Contacts of the strand formed by residues 1139 - 1151 (chain A) in PDB entry 6O0Z
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 VAL1139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1101A GLN* 3.7 15.8 - - - +
1137A PRO* 4.5 7.4 - - + +
1138A THR* 1.3 76.9 - - - +
1140A ALA* 1.3 62.8 + - - +
1141A TYR* 3.3 26.7 - - - +
1142A SER* 4.5 4.3 - - - +
1165A GLY* 3.8 10.8 - - - -
1166A ILE 3.4 20.6 - - - +
1167A THR* 4.5 3.1 - - + +
1216A SER* 4.0 13.2 - - - +
1217A ALA* 4.9 7.4 - - + +
33D G 3.9 21.1 - - - +
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Residues in contact with ALA1140 (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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1099A GLU 4.8 1.7 - - - +
1100A VAL* 4.3 4.6 - - + -
1101A GLN* 3.4 40.6 + - - +
1138A THR 3.6 3.8 + - - -
1139A VAL* 1.3 74.2 - - - +
1141A TYR* 1.3 68.8 + - + +
1166A ILE 2.9 15.7 + - - +
1168A ILE* 4.2 12.3 - - + -
1171A ARG* 3.9 30.3 - - + -
1200A LYS* 4.8 4.2 + - - +
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Residues in contact with TYR1141 (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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1100A VAL* 4.3 16.6 - - + -
1139A VAL* 3.3 7.5 - - - +
1140A ALA* 1.3 87.2 - - + +
1142A SER* 1.3 75.6 + - - +
1143A VAL* 4.1 18.8 - - + -
1166A ILE* 3.1 33.9 + - + +
1171A ARG* 3.8 34.9 + - + +
1174A PHE* 3.4 29.6 - + - -
1175A GLU* 5.0 7.3 + - - +
1197A LYS* 4.2 19.7 - - + +
1198A LEU 3.4 12.1 - - - +
1199A PRO* 3.9 15.7 - - + -
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Residues in contact with SER1142 (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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1139A VAL* 4.5 1.7 - - - +
1141A TYR* 1.3 80.5 + - - +
1143A VAL* 1.3 69.2 + - - +
1163A LEU* 3.9 17.7 - - - +
1164A LEU 3.4 13.7 + - - -
1165A GLY* 4.2 0.9 - - - -
1166A ILE* 4.7 0.9 - - - +
1198A LEU* 2.9 43.8 + - - -
1214A LEU* 4.4 9.4 - - - +
1216A SER 4.4 0.9 - - - -
1217A ALA* 4.0 24.6 + - - +
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Residues in contact with VAL1143 (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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1141A TYR* 4.1 14.6 - - + -
1142A SER* 1.3 81.6 - - - +
1144A LEU* 1.3 62.8 + - - +
1145A VAL* 3.7 5.0 + - + -
1163A LEU* 3.8 5.5 - - - +
1164A LEU* 3.1 40.1 + - + +
1166A ILE* 4.2 18.4 - - + -
1174A PHE* 4.0 27.8 - - + -
1182A LEU* 5.2 11.4 - - + -
1195A ILE* 4.1 18.2 - - + -
1196A ILE 3.3 10.3 - - - +
1197A LYS* 4.4 5.6 - - + -
1198A LEU* 5.4 1.8 - - - -
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Residues in contact with LEU1144 (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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1143A VAL* 1.3 72.1 - - - +
1145A VAL* 1.3 61.3 + - - +
1146A VAL* 4.3 4.0 + - + -
1161A LYS* 3.9 32.3 - - + -
1162A GLU 3.5 16.6 - - - +
1163A LEU* 4.8 5.4 - - + +
1194A LEU 3.3 23.1 - - - +
1195A ILE* 3.7 5.9 - - - +
1196A ILE* 3.0 35.5 + - + +
1198A LEU* 4.9 11.6 - - + +
1343A LEU* 4.1 18.6 - - + -
1362A LEU* 3.8 35.0 - - + -
1365A LEU* 5.7 4.0 - - + -
