Contacts of the helix formed by residues 1176 - 1191 (chain A) in PDB entry 6J8J
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 LYS1176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1175A GLY* 1.3 78.6 - - - +
1177A ILE* 1.3 60.7 + - - +
1178A TRP* 2.9 13.6 + - + +
1179A TRP* 3.1 41.1 + - + +
1180A ASN* 4.0 4.7 + - - +
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Residues in contact with ILE1177 (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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1175A GLY* 4.4 13.0 - - - +
1176A LYS* 1.3 77.0 - - - +
1178A TRP* 1.3 62.0 + - - +
1180A ASN* 3.2 22.3 + - - +
1181A ILE* 3.4 20.2 + - + +
182B TYR* 3.3 25.6 - - + +
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Residues in contact with TRP1178 (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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1176A LYS* 2.9 6.7 - - + -
1177A ILE* 1.3 80.0 - - - +
1179A TRP* 1.3 72.6 + + - +
1181A ILE* 3.3 22.5 + - + +
1182A ARG* 3.0 58.2 + - + +
1246A ILE* 3.9 31.2 - - + -
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Residues in contact with TRP1179 (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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1176A LYS* 3.1 37.4 + - + +
1178A TRP* 1.3 87.8 - + - +
1180A ASN* 1.3 66.4 + - - +
1182A ARG* 3.2 34.9 + - + +
1183A LYS* 2.9 69.5 + - + +
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Residues in contact with ASN1180 (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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1175A GLY 5.5 0.2 - - - +
1176A LYS 4.0 3.8 + - - +
1177A ILE* 3.2 24.1 + - - +
1179A TRP* 1.3 78.5 - - - +
1181A ILE* 1.3 62.2 + - - +
1183A LYS* 3.2 15.4 + - - +
1184A THR* 3.0 26.7 + - - -
182B TYR* 3.4 34.6 + - + +
185B ILE* 4.4 11.6 - - + +
186B ALA* 5.7 5.3 - - - +
189B THR* 4.4 20.2 - - - +
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Residues in contact with ILE1181 (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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1177A ILE* 3.5 23.1 - - + +
1178A TRP* 3.5 25.8 - - + +
1179A TRP 3.3 0.2 - - - -
1180A ASN* 1.3 75.6 - - - +
1182A ARG* 1.3 63.6 + - - +
1184A THR* 3.3 6.2 + - - -
1185A CYS* 3.1 30.4 + - - +
1246A ILE* 4.8 12.3 - - + -
182B TYR* 4.3 16.8 - - + -
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Residues in contact with ARG1182 (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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1178A TRP* 3.0 57.0 + - + +
1179A TRP* 3.6 32.9 - - + +
1180A ASN 3.2 0.2 - - - -
1181A ILE* 1.3 81.8 - - - +
1183A LYS* 1.3 62.0 + - + +
1185A CYS* 3.7 2.3 + - - +
1186A TYR* 3.4 19.6 + - - +
1245A TRP 4.5 1.4 + - - -
1246A ILE* 3.4 35.1 + - + +
1247A ALA* 4.1 8.0 + - - +
1248A TYR 3.6 25.1 + - - -
1249A GLY* 3.7 18.0 - - - -
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Residues in contact with LYS1183 (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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1179A TRP* 2.9 57.4 + - + +
1180A ASN* 3.2 15.2 + - - +
1182A ARG* 1.3 78.3 - - + +
1184A THR* 1.3 60.6 + - - +
1186A TYR* 3.1 11.5 - - - +
1187A LYS* 3.1 18.0 + - - +
185B ILE* 4.7 19.8 - - + +
189B THR* 5.2 11.5 - - - +
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Residues in contact with THR1184 (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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1180A ASN 3.0 16.8 + - - -
