Contacts of the helix formed by residues 1141 - 1155 (chain A) in PDB entry 6KJV
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 THR1141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1104A GLN* 3.2 30.2 + - - +
1137A TRP* 3.3 18.5 + - - +
1138A TYR 3.8 2.0 - - - -
1140A GLN* 1.3 92.1 - - + +
1142A PRO* 1.3 66.8 - - - +
1143A ASN 3.5 1.8 - - - -
1144A ARG* 3.8 8.9 + - - +
1145A ALA* 3.2 21.0 + - - +
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Residues in contact with PRO1142 (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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1138A TYR* 3.2 33.1 - - + +
1139A ASN* 4.3 6.1 - - - +
1140A GLN 3.6 8.1 - - - +
1141A THR* 1.3 85.4 - - - +
1143A ASN* 1.3 71.4 + - - +
1145A ALA* 3.2 3.1 + - + +
1146A LYS* 2.9 32.4 + - - +
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Residues in contact with ASN1143 (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 THR 3.5 0.6 - - - -
1142A PRO* 1.3 90.3 - - - +
1144A ARG* 1.3 60.5 + - - +
1146A LYS* 4.3 4.5 - - - +
1147A ARG* 3.4 40.9 + - - +
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Residues in contact with ARG1144 (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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1006A LEU* 3.5 20.4 - - - +
1009A ASP* 3.4 39.3 + - + +
1010A GLU* 2.7 37.7 + - - +
1100A ASN* 2.9 35.6 + - - +
1104A GLN* 3.3 42.3 + - - +
1137A TRP* 5.0 1.1 - - - +
1141A THR* 3.8 11.7 + - - +
1142A PRO 3.3 0.2 - - - -
1143A ASN* 1.3 77.2 - - - +
1145A ALA* 1.3 66.6 + - - +
1147A ARG* 3.2 18.0 + - - +
1148A VAL* 3.1 28.6 + - + +
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Residues in contact with ALA1145 (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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1137A TRP* 3.5 33.7 - - + +
1138A TYR* 3.7 29.2 - - + -
1141A THR 3.2 17.8 + - - +
1142A PRO 3.2 3.3 + - - +
1144A ARG* 1.3 79.4 - - - +
1146A LYS* 1.3 56.7 + - - +
1148A VAL* 3.3 1.0 + - - -
1149A ILE* 2.9 36.9 + - - +
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Residues in contact with LYS1146 (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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1138A TYR* 4.4 16.1 - - + +
1142A PRO 2.9 16.2 + - - +
1143A ASN* 4.3 5.2 - - - +
1144A ARG 3.3 0.2 - - - -
1145A ALA* 1.3 76.2 - - - +
1147A ARG* 1.3 58.5 + - + +
1149A ILE* 3.8 5.6 - - - +
1150A THR* 2.9 36.5 + - - +
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Residues in contact with ARG1147 (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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1008A ILE* 5.8 4.3 - - - -
1009A ASP* 3.0 34.7 + - - +
1143A ASN* 3.4 31.5 + - - +
1144A ARG* 3.2 29.2 + - - +
1146A LYS* 1.3 77.8 - - + +
1148A VAL* 1.3 64.0 + - - +
1150A THR* 3.3 3.6 + - - -
1151A THR* 3.0 25.6 + - - -
1159A ALA* 3.4 34.3 - - + +
1160A TYR* 3.7 26.7 - - + +
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Residues in contact with VAL1148 (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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1005A MET* 4.3 2.9 - - + -
1097A ALA* 3.7 20.0 - - + +
1100A ASN* 3.6 29.8 - - + +
1101A MET* 4.1 3.4 - - + -
1137A TRP* 3.7 28.3 - - + -
1144A ARG* 3.1 18.1 + - + +
1147A ARG* 1.3 75.0 - - - +
1149A ILE* 1.3 59.2 + - - +
1151A THR* 3.1 8.9 + - - -
1152A PHE* 2.9 50.5 + - + -
1160A TYR* 4.0 8.7 - - - +
