Contacts of the helix formed by residues 1149 - 1163 (chain B) in PDB entry 1JSP
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 GLU1149 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082B LYS 5.6 1.1 - - - +
1083B LYS* 5.6 7.3 - - - +
1087B PRO* 5.6 2.9 - - + -
1090B LEU* 3.4 12.3 - - + -
1146B GLN 5.2 0.9 + - - +
1147B TYR 3.3 0.4 - - - -
1148B GLN* 1.3 88.4 - - + +
1150B PRO* 1.3 73.9 - - + +
1151B TRP* 4.2 11.7 - - + +
1152B GLN* 2.9 23.1 + - + +
1153B TYR* 2.8 20.3 + - - +
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Residues in contact with PRO1150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082B LYS* 3.2 19.1 - - + +
1083B LYS 4.7 0.2 - - - +
1084B ILE* 3.1 29.8 - - + -
1090B LEU* 3.4 24.5 - - + -
1094B LEU* 6.3 0.2 - - + -
1148B GLN 3.3 1.1 - - - +
1149B GLU* 1.3 85.5 - - + +
1151B TRP* 1.3 56.2 + - - +
1153B TYR* 4.0 8.5 - - + -
1154B VAL* 2.5 42.3 + - + +
1192B VAL* 4.1 9.0 - - + -
1194B GLN* 3.2 29.6 - - + -
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Residues in contact with TRP1151 (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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1077B GLY 5.7 5.2 - - - -
1080B MET* 4.2 26.9 - - + -
1082B LYS* 4.0 34.4 + - + +
1149B GLU* 3.0 10.7 + - + -
1150B PRO* 1.3 79.1 - - - +
1152B GLN* 1.3 63.1 + - + +
1154B VAL* 4.3 1.7 - - - +
1155B ASP* 2.7 60.3 + - - +
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Residues in contact with GLN1152 (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 GLN 4.3 7.4 + - - +
1147B TYR* 2.9 68.3 + - + -
1149B GLU* 2.9 22.9 + - + +
1151B TRP* 1.3 86.2 - - + +
1153B TYR* 1.3 67.1 + - - +
1155B ASP* 3.1 7.8 - - - +
1156B ASP 3.0 19.2 + - - -
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Residues in contact with TYR1153 (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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1094B LEU* 3.0 28.7 - - + -
1097B THR* 3.5 34.1 + - + +
1098B LEU* 4.2 2.3 - - + +
1101B LEU* 3.7 18.4 - - + +
1138B ILE* 3.9 5.2 - - + -
1142B LEU* 3.1 41.2 - - + +
1147B TYR* 3.3 25.9 + - - +
1149B GLU 2.8 15.9 + - - +
1150B PRO* 3.9 5.4 - - + +
1152B GLN* 1.3 74.4 - - - +
1154B VAL* 1.3 74.4 + - + +
1155B ASP 3.0 0.3 + - - -
1156B ASP* 3.1 0.9 + - - +
1157B VAL* 2.8 51.5 + - + +
1185B PHE* 5.0 0.7 - - - -
1189B ILE* 4.8 11.9 - - + -
1192B VAL* 5.4 4.5 - - + -
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Residues in contact with VAL1154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082B LYS* 5.8 1.8 - - + +
1150B PRO* 2.5 38.8 + - + +
1151B TRP* 4.3 1.8 - - - +
1153B TYR* 1.3 80.3 - - + +
1155B ASP* 1.3 56.9 + - - +
1157B VAL* 4.0 8.7 - - + -
1158B TRP* 2.7 57.1 + - + +
1185B PHE* 5.5 4.5 - - + -
1189B ILE* 4.7 9.9 - - + -
1192B VAL* 5.9 0.2 - - + -
1194B GLN* 3.0 50.0 - - + +
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Residues in contact with ASP1155 (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 TYR* 5.3 0.2 - - + -
1151B TRP* 2.7 51.0 + - - +
1152B GLN* 3.1 10.5 - - - +
1153B TYR 3.0 0.4 + - - -
1154B VAL* 1.3 79.6 - - - +
1156B ASP* 1.3 63.3 + - - +
1158B TRP* 3.9 3.3 - - - +
1159B LEU* 2.9 32.2 + - - +
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Residues in contact with ASP1156 (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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1131B ASN* 5.4 1.4 - - - +
1133B MET* 3.5 32.6 - - + +
1138B ILE* 3.3 21.7 - - + +
1141B LYS* 3.3 24.6 + - - -
1147B TYR* 3.2 29.1 + - + -
1152B GLN 3.0 4.2 + - - +
1153B TYR 3.8 2.7 - - - +
1155B ASP* 1.3 79.7 - - - +
1157B VAL* 1.3 54.6 + - - +
1159B LEU* 4.2 1.6 - - - +
1160B MET* 2.5 41.3 + - - +
