Contacts of the helix formed by residues 1143 - 1161 (chain B) in PDB entry 5J67
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1141B LEU 4.2 0.4 - - - -
1142B VAL* 1.3 68.5 - - - +
1144B ASP* 1.3 60.9 + - - +
1145B ASN* 3.4 20.4 + - - +
1146B LYS* 3.6 26.3 + - + +
1147B ALA 3.0 21.7 + - - -
1181B MET* 3.5 16.2 - - - +
1237B SER* 5.4 1.6 - - - -
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Residues in contact with ASP1144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142B VAL* 3.1 8.8 + - + +
1143B ASP* 1.3 70.6 + - - +
1145B ASN* 1.3 60.2 + - - +
1147B ALA* 3.5 3.5 + - - +
1148B GLU* 3.1 27.5 + - - +
1184B ARG* 2.6 37.5 + - - +
1188B HIS* 2.7 18.2 + - - -
1234B TYR* 4.0 8.0 - - - +
1235B ILE* 2.8 46.6 + - + +
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Residues in contact with ASN1145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143B ASP* 3.3 12.3 + - - +
1144B ASP* 1.3 75.3 - - - +
1146B LYS* 1.3 60.0 + - - +
1148B GLU* 3.3 9.2 + - - +
1149B GLU* 2.9 33.0 + - - +
1286B LYS* 6.0 0.3 + - - -
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Residues in contact with LYS1146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143B ASP* 3.3 31.8 + - + +
1145B ASN* 1.3 79.1 - - - +
1147B ALA* 1.3 57.9 + - - +
1149B GLU* 3.4 27.3 + - - +
1150B ILE* 2.9 54.7 + - + +
1177B VAL* 6.0 0.9 - - + -
1181B MET* 4.0 7.2 - - + -
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Residues in contact with ALA1147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143B ASP 3.0 13.2 + - - +
1144B ASP 3.6 8.1 - - - +
1145B ASN 3.2 0.4 - - - -
1146B LYS* 1.3 77.0 - - - +
1148B GLU* 1.3 57.8 + - - +
1150B ILE 3.3 1.4 + - - -
1151B ALA* 3.1 26.3 + - - +
1181B MET* 3.6 18.6 - - + +
1184B ARG* 3.5 35.2 - - + -
1185B VAL* 3.5 15.1 - - + +
1188B HIS* 3.8 5.6 - - + -
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Residues in contact with GLU1148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144B ASP 3.1 16.3 + - - +
1145B ASN* 3.3 8.1 + - - +
1147B ALA* 1.3 76.1 - - - +
1149B GLU* 1.3 60.8 + - - +
1151B ALA* 3.7 1.2 + - - +
1152B ASP* 3.3 31.9 + - - +
1188B HIS* 3.6 35.1 + - + +
1192B HIS* 3.3 29.4 + - - +
1234B TYR* 6.0 1.6 - - - -
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Residues in contact with GLU1149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145B ASN* 2.9 19.6 + - - +
1146B LYS* 3.4 33.5 + - - +
1148B GLU* 1.3 74.5 - - - +
1150B ILE* 1.3 60.8 + - - +
1152B ASP* 3.2 9.2 + - - +
1153B LYS* 2.9 28.3 + - + +
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Residues in contact with ILE1150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146B LYS* 2.9 41.8 + - + +
1147B ALA 3.7 4.3 - - - +
1149B GLU* 1.3 77.5 - - + +
1151B ALA* 1.3 57.7 + - - +
1153B LYS* 3.1 14.8 + - + +
1154B ILE* 2.8 44.9 + - + +
1173B THR* 5.1 16.2 - - - +
1174B LEU* 4.2 9.6 - - + -
1177B VAL* 4.8 14.4 - - + -
1181B MET* 3.8 23.6 - - + -
1185B VAL* 3.7 17.0 - - + -
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Residues in contact with ALA1151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147B ALA 3.1 16.5 + - - +
1148B GLU 3.7 6.7 - - - +
1149B GLU 3.3 0.2 - - - -
1150B ILE* 1.3 76.0 - - - +
1152B ASP* 1.3 60.6 + - - +
1154B ILE* 3.6 5.6 + - - +
1155B TYR* 3.1 27.0 + - - +
1185B VAL* 3.6 26.4 - - - +
1188B HIS* 3.8 8.1 - - + -
1189B TYR* 3.7 26.8 - - - +
1192B HIS* 5.9 0.2 - - + -
1193B TYR* 3.9 2.2 - - + -
1199B PHE* 6.5 0.7 - - - -
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Residues in contact with ASP1152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148B GLU* 3.3 20.0 + - - +
1149B GLU* 3.2 9.6 + - - +
1151B ALA* 1.3 74.9 - - - +
1153B LYS* 1.3 67.3 + - - +
1155B TYR* 3.3 2.2 + - - +
