Contacts of the helix formed by residues 1178 - 1194 (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 SER1178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1140A PRO* 5.5 4.8 - - - +
1141A LEU 5.2 3.6 + - - -
1177A VAL* 1.3 82.7 - - - +
1179A ALA* 1.3 60.6 + - - +
1180A SER* 3.7 6.9 + - - -
1181A MET* 3.2 23.3 + - - +
1182A LEU* 2.9 25.5 + - - +
1218A ARG* 5.0 0.7 - - - +
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Residues in contact with ALA1179 (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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1178A SER* 1.3 74.5 - - - +
1180A SER* 1.3 58.2 + - - +
1182A LEU* 3.3 2.9 + - - +
1183A PHE* 2.9 23.9 + - - +
1218A ARG* 3.4 49.4 - - + +
1219A LEU* 4.4 2.6 - - - +
1221A ARG* 4.3 15.2 - - + +
1222A VAL* 3.3 18.9 - - + +
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Residues in contact with SER1180 (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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1111A ASP* 5.7 0.3 + - - -
1140A PRO* 3.4 33.0 - - - +
1141A LEU 5.4 0.4 - - - -
1142A VAL* 4.1 16.7 - - - +
1178A SER* 3.3 7.2 + - - -
1179A ALA* 1.3 75.3 - - - +
1181A MET* 1.3 59.6 + - - +
1183A PHE* 3.2 3.8 + - - +
1184A ARG* 2.9 27.0 + - - +
1222A VAL* 3.8 17.1 - - - +
1226A CYS* 5.3 0.2 - - - +
1230A LEU* 3.9 22.1 - - - +
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Residues in contact with MET1181 (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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1141A LEU 5.0 2.5 - - - +
1142A VAL* 3.7 23.6 - - + -
1143A ASP* 3.6 25.8 - - - +
1146A LYS* 4.1 9.2 - - + -
1147A ALA* 3.7 31.9 - - + +
1150A ILE* 3.9 21.8 - - + -
1177A VAL* 3.5 30.1 - - + -
1178A SER* 3.2 14.1 + - - +
1180A SER* 1.3 80.2 - - - +
1182A LEU* 1.3 56.4 + - - +
1184A ARG* 3.0 5.2 + - - +
1185A VAL* 2.8 37.9 + - + +
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Residues in contact with LEU1182 (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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1174A LEU* 3.6 52.9 - - + +
1175A MET* 4.5 1.1 - - + -
1177A VAL* 4.0 4.2 - - + +
1178A SER 2.9 14.0 + - - +
1179A ALA* 3.6 7.9 - - - +
1181A MET* 1.3 76.0 - - - +
1183A PHE* 1.3 62.5 + - - +
1185A VAL* 3.1 10.6 - - + +
1186A GLN* 3.0 22.7 + - - +
1199A PHE* 4.4 3.8 - - + -
1215A ILE* 3.3 43.5 - - + +
1218A ARG* 3.6 21.5 - - + -
1219A LEU* 3.6 14.3 - - + +
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Residues in contact with PHE1183 (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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1179A ALA 2.9 15.2 + - - +
1180A SER* 3.5 8.7 - - - +
1182A LEU* 1.3 76.5 - - - +
1184A ARG* 1.3 55.8 + - - +
1186A GLN* 3.5 22.4 + - - +
1187A HIS* 3.1 22.4 + - + +
1219A LEU* 3.5 25.0 - - + +
1222A VAL* 4.3 11.0 - - + -
1227A SER* 3.2 37.5 - - - -
1230A LEU* 3.5 33.4 - - + -
1231A ARG* 3.4 36.8 - - + -
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Residues in contact with ARG1184 (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* 3.8 15.9 - - + -
1144A ASP* 2.7 30.5 + - - +
1147A ALA* 3.5 21.5 - - + -
1180A SER 2.9 13.1 + - - +
1181A MET 3.0 7.8 + - - +
1183A PHE* 1.3 77.6 - - - +
1185A VAL* 1.3 60.4 + - - +
1186A GLN 3.2 0.4 - - - -
1187A HIS* 3.1 20.1 + - - +
1188A HIS* 3.0 40.4 + - + -
1230A LEU* 2.6 40.7 + - + -
1232A SER 2.9 22.8 + - - +
1233A ALA 3.1 28.3 + - - -
1234A TYR* 3.9 3.4 - - - +
1235A ILE* 3.7 21.0 - - - +
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Residues in contact with VAL1185 (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* 3.5 37.9 - - - +
1150A ILE* 4.0 20.2 - - + -
1151A ALA* 3.6 7.6 - - + +
1154A ILE* 6.1 0.2 - - + -
1174A LEU* 4.0 24.7 - - + -
1177A VAL* 5.4 2.2 - - + -
1181A MET* 2.8 27.4 + - + +
1182A LEU* 3.1 25.6 - - + +
1184A ARG* 1.3 73.0 - - - +
1186A GLN* 1.3 58.2 + - - +
1188A HIS* 4.4 0.9 - - - +
1189A TYR* 2.9 31.2 + - - +