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Residues in contact with VAL1145 (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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1143A VAL* 4.5 7.6 - - + +
1144A LEU* 1.3 75.8 - - - +
1146A VAL* 1.3 62.5 + - - +
1147A ALA* 4.1 20.4 - - + -
1160A VAL 4.1 1.0 - - - +
1161A LYS* 3.7 1.0 - - - -
1162A GLU* 2.9 44.2 + - - +
1164A LEU* 4.6 11.7 - - + -
1182A LEU* 4.4 24.0 - - + -
1187A TYR* 4.4 31.2 - - + +
1190A VAL* 4.5 7.4 - - + -
1195A ILE* 4.2 14.6 - - + -
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Residues in contact with VAL1146 (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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1144A LEU* 4.2 4.0 - - + +
1145A VAL* 1.3 72.6 - - - +
1147A ALA* 1.3 67.1 + - - +
1159A SER* 4.9 6.3 - - - +
1160A VAL 3.6 9.2 - - - +
1161A LYS* 4.6 19.3 - - + -
1189A GLU 4.6 0.2 - - - +
1190A VAL* 3.9 1.7 - - - +
1191A LYS* 3.7 23.6 + - + +
1194A LEU* 3.8 40.4 - - + +
1195A ILE* 5.5 0.6 - - - +
1365A LEU 5.7 0.7 - - - +
1366A GLY* 4.8 20.9 - - - +
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Residues in contact with ALA1147 (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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1145A VAL* 4.1 3.1 - - + -
1146A VAL* 1.3 77.7 - - - +
1148A LYS* 1.3 60.5 + - - +
1159A SER* 3.4 7.5 + - - -
1160A VAL* 2.7 38.8 + - - +
1187A TYR* 3.9 22.4 - - + -
1188A LYS 3.8 6.5 - - - +
1189A GLU 4.0 7.9 - - - -
1190A VAL* 3.8 27.6 - - + -
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Residues in contact with LYS1148 (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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1147A ALA* 1.3 80.2 - - - +
1149A VAL* 1.3 60.8 + - - +
1150A GLU* 5.0 0.5 - - - +
1157A LEU* 4.0 40.8 + - + +
1158A LYS 3.5 12.8 - - - +
1159A SER* 3.8 14.1 - - - -
1160A VAL* 4.2 1.6 - - - -
1187A TYR* 4.3 1.2 - - - -
1188A LYS* 3.1 42.9 + - + +
1189A GLU* 4.2 21.0 - - + +
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Residues in contact with VAL1149 (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 LYS* 1.3 75.0 - - - +
1150A GLU* 1.3 84.7 + - + +
1151A LYS* 3.4 1.2 + - + +
1156A LYS 3.0 12.9 - - - +
1157A LEU* 3.6 3.2 - - - -
1158A LYS* 3.2 20.1 + - + +
1160A VAL* 4.2 20.1 - - + +
1186A GLY 3.4 25.8 - - - +
1187A TYR* 5.1 9.6 - - + -
1188A LYS* 5.5 0.2 - - - -
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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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1149A VAL* 1.3 90.2 - - + +
1151A LYS* 1.3 59.8 + - - +
1152A GLY 4.2 4.7 + - - +
1155A LYS* 3.4 37.9 - - + +
1156A LYS 3.3 2.2 - - - -
1157A LEU* 3.3 20.7 - - - +
1186A GLY 5.7 0.7 - - - +
1188A LYS* 3.5 25.9 - - + +
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Residues in contact with LYS1151 (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 VAL* 5.9 0.7 - - + -
1150A GLU* 1.3 72.9 - - - +
1152A GLY* 1.3 65.0 + - - +
1154A SER* 4.2 2.1 + - - -
1155A LYS 3.7 1.0 + - - -
1156A LYS* 2.5 52.7 + - + +
1158A LYS* 3.8 23.3 - - + -
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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