1156B ASN* 3.0 37.6 + - - +
1192B HIS* 4.5 9.4 - - - -
1193B TYR* 2.7 34.7 + - - +
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Residues in contact with LYS1153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1149B GLU* 2.9 15.4 + - + +
1150B ILE* 3.4 18.4 - - + +
1152B ASP* 1.3 76.5 - - - +
1154B ILE* 1.3 63.1 + - + +
1156B ASN* 3.4 6.9 + - - +
1157B LEU* 3.1 43.3 + - + +
1169B MET* 3.4 30.2 - - - -
1173B THR* 3.8 33.4 - - - +
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Residues in contact with ILE1154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150B ILE* 2.8 28.0 + - + +
1151B ALA* 3.8 7.2 - - - +
1153B LYS* 1.3 75.5 - - + +
1155B TYR* 1.3 58.2 + - - +
1157B LEU* 3.4 6.3 + - + +
1158B TYR* 3.0 62.1 + - + +
1170B ALA* 3.6 37.5 - - + +
1173B THR* 3.7 11.9 - - - +
1174B LEU* 3.7 24.5 - - + -
1185B VAL* 5.9 0.2 - - + -
1189B TYR* 4.6 4.9 - - + -
1199B PHE* 4.4 13.9 - - + -
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Residues in contact with TYR1155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151B ALA 3.1 10.4 + - - +
1152B ASP 3.3 3.8 + - - +
1154B ILE* 1.3 76.1 - - - +
1156B ASN* 1.3 71.2 + - - +
1158B TYR* 3.3 3.6 + - - -
1159B ASN* 2.9 56.2 + - - +
1189B TYR* 3.6 19.7 - - + -
1193B TYR* 3.4 69.8 - + + -
1196B PHE* 3.9 27.2 - - + +
1202B ARG* 4.0 19.1 - - - -
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Residues in contact with ASN1156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1152B ASP* 3.0 31.9 + - - +
1153B LYS* 3.9 6.3 - - - +
1155B TYR* 1.3 87.2 - - - +
1157B LEU* 1.3 64.0 + - + +
1159B ASN* 3.8 8.2 + - - +
1160B GLY* 3.0 21.1 + - - -
1166B GLU* 4.4 1.9 - - - +
1193B TYR* 5.7 0.4 + - - -
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Residues in contact with LEU1157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1153B LYS* 3.1 38.1 + - + +
1154B ILE* 3.7 8.5 - - + +
1156B ASN* 1.3 80.0 - - + +
1158B TYR* 1.3 65.5 + - + +
1160B GLY* 3.0 3.3 + - - -
1161B TYR* 2.9 26.7 + - - +
1166B GLU* 3.5 60.3 - - + +
1169B MET* 4.6 9.2 - - + -
1170B ALA* 3.8 19.7 - - + +
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Residues in contact with TYR1158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1154B ILE* 3.0 44.8 + - + +
1155B TYR* 3.3 6.7 + - - +
1157B LEU* 1.3 79.2 - - + +
1159B ASN* 1.3 56.3 + - - +
1161B TYR* 3.2 16.6 - - - -
1170B ALA* 4.1 18.2 - - + -
1174B LEU* 3.9 6.2 - - - +
1189B TYR* 4.0 11.2 - + - -
1199B PHE* 4.8 2.0 - + - -
1202B ARG* 3.1 49.5 + - + +
1203B SER* 2.8 42.8 + - - -
1206B GLU* 3.3 32.9 - - + +
1207B LEU* 3.4 22.0 - - + +
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Residues in contact with ASN1159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155B TYR* 2.9 52.3 + - - +
1156B ASN* 4.0 9.3 + - - +
1158B TYR* 1.3 74.8 - - - +
1160B GLY* 1.3 59.2 + - - +
1161B TYR* 3.2 24.5 + - - -
1202B ARG* 4.2 7.9 + - - -
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Residues in contact with GLY1160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156B ASN 3.0 13.3 + - - -
1157B LEU 3.0 5.5 + - - -
1159B ASN* 1.3 77.3 - - - +
1161B TYR* 1.3 55.4 + - - +
1162B THR* 2.7 23.2 + - - -
1166B GLU* 3.7 20.5 - - - +
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Residues in contact with TYR1161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1157B LEU 2.9 11.7 + - - +
1158B TYR 3.2 14.1 + - - -
1159B ASN* 3.2 36.2 + - - -
1160B GLY* 1.3 70.4 - - - +
1162B THR* 1.3 70.9 + - - +
1163B SER 3.1 11.0 + - - +
1166B GLU* 3.9 3.5 - - - +
1167B GLN* 4.4 11.3 + - - +
1202B ARG* 3.6 13.1 + - - -
1206B GLU* 2.9 43.8 + - - +
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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