1199A PHE* 4.5 7.3 - - + -
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Residues in contact with GLN1186 (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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1182A LEU 3.0 18.1 + - - +
1183A PHE* 3.6 26.9 - - - +
1184A ARG 3.2 0.2 - - - -
1185A VAL* 1.3 75.6 - - - +
1187A HIS* 1.3 64.1 + - - +
1189A TYR* 3.9 0.2 - - - -
1190A ASN* 3.0 48.9 + - - +
1198A ASP* 5.4 0.6 + - - -
1199A PHE* 3.6 25.1 - - + -
1200A VAL* 3.6 29.1 - - - +
1219A LEU* 3.6 23.7 - - + +
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Residues in contact with HIS1187 (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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1183A PHE* 3.1 16.6 + - + +
1184A ARG* 3.1 31.5 + - - +
1186A GLN* 1.3 77.6 - - - +
1188A HIS* 1.3 62.7 + + - +
1190A ASN* 4.0 4.0 - - - +
1191A SER* 2.5 51.0 + - - -
1230A LEU 4.0 8.1 - - - +
1231A ARG* 3.4 33.0 + - + -
1232A SER 3.2 26.2 + - - -
1233A ALA* 4.6 4.7 - - - -
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Residues in contact with HIS1188 (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* 2.7 34.8 + - - -
1147A ALA* 3.8 7.2 - - + -
1148A GLU* 3.6 52.1 + - + +
1151A ALA* 3.8 18.2 - - + -
1184A ARG* 3.0 43.5 + - + +
1185A VAL 4.5 0.2 - - - -
1187A HIS* 1.3 83.8 + + - +
1189A TYR* 1.3 65.7 + - - +
1191A SER* 3.2 11.4 + - - -
1192A HIS* 3.1 28.4 + - + -
1233A ALA 5.0 2.9 - - - -
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Residues in contact with TYR1189 (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* 3.8 19.9 - - + +
1154A ILE* 4.6 4.9 - - + -
1155A TYR* 3.6 35.8 - + + -
1158A TYR* 3.8 11.8 - + - -
1185A VAL 2.9 20.0 + - - +
1186A GLN 3.9 3.4 - - - +
1188A HIS* 1.3 76.0 - - - +
1190A ASN* 1.3 59.3 + - - +
1193A TYR* 2.9 47.6 + + + +
1197A GLY 3.3 21.7 + - - -
1198A ASP 4.1 0.4 - - - -
1199A PHE* 3.5 45.5 - + + -
1202A ARG* 3.4 36.4 + - + +
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Residues in contact with ASN1190 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1186A GLN* 3.0 41.8 + - - +
1187A HIS* 4.2 3.3 - - - +
1189A TYR* 1.3 74.6 - - - +
1191A SER* 1.3 65.6 + - - +
1192A HIS 3.2 0.8 + - - -
1194A GLU* 3.2 44.9 + - - +
1197A GLY 4.9 0.2 - - - +
1198A ASP* 3.0 30.5 + - - +
1199A PHE* 3.0 18.3 + - - +
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Residues in contact with SER1191 (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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1187A HIS* 2.5 42.0 + - - -
1188A HIS* 3.2 11.3 + - - -
1190A ASN* 1.3 78.9 - - - +
1192A HIS* 1.3 67.8 + - - +
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Residues in contact with HIS1192 (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* 3.3 27.1 + - + +
1152A ASP* 4.7 11.9 - - - -
1188A HIS* 3.1 29.9 + - + +
1190A ASN 3.2 0.2 - - - -
1191A SER* 1.3 89.7 + - - +
1193A TYR* 1.3 89.9 + + + +
1194A GLU 3.5 2.4 + - - -
1195A LYS* 5.1 6.8 + - - +
1196A PHE* 5.3 4.0 - - - -
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Residues in contact with TYR1193 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1151A ALA* 3.9 8.3 - - + -
1152A ASP* 2.7 37.5 + - - +
1155A TYR* 3.4 66.2 - + + -
1156A ASN* 5.9 0.3 + - - -
1189A TYR* 2.9 45.8 + + + +
1192A HIS* 1.3 94.2 - + + +
1194A GLU* 1.3 63.2 + - - +
1195A LYS 3.2 3.7 + - - +
1196A PHE* 3.3 19.7 + + + +
1197A GLY 3.2 15.7 + - - +
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Residues in contact with GLU1194 (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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1189A TYR 4.0 0.4 + - - -
1190A ASN* 3.2 43.1 + - - +
1192A HIS 3.5 3.2 + - - -
1193A TYR* 1.3 78.1 - - - +
1195A LYS* 1.3 78.6 + - + +
1197A GLY* 3.4 17.1 + - - -
1198A ASP* 4.1 20.0 + - + +
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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