Contacts of the helix formed by residues 1130 - 1147 (chain D) in PDB entry 1W1W
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 SER1130 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLY* 3.3 9.5 + - - -
2224C AGS 2.6 65.8 + - - -
1128D TYR 3.7 1.4 + - - -
1129D LEU* 1.3 74.7 - - - +
1131D GLY* 1.3 55.3 + - - +
1133D GLU* 3.0 27.4 + - - +
1134D LYS* 2.6 34.9 + - - +
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Residues in contact with GLY1131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C GLN* 3.8 21.0 + - - +
2224C AGS 3.5 6.3 + - - -
155D GLU* 3.3 25.5 - - - +
1130D SER* 1.3 75.3 - - - +
1132D GLY* 1.3 60.0 + - - +
1134D LYS* 4.5 2.0 - - - +
1135D THR* 3.0 27.9 + - - -
1162D ALA* 4.0 4.5 - - - -
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Residues in contact with GLY1132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ASN* 3.6 13.5 - - - -
151C GLN* 4.9 0.2 - - - +
2224C AGS 2.7 22.7 + - - -
1131D GLY* 1.3 72.7 - - - -
1133D GLU* 1.3 60.8 + - - +
1135D THR* 3.0 13.7 + - - -
1136D VAL* 3.0 18.9 + - - +
1162D ALA 3.6 19.5 + - - -
1163D LEU* 4.1 7.6 - - - -
1167D ASN* 5.1 0.9 - - - -
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Residues in contact with GLU1133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ASN* 4.6 5.6 - - + +
36C GLY* 3.5 11.0 - - - +
2224C AGS 2.8 20.3 + - - -
1079D TYR* 4.9 3.2 + - - -
1118D PRO* 3.7 23.7 - - + +
1121D LYS* 2.8 31.2 - - - +
1129D LEU* 3.5 18.6 - - + +
1130D SER* 3.0 32.0 + - - +
1132D GLY* 1.3 75.1 - - - +
1134D LYS* 1.3 56.7 + - - +
1136D VAL* 3.3 7.2 + - - +
1137D ALA* 2.9 29.6 + - - +
1167D ASN* 6.1 0.2 - - - +
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Residues in contact with LYS1134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D GLU* 3.8 34.7 + - + +
158D ALA* 3.8 0.6 - - + +
159D ALA* 3.9 23.8 - - + +
1126D MET* 3.8 33.8 + - + +
1127D GLU* 5.5 2.4 + - - +
1129D LEU* 3.5 27.2 + - + +
1130D SER 2.6 18.2 + - - +
1131D GLY* 3.9 4.8 - - - +
1133D GLU* 1.3 73.6 - - - +
1135D THR* 1.3 57.2 + - - +
1137D ALA* 3.5 5.8 + - - +
1138D ALA* 2.9 30.5 + - - +
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Residues in contact with THR1135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D VAL* 3.9 10.1 - - + +
155D GLU* 3.3 21.1 + - - +
1131D GLY 3.0 17.1 + - - -
1132D GLY 3.0 9.7 + - - -
1134D LYS* 1.3 75.7 - - - +
1136D VAL* 1.3 63.1 + - - +
1138D ALA* 3.2 5.9 + - - +
1139D LEU* 2.8 35.6 + - + +
1159D VAL 3.2 25.7 + - - +
1162D ALA* 3.8 8.3 - - - +
1163D LEU* 3.6 24.7 - - + -
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Residues in contact with VAL1136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079D TYR* 4.2 7.2 - - + +
1082D LEU* 3.8 36.4 - - + +
1083D THR* 4.2 11.9 - - + -
1132D GLY 3.0 14.2 + - - +
1133D GLU* 3.8 7.4 - - - +
1135D THR* 1.3 75.9 - - - +
1137D ALA* 1.3 64.5 + - - +
1139D LEU* 3.2 8.6 + - - +
1140D ALA* 3.0 21.7 + - - +
1163D LEU* 3.8 17.0 - - + -
1167D ASN* 4.1 22.4 - - + +
1171D ILE* 4.8 8.1 - - + -
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Residues in contact with ALA1137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079D TYR* 3.7 15.0 - - + +
1114D TYR* 2.7 24.0 + - + +
1116D ALA* 3.8 26.7 - - + -
1126D MET* 4.0 17.9 - - + -
1129D LEU* 4.0 2.7 - - + -
1133D GLU 2.9 18.8 + - - +
1134D LYS 3.7 4.3 - - - +
1136D VAL* 1.3 75.5 - - - +
1138D ALA* 1.3 63.7 + - - +
1140D ALA* 3.2 1.7 + - - +
1141D LEU 3.1 10.6 + - - -
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Residues in contact with ALA1138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D VAL* 3.3 31.4 - - + +
155D GLU* 4.4 0.4 - - - -
157D ILE* 3.9 7.0 - - + +
158D ALA* 3.6 24.0 - - + +
1134D LYS 2.9 18.2 + - - +
1135D THR 3.5 4.5 - - - +
1136D VAL 3.2 0.2 - - - -
1137D ALA* 1.3 78.9 - - - +
1139D LEU* 1.3 63.4 + - - +
1141D LEU* 3.3 3.3 + - - +
1142D LEU* 2.9 25.6 + - - +
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Residues in contact with LEU1139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D VAL* 5.7 0.7 - - + -
154D VAL* 4.0 20.9 - - + -
1082D LEU* 4.2 9.2 - - + -