1181A ILE* 3.3 7.4 + - - -
1183A LYS* 1.3 72.3 - - - +
1185A CYS* 1.3 62.5 + - - +
1186A TYR 3.0 1.6 - - - -
1187A LYS* 2.7 29.9 + - + +
1188A ILE* 3.0 10.8 + - + +
178B MET* 4.5 12.1 - - + +
181B CYS* 3.3 35.0 - - + -
182B TYR* 4.0 13.5 - - + +
185B ILE* 3.5 23.9 - - + +
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Residues in contact with CYS1185 (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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1181A ILE* 3.1 24.9 + - - +
1182A ARG 4.1 3.6 - - - +
1184A THR* 1.3 76.1 - - - +
1186A TYR* 1.3 64.3 + - - +
1188A ILE* 3.0 19.9 + - - +
1189A VAL* 3.0 18.9 + - - +
1243A LEU* 3.6 31.9 - - + +
1246A ILE* 4.2 27.6 - - + -
1247A ALA* 4.0 7.0 - - + +
178B MET* 4.7 15.3 - - - -
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Residues in contact with TYR1186 (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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1182A ARG 3.4 11.3 + - - +
1183A LYS* 3.1 17.0 + - - +
1185A CYS* 1.3 80.0 - - - +
1187A LYS* 1.3 60.5 + - - +
1189A VAL* 3.1 12.0 - - - +
1190A GLU* 2.6 63.5 + - + +
1247A ALA* 3.5 25.7 - - + +
1248A TYR* 4.1 14.5 - + - -
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Residues in contact with LYS1187 (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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1183A LYS 3.1 9.2 + - - +
1184A THR* 2.7 19.3 + - - +
1186A TYR* 1.3 82.6 - - - +
1188A ILE* 1.3 59.7 + - - +
1190A GLU* 3.5 11.8 + - + +
1191A HIS* 3.2 24.1 + - + +
181B CYS* 4.8 15.9 - - - -
185B ILE* 4.8 20.1 - - + +
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Residues in contact with ILE1188 (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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1184A THR* 3.0 14.3 + - + +
1185A CYS* 3.0 11.3 + - - +
1187A LYS* 1.3 77.1 - - - +
1189A VAL* 1.3 63.2 - - - +
1191A HIS* 3.4 14.3 + - + +
1194A PHE* 3.3 39.1 - - + +
1243A LEU* 3.9 18.8 - - + -
174B LEU* 4.5 9.0 - - + -
177B GLU* 3.8 30.7 - - + +
178B MET* 5.5 10.1 - - - -
181B CYS* 3.8 26.9 - - + -
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Residues in contact with VAL1189 (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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1185A CYS 3.0 18.2 + - - +
1186A TYR* 3.1 21.3 - - - +
1188A ILE* 1.3 74.5 - - - +
1190A GLU* 1.3 70.5 + - - +
1191A HIS 3.5 5.5 + - - +
1194A PHE* 3.9 29.5 - - + -
1195A GLU* 4.7 7.1 + - - +
1243A LEU* 4.3 18.2 - - + -
1244A LYS* 3.5 37.4 - - + -
1247A ALA* 3.5 13.0 - - + -
1248A TYR* 4.5 6.7 - - + +
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Residues in contact with GLU1190 (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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1186A TYR* 2.6 73.0 + - + +
1187A LYS* 3.9 13.5 - - - +
1189A VAL* 1.3 82.7 - - - +
1191A HIS* 1.3 64.7 + - - +
1192A SER* 3.5 2.4 + - - -
1195A GLU* 5.2 2.9 - - - +
1248A TYR* 4.0 15.8 + - - -
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Residues in contact with HIS1191 (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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1187A LYS* 3.2 15.4 + - + +
1188A ILE* 3.6 18.2 - - + +
1189A VAL 3.3 2.0 - - - +
1190A GLU* 1.3 79.1 - - - +
1192A SER* 1.3 88.0 + - - +
1193A TRP* 3.4 52.4 + + + +
1194A PHE* 3.3 7.9 + - + +
1195A GLU* 3.1 18.0 + - - +
177B GLU* 5.7 3.4 - - - -
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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