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Residues in contact with ILE1149 (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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1129A ALA* 3.7 35.6 - - + +
1132A LEU* 3.8 33.2 - - + +
1133A ALA* 4.1 3.1 - - + +
1137A TRP* 4.0 18.8 - - + -
1138A TYR* 3.8 28.3 - - + -
1145A ALA 2.9 21.9 + - - +
1146A LYS* 3.9 4.3 - - - +
1148A VAL* 1.3 73.0 - - - +
1150A THR* 1.3 61.9 + - - +
1152A PHE* 3.2 8.8 + - + +
1153A ARG* 2.8 27.4 + - + +
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Residues in contact with THR1150 (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 LYS* 2.9 22.8 + - - +
1147A ARG 3.5 4.9 - - - -
1149A ILE* 1.3 77.6 - - - +
1151A THR* 1.3 63.6 + - - +
1153A ARG* 3.1 26.8 + - - +
1154A THR* 2.8 39.7 + - + +
1156A THR* 5.4 1.1 - - - +
1158A ASP* 5.4 5.4 - - + -
1159A ALA* 3.8 25.7 - - + +
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Residues in contact with THR1151 (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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1005A MET* 4.2 3.2 - - + +
1093A VAL* 3.7 32.5 - - + +
1094A ARG* 3.6 3.7 - - - +
1097A ALA* 3.9 11.7 - - + -
1147A ARG 3.0 16.1 + - - -
1148A VAL* 3.1 10.1 + - - -
1150A THR* 1.3 77.5 - - - +
1152A PHE* 1.3 56.3 + - - +
1154A THR* 4.3 0.4 - - - -
1155A GLY* 2.8 26.2 + - - -
1156A THR 3.6 24.7 + - - +
1157A TRP* 4.5 9.4 - - + -
1159A ALA* 4.9 1.7 - - - +
1160A TYR* 4.0 16.5 - - - -
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Residues in contact with PHE1152 (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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1090A LEU* 4.2 8.7 - - + -
1094A ARG* 2.7 61.8 + - + -
1097A ALA* 3.5 4.9 - - + -
1098A LEU* 3.5 28.0 - - + -
1101A MET* 3.8 19.3 - - - -
1120A LEU* 3.9 39.5 - - + -
1125A TRP* 4.0 9.1 - - - +
1128A ALA* 6.3 0.9 - - + -
1129A ALA* 6.2 2.2 - - + +
1132A LEU* 4.1 19.7 - - + -
1148A VAL* 2.9 47.2 + - + -
1149A ILE* 3.2 7.8 + - + +
1151A THR* 1.3 78.1 - - - +
1153A ARG* 1.3 54.0 + - - +
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Residues in contact with ARG1153 (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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171A HIS* 5.6 8.0 - - - +
1094A ARG* 3.6 6.1 + - - -
1125A TRP* 3.6 22.3 - - - +
1126A ASP* 3.8 29.7 + - - +
1129A ALA* 4.1 24.2 - - + -
1149A ILE* 2.8 17.0 + - - +
1150A THR* 3.1 20.6 + - - +
1152A PHE* 1.3 77.9 - - - +
1154A THR* 1.3 82.2 + - - +
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Residues in contact with THR1154 (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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171A HIS 5.9 3.8 - - - +
173A HIS 5.8 3.8 - - - +
174A CYS* 5.9 4.3 - - + -
1094A ARG* 3.5 10.3 + - - -
1150A THR* 2.8 26.1 + - + +
1153A ARG* 1.3 114.3 - - - +
1155A GLY* 1.3 64.0 + - - +
1156A THR* 2.9 33.2 + - - +
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Residues in contact with GLY1155 (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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345A ILE* 3.8 9.2 - - - +
1091A ASP* 4.5 2.1 - - - +
1093A VAL* 3.3 31.0 - - - +
1094A ARG* 3.4 22.4 - - - +
1151A THR 2.8 19.1 + - - -
1154A THR* 1.3 77.8 - - - +
1156A THR* 1.3 61.6 + - - +
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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