Contacts of the helix formed by residues 1169 - 1184 (chain A) in PDB entry 5W0N
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 SER1169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1161A GLY 4.7 0.9 - - - -
1163A ALA* 3.9 22.4 - - - +
1168A LEU* 1.3 75.5 - - - +
1170A SER* 1.3 63.2 + - - +
1171A TYR* 3.2 20.7 + - - +
1172A ALA* 2.8 32.7 + - - +
1173A TYR* 3.3 7.7 + - - -
1288A LEU* 4.8 11.1 + - - -
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Residues in contact with SER1170 (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 LYS* 3.9 33.4 + - - -
1155A THR* 5.7 2.2 - - - -
1156A LYS* 6.1 2.9 - - - -
1161A GLY* 4.2 13.6 + - - -
1168A LEU 3.7 2.0 + - - -
1169A SER* 1.3 75.2 + - - +
1171A TYR* 1.3 58.6 + - - +
1173A TYR* 3.2 14.8 + - - +
1174A THR* 3.0 30.1 + - - -
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Residues in contact with TYR1171 (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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1050A ASN* 5.6 2.7 - - - -
1130A ASN* 3.3 41.5 + - - +
1134A LEU* 3.8 32.3 - - + -
1169A SER* 3.1 11.9 + - - +
1170A SER* 1.3 82.6 + - - +
1172A ALA* 1.3 60.2 + - - +
1174A THR* 3.4 5.9 + - - -
1175A LEU* 3.2 40.4 + - + +
1280A ASP* 2.9 28.3 + - - -
1281A PRO* 3.4 13.2 - - - +
1286A HIS* 6.3 0.2 - + - -
1288A LEU* 4.0 21.5 - - + -
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Residues in contact with ALA1172 (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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1168A LEU* 4.3 11.7 - - + -
1169A SER* 2.8 22.2 + - - +
1171A TYR* 1.3 80.7 - - - +
1173A TYR* 1.3 59.4 + - - +
1175A LEU* 3.2 15.4 + - - +
1176A MET* 3.1 25.7 + - - +
1278A ILE* 4.1 14.1 - - + +
1288A LEU* 4.0 29.2 - - + -
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Residues in contact with TYR1173 (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 MET* 3.8 23.2 - - + +
1152A LYS* 5.9 1.3 - - - +
1155A THR* 3.6 39.5 - - + +
1160A ILE* 2.7 42.9 + - - +
1161A GLY* 3.9 6.3 - - - -
1168A LEU* 3.7 33.9 - - + +
1169A SER 3.3 14.8 + - - -
1170A SER* 3.2 14.4 + - - +
1172A ALA* 1.3 73.9 - - - +
1174A THR* 1.3 66.0 + - - +
1176A MET* 3.1 22.4 + - - +
1177A VAL* 3.1 25.6 + - - +
1300A ILE* 3.9 9.1 - - + +
1304A PHE* 4.2 15.5 - + - -
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Residues in contact with THR1174 (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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1050A ASN* 5.6 1.2 + - - -
1052A PHE* 3.8 27.5 - - + +
1134A LEU* 3.6 31.6 - - + +
1148A CYS* 4.0 15.0 + - - +
1151A MET* 5.7 0.2 - - - -
1152A LYS* 4.9 10.4 + - - -
1170A SER 3.0 15.3 + - - -
1171A TYR* 3.6 11.1 - - - -
1172A ALA 3.3 0.2 - - - -
1173A TYR* 1.3 76.4 - - - +
1175A LEU* 1.3 61.6 + - - +
1177A VAL* 3.1 9.2 + - - +
1178A LEU* 3.0 25.5 + - + +
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Residues in contact with LEU1175 (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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1134A LEU* 4.4 8.5 - - + -
1171A TYR* 3.2 47.8 + - + +
1172A ALA* 3.2 7.4 + - - +
1174A THR* 1.3 75.0 - - - +
1176A MET* 1.3 58.0 + - - +
1178A LEU* 3.3 4.4 + - + +
1179A TYR* 2.8 31.8 + - - +
1256A ILE* 4.6 2.5 - - + -
1258A ILE* 3.5 38.9 - - + +
1278A ILE* 3.9 26.2 - - + -
1279A GLU 4.1 6.5 - - - +
1280A ASP* 4.6 0.4 - - - -
1281A PRO* 4.0 19.5 - - + -
1288A LEU* 4.4 8.3 - - + -
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Residues in contact with MET1176 (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 MET* 4.4 5.2 - - + -
1168A LEU* 4.8 3.6 - - - -
1172A ALA 3.1 11.1 + - - +
1173A TYR* 3.1 36.2 + - - +
1175A LEU* 1.3 76.4 - - - +
1177A VAL* 1.3 61.6 + - - +
1180A PHE* 3.0 13.9 + - - +
1245A TYR* 2.6 66.2 + - + +
1251A PHE* 4.6 9.0 - - + -
1256A ILE* 4.0 17.9 - - + -
1276A ILE* 5.1 4.5 - - + -
1278A ILE* 3.8 25.1 - - + -
1304A PHE* 4.8 12.6 - - + -
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Residues in contact with VAL1177 (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 LEU* 3.9 25.8 - - + +
1148A CYS* 3.7 26.0 - - - -
