Contacts of the helix formed by residues 1178 - 1194 (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 SER1178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1140B PRO* 5.6 4.3 - - - +
1141B LEU 5.3 3.3 + - - -
1176B GLU 4.3 0.2 + - - -
1177B VAL* 1.3 81.1 - - - +
1179B ALA* 1.3 58.7 + - - +
1180B SER* 3.6 7.7 + - - -
1181B MET* 3.1 25.2 + - - +
1182B LEU* 2.9 25.6 + - - +
1218B ARG* 5.4 0.2 - - - +
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Residues in contact with ALA1179 (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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1178B SER* 1.3 74.0 - - - +
1180B SER* 1.3 57.5 + - - +
1182B LEU* 3.3 4.2 + - - +
1183B PHE* 2.9 23.2 + - - +
1218B ARG* 3.5 48.9 - - + +
1219B LEU* 4.4 2.3 - - - +
1221B ARG* 4.3 14.7 - - + +
1222B VAL* 3.5 19.3 - - + +
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Residues in contact with SER1180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140B PRO* 3.2 35.8 - - - +
1141B LEU 5.5 0.4 - - - -
1142B VAL* 4.1 15.2 - - - +
1178B SER* 3.2 6.6 + - - -
1179B ALA* 1.3 76.2 - - - +
1181B MET* 1.3 59.2 + - - +
1183B PHE* 3.2 4.5 + - - +
1184B ARG* 2.9 27.5 + - - +
1222B VAL* 3.8 14.3 - - - +
1226B CYS* 5.4 0.5 - - - +
1230B LEU* 3.9 23.1 - - - +
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Residues in contact with MET1181 (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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1141B LEU 5.1 2.2 - - - +
1142B VAL* 3.9 22.9 - - + +
1143B ASP* 3.5 26.7 - - - +
1146B LYS* 4.0 9.0 - - + -
1147B ALA* 3.6 32.5 - - + +
1150B ILE* 3.8 22.7 - - + -
1177B VAL* 3.4 25.8 - - + -
1178B SER* 3.1 19.3 + - - +
1180B SER* 1.3 75.8 - - - +
1182B LEU* 1.3 53.5 + - - +
1184B ARG* 3.1 5.4 + - - +
1185B VAL* 2.8 41.2 + - + +
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Residues in contact with LEU1182 (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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1174B LEU* 3.6 52.3 - - + +
1175B MET* 4.7 1.6 - - + -
1177B VAL* 4.1 3.5 - - + +
1178B SER 2.9 13.7 + - - +
1179B ALA* 3.5 8.3 - - - +
1180B SER 3.3 0.2 - - - -
1181B MET* 1.3 75.8 - - - +
1183B PHE* 1.3 62.5 + - - +
1185B VAL* 3.2 9.8 - - + +
1186B GLN* 3.0 23.2 + - - +
1199B PHE* 4.4 3.8 - - + -
1215B ILE* 3.5 40.8 - - + +
1218B ARG* 3.6 22.4 - - + -
1219B LEU* 3.6 15.7 - - + +
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Residues in contact with PHE1183 (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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1179B ALA 2.9 13.8 + - - +
1180B SER* 3.2 9.2 + - - +
1182B LEU* 1.3 76.6 - - - +
1184B ARG* 1.3 57.5 + - - +
1186B GLN* 3.4 23.0 - - - +
1187B HIS* 3.1 23.0 + - + +
1219B LEU* 3.4 27.0 - - + +
1222B VAL* 4.2 11.0 - - + -
1227B SER* 3.2 38.8 - - - -
1230B LEU* 3.5 33.0 - - + -
1231B ARG* 3.4 35.4 - - + -
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Residues in contact with ARG1184 (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* 3.8 15.9 - - + -
1144B ASP* 2.6 36.2 + - - +
1147B ALA* 3.5 22.2 - - + -
1180B SER 2.9 14.3 + - - +
1181B MET 3.1 8.0 + - - +
1183B PHE* 1.3 76.6 - - - +
1185B VAL* 1.3 64.6 + - - +
1186B GLN 3.1 0.2 - - - -
1187B HIS* 3.1 25.8 + - - +
1188B HIS* 3.0 36.3 + - + -
1230B LEU* 2.7 40.0 + - + -
1232B SER 2.8 29.7 + - - -
1233B ALA 3.7 1.4 + - - -
1234B TYR* 3.6 5.1 - - - +
1235B ILE* 3.4 29.4 - - - +
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Residues in contact with VAL1185 (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* 3.5 35.0 - - - +
1150B ILE* 3.7 26.5 - - + -
1151B ALA* 3.6 8.7 - - + +
1154B ILE* 5.9 0.2 - - + -
1174B LEU* 3.8 27.8 - - + -
1177B VAL* 5.3 2.7 - - + -
1181B MET* 2.8 25.2 + - + +
1182B LEU* 3.2 23.8 + - + +
1184B ARG* 1.3 71.5 - - - +
1186B GLN* 1.3 56.8 + - - +
1188B HIS* 4.5 0.4 - - - +
1189B TYR* 2.8 30.8 + - - +
1199B PHE* 4.3 7.4 - - + -
