Contacts of the helix formed by residues 1138 - 1148 (chain A) in PDB entry 5JQE
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 ASN1138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020A ALA* 4.7 17.0 - - - +
1117A LEU* 3.9 8.1 - - + -
1136A ASP 4.1 1.8 + - - -
1137A MET* 1.3 76.6 - - - +
1139A LEU* 1.3 64.6 + - - +
1140A LEU* 3.3 17.0 + - - +
1141A ASP* 2.7 57.6 + - - +
1142A ILE* 3.1 10.7 + - - +
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Residues in contact with LEU1139 (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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1108A ILE* 4.2 3.6 - - + +
1109A SER* 3.6 33.2 - - - +
1112A VAL* 3.8 31.0 - - + -
1117A LEU* 3.6 22.3 - - + +
1120A PHE* 3.9 40.8 - - + -
1138A ASN* 1.3 74.2 - - - +
1140A LEU* 1.3 56.5 + - - +
1142A ILE* 3.2 7.0 + - + -
1143A PHE* 3.0 53.4 + - + -
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Residues in contact with LEU1140 (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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1020A ALA* 4.4 13.0 - - + +
1021A SER* 4.6 12.3 - - - +
1024A PHE* 3.8 52.1 - - + -
1105A LEU 4.5 3.4 - - - +
1106A TYR* 4.5 9.0 - - + -
1109A SER* 3.7 31.2 - - - +
1138A ASN* 3.1 16.4 + - - +
1139A LEU* 1.3 74.8 - - - +
1141A ASP* 1.3 65.9 + - - +
1142A ILE 3.1 1.3 - - - -
1143A PHE* 3.1 11.9 + - + +
1144A ILE* 3.1 29.3 + - + +
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Residues in contact with ASP1141 (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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1136A ASP 4.4 3.8 - - - +
1137A MET* 3.9 27.1 - - + +
1138A ASN* 2.7 38.9 + - - +
1140A LEU* 1.3 73.4 - - - +
1142A ILE* 1.3 57.6 + - - +
1144A ILE* 4.1 15.2 - - - +
1145A GLU* 3.2 25.8 + - - +
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Residues in contact with ILE1142 (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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1117A LEU* 3.8 29.2 - - + -
1120A PHE* 3.6 32.5 - - + -
1121A LYS* 4.3 16.8 - - + -
1124A LEU* 4.8 4.5 - - + -
1131A CYS* 5.8 0.9 - - - -
1133A LEU* 4.2 26.5 - - + -
1137A MET* 4.4 12.8 - - + +
1138A ASN 3.1 11.3 + - - +
1139A LEU* 3.4 10.1 - - + +
1140A LEU 3.1 1.0 - - - -
1141A ASP* 1.3 78.3 - - - +
1143A PHE* 1.3 58.9 + - - +
1145A GLU* 3.4 6.2 + - - +
1146A MET* 2.9 38.9 + - + +
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Residues in contact with PHE1143 (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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1024A PHE* 4.3 9.2 - - + -
1105A LEU* 3.6 53.4 - - + -
1108A ILE* 4.1 11.7 - - + -
1109A SER* 4.7 0.9 - - - -
1120A PHE* 4.1 9.0 - + - -
1139A LEU* 3.0 46.8 + - + -
1140A LEU* 3.1 15.5 + - + +
1142A ILE* 1.3 74.6 - - - +
1144A ILE* 1.3 60.1 + - - +
1146A MET* 3.0 9.1 + - - +
1147A GLU* 2.8 35.0 + - - +
1152A LEU* 3.5 24.0 - - + +
1160A LEU* 3.7 28.3 - - + -
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Residues in contact with ILE1144 (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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1024A PHE* 4.0 11.9 - - + -
1027A LEU* 3.6 39.3 - - + -
1032A GLN* 4.3 22.2 - - + +
1140A LEU* 3.1 17.4 + - + +
1141A ASP* 4.3 15.5 - - - +
1143A PHE* 1.3 75.2 - - - +
1145A GLU* 1.3 58.0 + - + +
1147A GLU* 3.4 15.4 + - - +
1148A LYS* 2.8 44.4 + - + +
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Residues in contact with GLU1145 (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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1131A CYS* 3.5 23.3 - - - -
1132A LYS* 4.0 14.9 + - - +
1133A LEU* 4.9 4.7 - - + -
1137A MET* 5.1 10.2 - - + +
1141A ASP 3.2 19.5 + - - +
1142A ILE* 3.6 5.2 - - - +
1143A PHE 3.1 0.8 - - - -
1144A ILE* 1.3 78.0 - - + +
1146A MET* 1.3 56.8 + - - +
1148A LYS* 3.2 32.7 + - - +
1149A ARG* 2.5 65.5 + - - +
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Residues in contact with MET1146 (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 PHE* 4.4 8.7 - - + -
1124A LEU* 3.8 22.4 - - + -
1131A CYS* 5.1 6.1 - - - -
1142A ILE* 2.9 31.8 + - + +
1143A PHE* 3.0 17.9 + - + +
1145A GLU* 1.3 78.1 - - - +
1147A GLU* 1.3 61.1 + - - +
1148A LYS 3.1 0.9 - - - -
1149A ARG* 3.3 1.7 + - - +
1150A VAL 2.9 21.3 + - - -
1151A ILE* 3.0 36.8 + - + +
1152A LEU* 3.8 26.9 - - + -
1159A ILE* 3.9 29.2 - - + -
1160A LEU* 4.9 6.1 - - + +
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Residues in contact with GLU1147 (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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1024A PHE* 5.9 0.2 - - - -
1027A LEU* 5.4 0.3 - - - +
1101A TYR* 2.7 35.9 + - - +
1102A ARG* 3.2 32.2 + - - -
1105A LEU* 5.2 2.0 - - - -
1143A PHE 2.8 18.7 + - - +
1144A ILE* 3.6 18.8 - - - +
1146A MET* 1.3 73.1 - - - +
1148A LYS* 1.3 56.9 + - - +
1150A VAL* 2.9 24.9 + - - +
1152A LEU* 3.3 25.9 + - + +
1153A GLY* 5.2 0.7 - - - -
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Residues in contact with LYS1148 (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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1032A GLN* 5.6 2.9 - - - +
1144A ILE* 2.8 32.1 + - + +
1145A GLU* 3.2 30.1 + - - +
1146A MET 3.1 0.4 - - - -
1147A GLU* 1.3 76.7 - - - +
1149A ARG* 1.3 68.8 + - - +
1150A VAL* 3.7 5.4 + - - +
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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