Contacts of the helix formed by residues 1186 - 1202 (chain B) in PDB entry 2NVU
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 ASN1186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1166B GLY 2.6 25.9 + - - +
1168B TYR* 3.9 19.6 + - - -
1182B VAL 5.5 0.2 + - - -
1183B GLY* 3.9 11.6 + - - -
1185B ASP* 1.3 82.1 - - - +
1187B ALA* 1.3 59.4 + - - +
1188B GLY* 2.9 8.0 + - - +
1189B ALA* 2.8 32.2 + - - +
1190B LYS* 3.0 13.1 + - - +
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Residues in contact with ALA1187 (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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1165B ASP* 4.4 3.4 - - - +
1186B ASN* 1.3 74.2 - - - +
1188B GLY* 1.3 62.8 + - - +
1190B LYS* 4.3 11.6 - - - +
1191B ALA* 3.0 28.2 + - - +
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Residues in contact with GLY1188 (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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1162B ILE 2.9 16.6 - - - +
1165B ASP* 3.4 45.1 - - - +
1166B GLY* 3.9 5.2 - - - -
1186B ASN* 2.9 11.8 + - - -
1187B ALA* 1.3 80.6 - - - +
1189B ALA* 1.3 57.4 + - - +
1192B GLY* 3.8 7.6 + - - -
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Residues in contact with ALA1189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1162B ILE* 3.5 27.6 - - + +
1167B GLY* 4.7 3.1 - - - -
1183B GLY 4.4 4.0 - - - +
1184B VAL* 3.8 28.9 - - - +
1186B ASN* 2.8 15.6 + - - +
1188B GLY* 1.3 76.9 - - - +
1190B LYS* 1.3 61.2 + - - +
1191B ALA 3.1 1.8 - - - -
1192B GLY* 3.0 2.8 + - - -
1193B LEU* 2.8 30.8 + - - +
1362B LEU* 3.8 4.3 - - + -
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Residues in contact with LYS1190 (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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1185B ASP* 3.2 33.7 + - - +
1186B ASN 3.0 17.5 + - - +
1187B ALA* 4.2 7.6 - - - +
1189B ALA* 1.3 75.5 - - - +
1191B ALA* 1.3 60.4 + - - +
1194B THR* 2.8 31.5 + - - -
1358B VAL* 3.8 9.0 - - + +
1359B ASP* 3.5 47.7 + - - +
1362B LEU* 3.5 24.7 - - + +
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Residues in contact with ALA1191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1165B ASP* 4.4 12.1 - - - +
1187B ALA 3.0 20.0 + - - +
1188B GLY 4.3 2.7 - - - +
1190B LYS* 1.3 77.1 - - - +
1192B GLY* 1.3 64.3 + - - +
1193B LEU 3.2 1.0 + - - -
1194B THR* 3.3 14.3 + - - -
1195B PHE* 3.3 13.3 + - - +
1251B PHE* 4.2 14.1 - - + -
1252B LYS* 5.9 3.8 - - + -
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Residues in contact with GLY1192 (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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1161B LEU* 3.9 16.9 - - - +
1162B ILE* 4.0 23.1 - - - +
1188B GLY 3.8 4.0 + - - -
1189B ALA 3.0 7.4 + - - -
1191B ALA* 1.3 81.1 - - - +
1193B LEU* 1.3 58.8 + - - +
1195B PHE* 3.7 3.6 + - - +
1196B LEU* 3.5 15.2 + - - +
1251B PHE* 4.0 18.3 - - - -
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Residues in contact with LEU1193 (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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1162B ILE* 4.4 23.0 - - + +
1189B ALA 2.8 17.4 + - - +
1192B GLY* 1.3 68.8 - - - +
1194B THR* 1.3 67.7 + - - +
1195B PHE 3.1 1.6 - - - -
1196B LEU* 3.2 18.4 + - + -
1197B VAL* 3.0 35.5 + - + +
1347B ALA 3.8 14.8 - - - +
1348B VAL* 4.5 13.9 - - + -
1351B ALA* 4.1 12.6 - - + -
1352B ALA* 6.3 0.2 - - + -
1358B VAL* 3.4 34.8 - - + +
1362B LEU* 3.6 26.7 - - + -
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Residues in contact with THR1194 (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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1190B LYS* 2.8 22.9 + - - +
1191B ALA* 3.3 6.9 + - - -
1193B LEU* 1.3 75.5 - - - +
1195B PHE* 1.3 63.0 + - - +
1197B VAL* 3.3 5.1 + - + +
1198B ASP* 2.9 41.0 + - - +
1358B VAL* 3.9 22.0 - - + +
