Contacts of the helix formed by residues 1143 - 1161 (chain A) in PDB entry 5J68
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 ASP1143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1141A LEU 4.3 0.8 + - - -
1142A VAL* 1.3 68.5 - - - +
1144A ASP* 1.3 60.2 + - - +
1145A ASN* 3.4 20.2 + - - +
1146A LYS* 3.6 25.8 + - + +
1147A ALA* 3.0 22.3 + - - +
1181A MET* 3.6 14.8 - - - +
1237A SER* 5.9 0.4 - - - -
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Residues in contact with ASP1144 (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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1142A VAL* 3.1 8.1 + - - -
1143A ASP* 1.3 70.8 + - - +
1145A ASN* 1.3 65.4 + - - +
1147A ALA* 3.4 2.6 + - - -
1148A GLU* 3.1 23.7 + - - +
1184A ARG* 2.7 33.8 + - - +
1188A HIS* 2.7 31.7 + - - -
1233A ALA 4.0 1.7 - - - +
1234A TYR* 3.9 10.9 - - - +
1235A ILE* 3.3 36.6 + - + +
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Residues in contact with ASN1145 (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 ASP* 3.3 10.9 + - - +
1144A ASP* 1.3 79.2 - - - +
1146A LYS* 1.3 56.6 + - - +
1148A GLU* 3.4 9.1 + - - +
1149A GLU* 2.9 32.8 + - - +
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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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1143A ASP* 3.3 32.4 + - + +
1145A ASN* 1.3 78.2 - - - +
1147A ALA* 1.3 57.8 + - - +
1149A GLU* 3.3 28.6 + - - +
1150A ILE* 2.9 55.9 + - + +
1177A VAL* 6.0 1.1 - - + -
1181A MET* 4.1 7.6 - - + -
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Residues in contact with ALA1147 (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 ASP 3.0 15.9 + - - +
1144A ASP 3.7 4.3 - - - +
1145A ASN 3.2 0.2 - - - -
1146A LYS* 1.3 77.4 - - - +
1148A GLU* 1.3 62.7 + - - +
1150A ILE 3.3 1.2 + - - -
1151A ALA* 3.0 22.2 + - - +
1181A MET* 3.7 13.2 - - + +
1184A ARG* 3.5 32.3 - - + -
1185A VAL* 3.5 23.6 - - + +
1188A HIS* 3.8 5.8 - - + -
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Residues in contact with GLU1148 (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 ASP 3.1 16.6 + - - +
1145A ASN* 4.0 7.5 - - - +
1147A ALA* 1.3 76.9 - - - +
1149A GLU* 1.3 60.7 - - - +
1151A ALA* 3.6 0.5 + - - +
1152A ASP* 3.2 36.5 + - - +
1188A HIS* 3.6 35.9 + - + +
1192A HIS* 3.3 28.9 + - - +
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Residues in contact with GLU1149 (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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1145A ASN* 2.9 18.6 + - - +
1146A LYS* 3.5 30.9 + - + +
1148A GLU* 1.3 75.4 - - - +
1150A ILE* 1.3 66.2 + - + +
1152A ASP* 3.3 8.0 + - - +
1153A LYS* 3.0 21.8 + - + +
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Residues in contact with ILE1150 (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 41.0 + - + +
1147A ALA 3.3 4.9 + - - +
1149A GLU* 1.3 76.8 - - + +
1151A ALA* 1.3 58.4 + - - +
1153A LYS* 3.0 14.6 + - + +
1154A ILE* 2.8 44.8 + - + +
1173A THR* 5.0 16.2 - - - +
1174A LEU* 4.2 11.2 - - + -
1177A VAL* 4.8 15.9 - - + -
1181A MET* 3.9 22.2 - - + -
1185A VAL* 4.0 14.1 - - + -
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Residues in contact with ALA1151 (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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1147A ALA 3.0 15.9 + - - +
1148A GLU 3.9 3.8 - - - +
1149A GLU 3.3 0.2 - - - -
1150A ILE* 1.3 78.9 - - - +
1152A ASP* 1.3 60.9 + - - +
1154A ILE* 3.5 5.9 + - - +
1155A TYR* 3.1 27.2 + - - +
1185A VAL* 3.6 25.8 - - - +
1188A HIS* 3.8 10.1 - - + -
1189A TYR* 3.8 27.2 - - - +
1193A TYR* 3.9 2.1 - - + -
1199A PHE* 6.5 0.7 - - - -
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Residues in contact with ASP1152 (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 GLU* 3.2 24.2 + - - +
1149A GLU* 3.7 8.9 - - - +
1150A ILE 3.2 0.4 - - - -
1151A ALA* 1.3 78.7 - - - +
1153A LYS* 1.3 65.2 + - - +
1155A TYR* 3.2 1.8 + - - +
1156A ASN* 3.0 37.4 + - - +
1192A HIS* 4.7 5.5 + - - -
1193A TYR* 2.7 29.5 + - - +