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Residues in contact with VAL1157 (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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1101B LEU* 4.0 10.3 - - + -
1138B ILE* 3.1 12.1 - - + -
1153B TYR* 2.8 62.1 + - + +
1154B VAL* 3.8 5.8 - - - +
1156B ASP* 1.3 72.5 - - - +
1158B TRP* 1.3 57.3 + - - +
1160B MET* 3.3 5.7 - - - +
1161B PHE* 2.7 42.5 + - + -
1185B PHE* 2.9 43.3 - - + -
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Residues in contact with TRP1158 (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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1082B LYS* 6.0 3.6 - - - -
1154B VAL* 2.7 44.9 + - + +
1155B ASP* 3.9 3.8 - - - +
1157B VAL* 1.3 75.1 - - - +
1159B LEU* 1.3 59.9 + - - +
1161B PHE* 3.0 12.9 + - + +
1162B ASN* 2.7 48.0 + - + +
1185B PHE* 5.1 10.3 - + - -
1189B ILE* 5.6 5.4 - - + -
1194B GLN* 5.0 10.1 - - - -
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Residues in contact with LEU1159 (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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1129B VAL* 3.8 15.7 - - + +
1130B LYS* 5.8 0.7 - - + -
1131B ASN* 2.8 52.9 - - + +
1132B PRO* 3.7 9.4 - - + -
1133B MET* 3.7 9.4 - - + -
1155B ASP 2.9 21.4 + - - +
1156B ASP* 3.7 3.6 - - - +
1158B TRP* 1.3 77.4 - - - +
1160B MET* 1.3 56.3 + - - +
1161B PHE 2.9 0.2 + - - -
1162B ASN* 3.0 8.6 + - + -
1163B ASN* 2.5 38.5 + - + +
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Residues in contact with MET1160 (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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1101B LEU* 6.4 0.2 - - + -
1111B PHE* 3.3 43.1 - - + +
1114B PRO* 4.1 3.4 - - + -
1133B MET* 2.7 49.8 - - + +
1134B ASP* 3.4 11.0 - - - -
1135B LEU* 3.5 20.4 - - + -
1138B ILE* 5.2 3.8 - - + -
1156B ASP 2.5 25.3 + - - +
1157B VAL* 3.3 8.5 - - - +
1159B LEU* 1.3 74.9 - - - +
1161B PHE* 1.3 62.2 + - + +
1163B ASN* 3.2 26.1 - - - +
1164B ALA* 3.8 2.5 + - + -
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Residues in contact with PHE1161 (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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1101B LEU* 3.1 35.4 - - + -
1111B PHE* 3.4 22.7 - + - -
1157B VAL* 2.7 31.3 + - + -
1158B TRP* 3.0 11.7 - - + +
1159B LEU 2.9 0.2 + - - -
1160B MET* 1.3 76.2 - - + +
1162B ASN* 1.3 57.8 + - - +
1163B ASN 2.9 0.9 - - - -
1164B ALA* 2.6 36.0 + - - -
1165B TRP* 3.1 19.7 + - + +
1178B CYS 3.4 9.6 - - - -
1181B LEU* 3.2 2.7 - - + -
1182B ALA* 3.1 42.8 - - + -
1185B PHE* 3.2 28.3 - + - -
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Residues in contact with ASN1162 (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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1128B ILE 3.4 14.5 - - - +
1129B VAL* 4.3 1.1 - - - +
1158B TRP* 2.7 39.7 + - + +
1159B LEU* 3.5 10.5 - - + +
1161B PHE* 1.3 72.7 - - - +
1163B ASN* 1.3 63.4 + - - +
1164B ALA 2.9 1.0 + - - -
1165B TRP* 3.1 19.5 + - - +
1166B LEU* 2.7 51.7 + - - +
1167B TYR 5.1 0.2 + - - -
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Residues in contact with ASN1163 (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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382A ALY 3.3 9.7 - - - +
1114B PRO* 3.4 15.6 - - - +
1115B VAL 4.4 1.6 + - - -
1125B TYR* 2.5 39.8 + - - -
1129B VAL* 3.3 23.6 - - + +
1132B PRO* 3.2 30.1 - - + +
1133B MET 3.6 0.2 - - - +
1159B LEU* 2.5 21.9 + - - +
1160B MET* 3.2 34.5 - - - +
1162B ASN* 1.3 74.1 - - - +
1164B ALA* 1.3 57.8 + - - +
1165B TRP 4.1 0.2 + - - -
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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