1135D THR* 2.8 31.3 + - + +
1136D VAL* 3.2 4.7 + - - +
1138D ALA* 1.3 75.5 - - - +
1140D ALA* 1.3 58.1 + - - +
1142D LEU* 3.6 12.5 - - + +
1143D PHE* 2.9 54.2 + - + -
1156D LEU* 4.9 6.1 - - + -
1159D VAL* 4.1 23.6 - - + +
1163D LEU* 4.9 0.4 - - + -
1171D ILE* 3.6 44.9 - - + -
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Residues in contact with ALA1140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075D LEU* 4.2 5.6 - - + -
1078D ILE* 3.9 6.6 - - + +
1079D TYR* 3.7 44.9 - - + +
1082D LEU* 3.8 11.4 - - + +
1114D TYR* 4.0 3.6 - - - +
1136D VAL 3.0 7.7 + - - +
1137D ALA 3.4 9.0 - - - +
1138D ALA 3.1 0.2 - - - -
1139D LEU* 1.3 73.8 - - - +
1141D LEU* 1.3 55.3 + - - +
1143D PHE* 3.1 3.5 + - - +
1144D ALA* 2.7 35.7 + - - +
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Residues in contact with LEU1141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D ILE* 3.6 30.1 - - + +
160D GLN* 4.4 0.9 - - - +
165D LEU* 4.3 19.7 - - + -
1071D VAL* 4.8 2.2 - - + -
1075D LEU* 4.3 7.0 - - + -
1099D LEU* 4.6 20.4 - - + -
1114D TYR* 3.8 39.6 + - + -
1137D ALA 3.1 9.9 + - - +
1138D ALA* 3.8 6.1 - - - +
1140D ALA* 1.3 77.4 - - - +
1142D LEU* 1.3 57.6 + - - +
1144D ALA* 3.1 1.4 + - + +
1145D ILE* 2.8 63.7 + - + +
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Residues in contact with LEU1142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ASN* 3.2 34.2 - - + +
148D LEU 5.6 0.4 - - - +
149D VAL* 4.0 17.9 - - + -
157D ILE* 3.7 32.0 - - + +
1138D ALA 2.9 18.0 + - - +
1139D LEU* 3.6 10.5 - - + +
1141D LEU* 1.3 76.0 - - - +
1143D PHE* 1.3 78.6 + - + +
1145D ILE* 3.9 7.7 - - + +
1146D ASN* 3.2 20.8 + - - +
1154D PHE* 3.5 29.6 - - + -
1156D LEU* 4.4 3.4 - - + -
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Residues in contact with PHE1143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078D ILE* 3.9 8.9 - - + +
1082D LEU* 4.3 11.7 - - + -
1139D LEU* 2.9 46.9 + - + +
1140D ALA 3.6 2.7 - - - +
1142D LEU* 1.3 91.4 - - + +
1144D ALA* 1.3 65.5 + - - +
1146D ASN* 3.2 3.6 + - - +
1147D SER* 3.2 20.6 + - - -
1154D PHE* 3.6 34.8 - + - -
1156D LEU* 4.6 9.6 - - + -
1171D ILE* 5.4 3.4 - - + -
1174D TYR* 3.6 47.8 - + - +
1175D ILE* 5.0 4.3 - - + -
1185D PHE* 3.9 20.6 - + - -
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Residues in contact with ALA1144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071D VAL* 3.4 25.1 - - + +
1074D HIS 5.3 0.7 - - - -
1075D LEU* 3.7 35.0 - - + +
1078D ILE* 3.6 13.6 - - + +
1140D ALA 2.7 19.8 + - - +
1141D LEU* 3.6 4.9 - - + +
1143D PHE* 1.3 71.1 - - - +
1145D ILE* 1.3 61.8 + - - +
1147D SER* 2.6 26.1 + - - -
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Residues in contact with ILE1145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ASN* 4.4 11.7 - - + +
157D ILE* 5.3 1.8 - - + -
165D LEU* 4.8 7.9 - - + -
168D MET* 3.8 27.1 - - + -
169D PHE* 4.5 13.0 - - + -
172D VAL* 4.0 35.0 - - + +
1071D VAL* 3.4 25.7 - - + +
1141D LEU* 2.8 54.1 + - + +
1142D LEU* 3.9 8.5 - - + +
1144D ALA* 1.3 72.3 - - - +
1146D ASN* 1.3 61.8 + - - +
1147D SER 3.1 1.3 + - - -
1148D TYR* 3.7 9.2 + - - +
1149D GLN 5.1 0.2 + - - -
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Residues in contact with ASN1146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ASN 5.1 0.4 + - - -
146D ASN* 3.7 24.9 + - - +
147D PHE* 4.8 0.2 - - - +
1142D LEU 3.2 13.4 + - - +
1143D PHE 3.2 5.1 + - - +
1145D ILE* 1.3 77.7 - - - +
1147D SER* 1.3 63.3 + - - +
1148D TYR 3.3 0.7 - - - -
1149D GLN 3.8 5.5 + - - +
1150D PRO* 3.1 20.1 - - - +
1151D SER* 3.0 44.8 + - - +
1154D PHE* 3.6 34.9 - - + -
1183D LEU* 5.2 3.5 - - - +
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Residues in contact with SER1147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070D TYR* 3.3 31.7 + - - -
1071D VAL* 4.4 1.0 - - - -
1074D HIS* 4.2 16.6 - - - +
1078D ILE* 4.9 4.9 - - - -
1143D PHE 3.2 9.8 + - - -
1144D ALA* 2.6 23.6 + - - -
1146D ASN* 1.3 78.1 - - - +
1148D TYR* 1.3 66.1 + - - +
1150D PRO* 3.2 15.5 - - - +
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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