
1156A ILE* 1.3 77.4 - - - +
1158A SER* 1.3 62.7 + - - +
1160A VAL* 3.6 1.9 + - - +
1161A ALA* 3.2 22.5 + - + +
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Residues in contact with SER1158 (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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1120A TRP* 3.9 18.0 - - - -
1154A ASP 3.0 16.1 + - - -
1155A ARG* 3.7 4.0 - - - -
1157A LYS* 1.3 77.3 - - - +
1159A TRP* 1.3 63.8 + - - +
1161A ALA* 3.3 8.4 + - - +
1162A GLN* 3.1 21.7 + - - +
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Residues in contact with TRP1159 (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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1022A ILE* 3.9 30.5 - - + -
1051A ILE* 4.1 11.0 - - + -
1084A ALA* 3.8 17.3 - - + -
1085A TYR 3.1 34.5 - - - -
1086A PHE* 3.9 5.8 - - + -
1118A GLY* 2.9 28.2 + - - -
1120A TRP* 3.5 30.7 - + + -
1141A LEU* 3.5 30.6 - - + +
1155A ARG 2.9 17.7 + - - +
1156A ILE 3.8 2.2 - - - +
1158A SER* 1.3 78.3 - - - +
1160A VAL* 1.3 61.5 + - + +
1162A GLN* 3.0 13.3 + - - +
1163A LEU* 2.8 60.0 + - + +
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Residues in contact with VAL1160 (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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1022A ILE* 4.2 7.6 - - + +
1025A GLU* 3.6 33.4 - - + +
1026A PHE* 3.8 46.7 - - + +
1156A ILE* 2.8 34.4 + - + +
1157A LYS 4.0 2.7 - - - +
1159A TRP* 1.3 75.0 - - + +
1161A ALA* 1.3 67.0 + - - +
1163A LEU* 3.7 6.5 - - - +
1164A LYS* 2.9 30.2 + - + +
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Residues in contact with ALA1161 (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 LYS* 3.2 14.9 + - + +
1158A SER* 3.5 11.2 - - - +
1159A TRP 3.2 0.2 - - - -
1160A VAL* 1.3 77.8 - - - +
1162A GLN* 1.3 62.3 + - - +
1164A LYS* 3.4 11.7 + - - +
1165A SER* 3.4 18.4 + - - -
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Residues in contact with GLN1162 (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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1118A GLY* 3.4 12.8 - - - -
1119A TYR* 3.0 28.5 + - - +
1120A TRP* 3.9 19.4 - - - -
1158A SER* 3.1 11.9 + - - +
1159A TRP* 3.0 12.4 + - - +
1161A ALA* 1.3 77.6 - - - +
1163A LEU* 1.3 58.1 + - - +
1165A SER* 3.1 8.7 + - - -
1166A GLU* 2.9 61.2 + - + +
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Residues in contact with LEU1163 (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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1026A PHE* 3.7 28.5 - - + -
1051A ILE* 4.1 7.4 - - + -
1084A ALA* 3.7 20.0 - - + -
1117A VAL* 4.3 7.2 - - + -
1118A GLY* 3.7 32.3 - - - +
1159A TRP* 2.8 61.6 + - + +
1160A VAL* 3.7 0.9 - - - +
1162A GLN* 1.3 70.7 - - - +
1164A LYS* 1.3 59.6 + - - +
1166A GLU* 4.1 4.7 - - - +
1167A PHE* 2.6 46.0 + - + +
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Residues in contact with LYS1164 (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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1025A GLU 5.6 1.6 - - - +
1026A PHE* 3.8 28.9 - - + +
1160A VAL* 2.9 29.2 + - + +
1161A ALA* 3.7 10.3 - - - +
1162A GLN 3.3 0.2 - - - -
1163A LEU* 1.3 76.1 - - - +
1165A SER* 1.3 57.9 + - - +
1167A PHE* 4.7 1.3 - - - -
1168A GLY* 2.9 7.3 + - - -
1169A LEU* 2.8 59.8 + - + +
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Residues in contact with SER1165 (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 ALA 3.4 8.7 + - - -
1162A GLN* 3.1 11.3 + - - -
1164A LYS* 1.3 81.3 - - - +
1166A GLU* 1.3 64.1 + - - +
1168A GLY* 3.4 11.1 + - - -
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Residues in contact with GLU1166 (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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1082A LEU* 3.7 12.9 - - - +
1117A VAL* 3.9 22.9 - - + +
1118A GLY* 2.7 32.8 + - - -
1119A TYR* 5.1 3.5 + - - -
1162A GLN* 2.9 45.8 + - + +
1163A LEU* 4.1 4.9 - - - +
1165A SER* 1.3 78.6 - - - +
1167A PHE* 1.3 63.9 + - - +
1168A GLY* 3.6 0.3 + - - -
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Residues in contact with PHE1167 (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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1004A ILE* 4.0 28.5 - - + -
1026A PHE* 4.3 2.5 - + - -
1049A TYR* 3.4 42.2 + + + -
1050A LEU 3.8 19.5 - - - -
1051A ILE* 4.3 6.5 - - + -
1082A LEU* 3.7 33.5 - - + +
1083A VAL 4.3 0.2 - - - -
1084A ALA* 4.0 13.2 - - + -
1117A VAL* 3.5 23.3 - - + -
1163A LEU* 2.6 46.7 + - + +
1166A GLU* 1.3 73.7 - - - +
1168A GLY* 1.3 60.2 + - - +
1169A LEU* 3.8 19.3 - - + +
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Residues in contact with GLY1168 (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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1049A TYR* 5.2 0.7 + - - -
1164A LYS 2.9 8.2 + - - -
1165A SER* 3.4 7.6 + - - -
1166A GLU 3.2 3.2 - - - -
1167A PHE* 1.3 81.3 - - - +
1169A LEU* 1.3 67.2 + - - +
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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