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Residues in contact with PHE1195 (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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1130B TRP* 3.5 58.3 - + + -
1131B GLU* 4.9 6.7 - - - -
1134B PRO* 4.5 7.4 - - + -
1161B LEU* 3.5 19.5 - - + -
1191B ALA 3.3 9.3 + - - +
1192B GLY 3.8 7.4 - - - +
1193B LEU 3.1 0.4 - - - -
1194B THR* 1.3 77.2 - - - +
1196B LEU* 1.3 66.0 + - - +
1198B ASP* 3.0 23.2 + - + +
1199B LEU* 3.2 46.7 + - + +
1251B PHE* 4.0 21.5 - + + -
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Residues in contact with LEU1196 (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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1130B TRP* 5.9 2.0 - - + -
1150B PHE* 4.5 9.0 - - + -
1152B LEU* 4.1 21.5 - - + -
1158B THR* 4.0 33.2 - - + +
1161B LEU* 4.5 12.3 - - + -
1162B ILE* 5.6 3.1 - - + -
1192B GLY 3.5 9.4 + - - +
1193B LEU* 3.2 24.5 + - + +
1195B PHE* 1.3 85.4 - - - +
1197B VAL* 1.3 60.8 + - + +
1199B LEU* 3.5 9.9 + - + +
1200B ILE* 3.1 30.2 + - + +
1205B MET* 4.5 16.2 - - - -
1348B VAL* 4.5 9.9 - - + -
1352B ALA* 5.5 4.3 - - + -
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Residues in contact with VAL1197 (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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1193B LEU* 3.0 20.1 + - + +
1194B THR* 3.5 8.7 - - + +
1195B PHE 3.1 0.2 - - - -
1196B LEU* 1.3 74.6 - - + +
1198B ASP* 1.3 57.0 + - - +
1200B ILE* 2.7 35.5 + - + +
1201B LYS* 3.0 24.9 + - + +
1351B ALA* 4.1 10.8 - - + +
1352B ALA* 3.8 35.0 - - + +
1354B GLY* 5.9 0.4 - - - +
1358B VAL* 3.9 20.4 - - + -
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Residues in contact with ASP1198 (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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1194B THR* 2.9 35.3 + - - +
1195B PHE* 3.0 13.9 + - + +
1197B VAL* 1.3 70.6 - - - +
1199B LEU* 1.3 55.5 + - + +
1200B ILE 2.8 4.5 - - - -
1201B LYS* 2.7 18.3 + - - +
1202B ASN* 2.6 50.4 + - - +
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Residues in contact with LEU1199 (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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1130B TRP* 4.8 9.4 - - + -
1133B ILE* 5.4 5.8 - - + -
1134B PRO* 3.7 32.5 - - + -
1148B LEU* 5.8 0.2 - - + -
1195B PHE* 3.2 50.8 + - + +
1196B LEU* 3.7 11.7 - - + +
1197B VAL 3.3 0.2 - - - -
1198B ASP* 1.3 77.3 - - + +
1200B ILE* 1.3 58.8 + - - +
1202B ASN* 4.0 2.9 - - - +
1204B HIS* 3.0 30.9 + - + +
1205B MET* 2.8 48.5 + - + -
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Residues in contact with ILE1200 (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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1152B LEU* 4.2 7.9 - - + -
1196B LEU* 3.1 25.1 - - + +
1197B VAL* 2.7 19.3 + - + +
1199B LEU* 1.3 79.8 - - - +
1201B LYS* 1.3 61.9 + - + +
1203B LYS* 3.7 11.3 + - - +
1205B MET* 3.5 26.1 - - + +
1206B ASN* 3.9 7.5 - - - +
1207B ALA* 3.6 36.1 - - + +
1352B ALA* 3.2 37.7 - - + +
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Residues in contact with LYS1201 (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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1197B VAL* 3.0 28.3 + - + +
1198B ASP* 2.7 21.4 + - - +
1200B ILE* 1.3 74.1 - - + +
1202B ASN* 1.3 63.8 + - - +
1203B LYS* 2.9 18.3 + - - +
1352B ALA 5.9 1.6 - - - +
1354B GLY* 5.5 11.3 - - - -
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Residues in contact with ASN1202 (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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1137B ASP* 5.4 0.5 - - - +
1198B ASP* 2.6 34.6 + - - +
1199B LEU* 5.5 1.4 - - - +
1201B LYS* 1.3 75.9 - - - +
1203B LYS* 1.3 63.1 + - - +
1204B HIS* 3.1 43.0 + - + +
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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