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Residues in contact with GLN1186 (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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1182B LEU 3.0 13.0 + - - +
1183B PHE* 3.4 33.5 - - - +
1185B VAL* 1.3 76.3 - - - +
1187B HIS* 1.3 66.3 + - - +
1189B TYR* 3.2 0.7 + - - -
1190B ASN* 2.9 48.5 + - - +
1198B ASP* 5.4 1.0 + - - -
1199B PHE* 3.6 25.7 - - + +
1200B VAL* 3.6 28.9 - - - +
1216B LEU* 5.6 0.4 - - - +
1219B LEU* 3.7 18.4 - - + +
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Residues in contact with HIS1187 (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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1183B PHE* 3.1 11.0 + - + +
1184B ARG* 3.1 31.9 + - - +
1186B GLN* 1.3 80.0 - - - +
1188B HIS* 1.3 60.9 + + - +
1190B ASN* 4.0 4.0 - - - +
1191B SER* 2.6 50.1 + - - -
1230B LEU 4.0 9.0 - - - +
1231B ARG* 3.3 41.1 + - + -
1232B SER 3.3 19.0 + - - -
1233B ALA* 3.5 17.4 - - - -
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Residues in contact with HIS1188 (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* 2.7 34.8 + - - -
1147B ALA* 3.8 7.4 - - + -
1148B GLU* 3.6 52.4 + - + +
1151B ALA* 3.8 17.7 - - + -
1184B ARG* 3.0 43.3 + - + +
1185B VAL 3.9 0.2 - - - +
1187B HIS* 1.3 81.3 + + - +
1189B TYR* 1.3 65.8 + - - +
1191B SER* 3.0 15.9 + - - -
1192B HIS* 3.2 24.5 + - + -
1233B ALA 5.4 1.8 - - - -
1234B TYR* 6.0 3.8 - + - -
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Residues in contact with TYR1189 (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* 3.7 21.6 - - + +
1154B ILE* 4.6 4.9 - - + -
1155B TYR* 3.6 38.5 - + + -
1158B TYR* 4.0 11.9 - + - -
1185B VAL 2.8 23.1 + - - +
1186B GLN 3.2 3.6 + - - +
1188B HIS* 1.3 71.9 - - - +
1190B ASN* 1.3 60.5 + - - +
1193B TYR* 2.9 44.4 + + + +
1197B GLY 3.4 22.4 + - - -
1198B ASP 4.2 0.4 - - - -
1199B PHE* 3.6 43.7 - + + -
1202B ARG* 3.5 35.6 + - + +
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Residues in contact with ASN1190 (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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1186B GLN* 2.9 41.8 + - - +
1187B HIS* 4.2 3.9 - - - +
1189B TYR* 1.3 74.2 - - - +
1191B SER* 1.3 65.1 + - - +
1192B HIS 3.2 2.0 + - - -
1194B GLU* 3.2 44.5 + - - +
1198B ASP* 3.2 20.2 + - - +
1199B PHE* 3.0 27.8 + - - +
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Residues in contact with SER1191 (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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1187B HIS* 2.6 38.3 + - - -
1188B HIS* 3.0 14.1 + - - -
1190B ASN* 1.3 76.5 - - - +
1192B HIS* 1.3 71.2 + - - +
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Residues in contact with HIS1192 (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 27.9 + - + +
1151B ALA* 5.9 0.2 - - + -
1152B ASP* 4.5 13.6 + - - -
1188B HIS* 3.2 29.4 + - + +
1191B SER* 1.3 90.0 + - - +
1193B TYR* 1.3 89.6 + + + +
1194B GLU 3.6 2.6 + - - -
1195B LYS* 5.1 6.6 + - - +
1196B PHE* 5.3 3.6 - - - -
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Residues in contact with TYR1193 (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* 3.9 8.1 - - + -
1152B ASP* 2.7 37.6 + - - +
1155B TYR* 3.4 67.8 - + + -
1156B ASN* 5.7 0.5 + - - -
1189B TYR* 2.9 42.0 + + + +
1192B HIS* 1.3 91.7 - + + +
1194B GLU* 1.3 62.6 + - - +
1195B LYS 3.2 3.1 - - - -
1196B PHE* 3.3 21.9 + + + +
1197B GLY 3.2 15.3 + - - +
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Residues in contact with GLU1194 (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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1189B TYR 4.0 0.8 + - - -
1190B ASN* 3.2 39.9 + - - +
1192B HIS 3.6 2.8 - - - -
1193B TYR* 1.3 77.7 - - - +
1195B LYS* 1.3 79.0 + - + +
1197B GLY* 3.3 18.2 + - - -
1198B ASP* 3.9 22.6 + - + +
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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