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Residues in contact with LYS1153 (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 GLU* 3.0 15.0 + - + +
1150A ILE* 3.0 18.5 + - + +
1152A ASP* 1.3 77.3 - - - +
1154A ILE* 1.3 63.3 + - + +
1156A ASN* 3.5 5.4 + - - +
1157A LEU* 3.2 42.6 + - + +
1169A MET* 3.3 29.3 - - - -
1173A THR* 3.8 33.7 - - + +
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Residues in contact with ILE1154 (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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1150A ILE* 2.8 27.3 + - + +
1151A ALA* 3.8 7.4 - - - +
1153A LYS* 1.3 75.9 - - + +
1155A TYR* 1.3 58.4 + - - +
1157A LEU* 3.3 6.0 + - + +
1158A TYR* 3.0 60.0 + - + +
1170A ALA* 3.6 37.2 - - + +
1173A THR* 3.7 12.8 - - - +
1174A LEU* 3.8 22.4 - - + -
1185A VAL* 6.1 0.2 - - + -
1189A TYR* 4.6 4.3 - - + -
1199A PHE* 4.4 15.5 - - + -
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Residues in contact with TYR1155 (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 ALA 3.1 18.6 + - - +
1152A ASP 3.2 3.3 + - - +
1154A ILE* 1.3 78.0 - - - +
1156A ASN* 1.3 70.5 + - - +
1158A TYR* 3.2 5.0 + - + +
1159A ASN* 2.9 56.3 + - - +
1189A TYR* 3.6 19.9 - - + -
1193A TYR* 3.4 60.3 - + + -
1196A PHE* 3.9 26.6 - - + +
1202A ARG* 4.0 18.6 - - - -
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Residues in contact with ASN1156 (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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1152A ASP* 3.0 28.4 + - - +
1153A LYS* 4.1 5.9 - - - +
1155A TYR* 1.3 90.4 - - - +
1157A LEU* 1.3 61.4 + - + +
1159A ASN* 3.6 8.7 + - - +
1160A GLY* 3.1 20.1 + - - -
1166A GLU* 4.5 1.2 - - - +
1193A TYR* 5.9 0.4 + - - -
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Residues in contact with LEU1157 (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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1153A LYS* 3.2 39.6 + - + +
1154A ILE* 3.6 7.6 - - + +
1155A TYR 3.2 0.2 - - - -
1156A ASN* 1.3 78.2 - - + +
1158A TYR* 1.3 64.8 + - + +
1159A ASN 3.1 0.2 - - - -
1160A GLY* 2.9 16.1 + - - -
1161A TYR* 2.9 13.2 + - - +
1166A GLU* 3.5 61.0 - - + +
1169A MET* 4.6 8.3 - - + -
1170A ALA* 3.7 20.9 - - + +
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Residues in contact with TYR1158 (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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1154A ILE* 3.0 44.1 + - + +
1155A TYR* 3.2 6.0 + - - +
1157A LEU* 1.3 79.9 - - + +
1159A ASN* 1.3 57.1 + - - +
1161A TYR* 3.2 14.7 - - - -
1167A GLN* 6.3 0.2 - - - -
1170A ALA* 4.1 16.6 - - + -
1174A LEU* 4.0 5.0 - - - +
1189A TYR* 3.8 12.1 - + - -
1199A PHE* 4.8 1.8 - + - -
1202A ARG* 3.2 35.6 + - + +
1203A SER* 2.8 43.2 + - - -
1206A GLU* 3.1 46.7 - - + +
1207A LEU* 3.3 25.0 - - + +
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Residues in contact with ASN1159 (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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1155A TYR* 2.9 52.4 + - - +
1156A ASN* 3.8 10.0 + - - +
1157A LEU 3.1 0.2 - - - -
1158A TYR* 1.3 77.6 - - - +
1160A GLY* 1.3 58.1 + - - +
1161A TYR* 3.1 23.9 + - - -
1202A ARG* 4.1 8.1 + - - -
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Residues in contact with GLY1160 (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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1156A ASN 3.1 11.3 + - - -
1157A LEU 2.9 8.2 + - - -
1159A ASN* 1.3 77.5 - - - +
1161A TYR* 1.3 57.2 + - - +
1162A THR* 2.6 25.2 + - - -
1166A GLU* 3.7 15.6 - - - +
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Residues in contact with TYR1161 (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 LEU 2.9 11.4 + - - +
1158A TYR 3.2 14.6 + - - -
1159A ASN* 3.1 35.9 + - - -
1160A GLY* 1.3 70.8 - - - +
1162A THR* 1.3 73.4 + - - +
1163A SER 3.1 10.2 + - - +
1166A GLU* 3.8 3.9 - - - +
1167A GLN* 4.4 12.5 + - - +
1202A ARG* 3.5 13.2 + - - -
1206A GLU* 3.0 39.6 + - - +
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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
------------------------------------------------------------
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