Contacts of the helix formed by residues 1206 - 1222 (chain B) in PDB entry 2VE7
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 ASN1206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1201B VAL* 4.8 2.5 - - - +
1204B THR* 2.7 26.9 + - + +
1205B ASN* 1.3 72.1 - - - +
1207B PHE* 1.3 59.9 + - - +
1208B SER* 3.2 27.9 + - - +
1209B ALA* 3.4 19.0 - - - +
1210B PHE* 3.1 21.8 + - - +
1148D LYS* 5.0 7.5 - - - +
1194D ASP 5.4 0.3 - - - +
1196D GLU 3.7 9.4 - - - +
1197D TRP* 4.1 20.3 + - + +
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Residues in contact with PHE1207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1154B LEU* 5.4 2.7 - - + -
1156B PHE* 4.2 22.0 - + - -
1174B LEU* 4.7 15.3 - - + -
1180B ARG* 3.2 35.9 - - - -
1201B VAL* 4.8 2.4 - - + +
1205B ASN* 3.1 8.2 + - - -
1206B ASN* 1.3 71.4 - - - +
1208B SER* 1.3 69.4 + - - +
1210B PHE* 3.5 23.4 - + + +
1211B LEU* 3.0 43.0 + - + +
1138D TYR* 5.0 7.2 - - - -
1142D LEU* 4.3 22.0 - - + -
1145D GLN* 3.8 29.1 - - + +
1146D VAL* 3.6 20.1 - - + +
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Residues in contact with SER1208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1206B ASN* 3.2 13.8 - - - +
1207B PHE* 1.3 78.5 - - - +
1209B ALA* 1.3 54.0 - - - +
1211B LEU* 3.9 1.0 - - - +
1212B ALA* 2.8 38.4 + - - +
1145D GLN* 3.2 15.9 + - - +
1146D VAL* 2.9 28.6 + - - +
1148D LYS* 3.3 21.9 - - - +
1190D TRP* 4.6 0.2 - - - -
1193D VAL* 4.0 10.7 - - - +
1194D ASP* 4.7 4.5 - - - -
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Residues in contact with ALA1209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1206B ASN* 3.4 23.2 - - - +
1208B SER* 1.3 79.7 - - - +
1210B PHE* 1.3 53.9 + - - +
1212B ALA* 4.1 1.1 - - - -
1213B ASN* 2.5 47.4 + - - +
1194D ASP 3.7 14.3 + - - +
1196D GLU 3.4 18.8 - - - +
1197D TRP* 3.6 21.5 - - + +
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Residues in contact with PHE1210 (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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1172B PHE* 3.7 32.5 - + - -
1174B LEU* 4.4 15.7 - - + -
1183B GLU* 6.1 1.8 - - + -
1194B LEU* 4.4 11.0 - - + -
1197B PHE* 3.7 33.9 - - + -
1198B GLN* 4.2 5.2 - - + -
1201B VAL* 3.3 35.2 - - + -
1206B ASN 3.1 15.6 + - - +
1207B PHE* 3.5 21.1 - + - +
1208B SER 3.1 0.2 + - - -
1209B ALA* 1.3 76.9 - - - +
1211B LEU* 1.3 72.8 + - + +
1213B ASN* 3.7 2.1 - - - +
1214B VAL* 2.8 42.8 + - + +
1197D TRP* 3.9 9.8 - + + +
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Residues in contact with LEU1211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144B LEU* 3.8 21.8 - - + -
1156B PHE* 3.4 37.9 - - + -
1158B PHE* 3.9 11.3 - - + -
1172B PHE* 4.5 7.9 - - + -
1207B PHE* 3.0 32.7 + - + +
1210B PHE* 1.3 90.2 - - + +
1212B ALA* 1.3 67.8 + - - +
1214B VAL* 3.4 5.9 - - - +
1215B ARG* 2.8 26.2 + - - +
1146D VAL* 3.6 31.2 - - + -
1190D TRP* 3.9 7.2 - - + -
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Residues in contact with ALA1212 (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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1208B SER 2.8 23.7 + - - +
1209B ALA* 3.7 5.8 - - - +
1211B LEU* 1.3 74.8 - - - +
1213B ASN* 1.3 63.9 + - - +
1215B ARG* 3.3 9.9 + - - +
1216B LYS* 3.3 16.6 + - - +
1190D TRP* 3.7 17.3 - - + +
1193D VAL* 3.7 24.2 - - + +
1194D ASP 4.1 1.1 - - - +
1195D THR* 3.8 19.7 - - - +
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Residues in contact with ASN1213 (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 PHE* 4.9 16.0 - - + -
1209B ALA* 2.5 36.5 + - - +
1210B PHE 3.7 2.9 - - - +
1212B ALA* 1.3 71.5 - - - +
1214B VAL* 1.3 64.8 + - - +
1216B LYS* 3.1 11.0 + - - +
1217B ALA* 3.0 22.2 + - - +
1195D THR* 2.9 46.5 + - - +
1197D TRP* 3.3 30.6 - - + -