1151A MET* 3.6 37.2 - - + -
1173A TYR 3.1 15.2 + - - +
1174A THR* 3.1 6.9 + - - +
1176A MET* 1.3 76.2 - - - +
1178A LEU* 1.3 64.0 + - - +
1180A PHE* 3.2 4.2 + - - +
1181A LEU* 3.0 39.1 + - + +
1241A LEU* 4.0 16.2 - - + -
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Residues in contact with LEU1178 (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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1052A PHE* 5.1 1.8 - - + -
1134A LEU* 4.0 28.5 - - + -
1137A TYR* 3.9 28.7 - - + -
1144A VAL* 3.8 28.9 - - + -
1148A CYS* 4.6 7.4 - - - -
1174A THR* 3.0 21.7 + - + +
1175A LEU* 3.8 4.3 - - - +
1177A VAL* 1.3 75.7 - - - +
1179A TYR* 1.3 58.4 + - - +
1181A LEU* 3.2 3.1 + - + -
1182A GLN* 2.9 34.8 + - - +
1189A ILE* 3.6 22.0 - - + +
1258A ILE* 4.0 20.9 - - + -
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Residues in contact with TYR1179 (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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1175A LEU 2.8 18.7 + - - +
1176A MET 3.9 1.8 - - - +
1178A LEU* 1.3 77.6 - - - +
1180A PHE* 1.3 61.4 + - - +
1182A GLN* 3.2 7.7 + - - +
1183A GLN* 3.0 58.5 + - + +
1244A PHE* 4.3 7.2 - + - -
1245A TYR* 3.7 14.6 - - - -
1249A PHE* 3.6 34.7 - + - -
1254A HIS* 5.0 1.7 - - - +
1255A VAL 3.9 12.4 + - - -
1256A ILE* 3.7 20.2 - - + -
1257A SER* 3.2 36.8 - - - -
1258A ILE* 3.6 8.7 - - + +
1260A ARG 5.1 1.1 - - - -
1263A LEU* 4.2 19.0 - - - +
1264A LEU 6.3 0.4 - - - -
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Residues in contact with PHE1180 (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 LEU* 4.9 1.8 - - + -
1176A MET 3.0 14.7 + - - +
1177A VAL 3.2 5.4 + - - +
1179A TYR* 1.3 77.4 - - - +
1181A LEU* 1.3 80.4 + - + +
1183A GLN* 3.3 3.6 + - - +
1184A ARG* 2.9 67.5 + - - +
1237A LEU* 3.4 25.6 - - + -
1240A GLY 3.7 14.6 - - - -
1241A LEU* 3.5 36.6 - - + -
1244A PHE* 3.7 37.2 - + + -
1245A TYR* 3.9 6.0 + - + +
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Residues in contact with LEU1181 (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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1144A VAL* 4.2 31.9 - - + +
1147A LEU* 3.6 29.4 - - + -
1177A VAL* 3.0 36.1 + - + +
1178A LEU* 3.7 2.0 - - - +
1180A PHE* 1.3 92.8 - - + +
1182A GLN* 1.3 60.4 + - - +
1184A ARG* 3.8 5.2 + - + +
1187A PRO* 3.6 2.3 - - - +
1188A VAL* 3.0 55.0 + - + -
1189A ILE* 3.6 20.8 + - + -
1237A LEU* 4.4 3.4 - - + -
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Residues in contact with GLN1182 (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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1137A TYR* 2.9 32.5 + - - -
1178A LEU* 2.9 20.4 + - - +
1179A TYR* 3.7 7.4 - - - +
1181A LEU* 1.3 77.0 - - - +
1183A GLN* 1.3 68.9 + - + +
1187A PRO* 3.5 17.2 - - - +
1189A ILE* 3.7 14.9 - - + +
1190A PRO 3.1 22.3 + - - +
1191A VAL* 3.6 17.5 - - + +
1257A SER 4.3 2.1 - - - +
1258A ILE* 3.1 44.8 + - - +
1260A ARG 5.0 0.7 - - - +
1261A LYS* 3.7 16.3 + - + -
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Residues in contact with GLN1183 (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 TYR* 3.0 53.3 + - + +
1180A PHE 3.7 2.5 - - - +
1182A GLN* 1.3 76.1 + - - +
1184A ARG* 1.3 67.9 + - - +
1185A ASN* 3.5 3.3 + - - +
1244A PHE* 4.7 16.4 - - + -
1260A ARG 4.5 1.0 + - - -
1261A LYS* 2.9 50.6 + - - +
1262A SER 5.3 0.2 - - - -
1263A LEU* 3.3 25.0 - - - +
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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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1180A PHE* 2.9 50.5 + - + +
1181A LEU* 3.9 12.3 - - - +
1182A GLN 3.3 1.9 - - - +
1183A GLN* 1.3 80.3 - - - +
1185A ASN* 1.3 66.0 + - - +
1186A PRO 3.3 12.6 - - - +
1187A PRO* 2.9 24.1 - - - +
1188A VAL* 4.6 3.1 - - + +
1230A ASN* 3.8 3.4 - - - +
1232A GLU* 2.8 43.8 + - - +
1236A GLN* 4.3 6.5 + - - +
1237A LEU* 3.9 7.7 - - + +
1240A GLY* 4.0 21.6 + - - -
1244A PHE* 5.9 0.2 - - - -
1248A GLU* 5.1 8.1 + - - -
1261A LYS* 5.2 1.9 + - - -
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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