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Residues in contact with VAL1214 (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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1158B PHE* 3.9 4.7 - - + -
1172B PHE* 3.6 27.1 - - + -
1194B LEU* 4.9 9.0 - - + -
1197B PHE* 4.6 11.9 - - + -
1210B PHE* 2.8 57.0 + - + +
1211B LEU* 3.4 12.1 - - - +
1213B ASN* 1.3 71.8 - - - +
1215B ARG* 1.3 57.6 + - - +
1217B ALA* 3.1 9.1 + - - +
1218B PHE* 2.8 48.2 + - + +
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Residues in contact with ARG1215 (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 LEU 4.6 1.6 + - - -
1158B PHE* 3.5 32.1 - - + -
1160B ASN* 3.4 22.0 + - - +
1161B ILE* 3.8 17.1 - - + +
1211B LEU 2.8 15.8 + - - +
1212B ALA* 3.5 11.9 - - - +
1214B VAL* 1.3 73.7 - - - +
1216B LYS* 1.3 59.5 + - + +
1218B PHE* 3.2 8.3 + - - +
1219B THR* 2.8 36.2 + - - +
1186D SER* 3.8 17.4 - - - -
1187D ASP* 2.8 33.5 + - - +
1190D TRP* 3.5 49.1 - - + +
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Residues in contact with LYS1216 (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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1212B ALA 3.3 9.4 + - - +
1213B ASN* 3.1 11.0 + - - +
1215B ARG* 1.3 76.6 - - + +
1217B ALA* 1.3 56.9 + - - +
1219B THR* 3.1 11.2 + - - +
1220B ALA* 2.8 29.9 + - - +
1224B GLN* 5.6 0.2 + - - -
1191D SER* 5.7 8.3 - - - +
1195D THR* 3.7 35.7 - - + +
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Residues in contact with ALA1217 (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 LEU* 6.6 0.2 - - + -
1197B PHE* 3.8 28.3 - - + -
1213B ASN 3.0 12.1 + - - +
1214B VAL* 3.3 9.9 - - + +
1216B LYS* 1.3 74.4 - - - +
1218B PHE* 1.3 57.9 + - - +
1220B ALA* 3.1 11.1 + - - +
1221B THR* 2.9 29.9 + - - -
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Residues in contact with PHE1218 (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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1158B PHE* 3.8 14.6 - + - -
1161B ILE* 4.0 13.7 - - + +
1170B PHE* 3.4 49.4 - + + -
1171B MET 3.7 19.5 - - - -
1172B PHE* 4.1 11.7 - + + -
1186B ASP* 3.7 15.9 - - - -
1187B SER 3.5 23.1 - - - -
1188B ALA 4.7 6.7 - - - -
1194B LEU* 6.0 3.1 - - + -
1214B VAL* 2.8 37.1 + - + -
1215B ARG* 3.4 8.5 - - - +
1217B ALA* 1.3 76.5 - - - +
1219B THR* 1.3 62.2 + - - +
1221B THR* 3.0 27.2 + - + -
1222B VAL 3.8 2.9 + - - -
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Residues in contact with THR1219 (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 ILE* 3.7 31.8 + - - +
1215B ARG* 2.8 25.5 + - - +
1216B LYS* 3.1 13.9 + - - +
1218B PHE* 1.3 72.9 - - - +
1220B ALA* 1.3 63.9 + - - +
1221B THR 3.4 0.2 + - - -
1222B VAL 3.9 4.2 + - - +
1224B GLN* 3.3 47.6 + - + +
1183D LYS* 5.7 2.4 + - - -
1187D ASP* 5.7 0.3 + - - -
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Residues in contact with ALA1220 (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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1216B LYS 2.8 12.7 + - - +
1217B ALA* 3.3 12.1 - - - +
1219B THR* 1.3 75.2 - - - +
1221B THR* 1.3 67.0 + - - +
1223B TYR* 2.9 26.2 + - - -
1224B GLN* 4.4 14.1 - - - +
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Residues in contact with THR1221 (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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1170B PHE* 4.5 5.8 - - + -
1188B ALA* 3.7 33.4 + - + +
1217B ALA 2.9 17.0 + - - -
1218B PHE* 3.0 24.3 + - - -
1220B ALA* 1.3 76.5 - - - +
1222B VAL* 1.3 70.9 + - + +
1223B TYR* 3.1 24.5 + - - -
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Residues in contact with VAL1222 (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 ASP* 5.8 10.5 - - + +
1163B PRO* 5.8 1.9 - - - +
1170B PHE* 3.8 26.7 - - + -
1218B PHE 3.8 3.6 + - - -
1219B THR 3.9 3.5 + - - +
1220B ALA 3.4 0.6 - - - -
1221B THR* 1.3 89.5 - - + +
1223B TYR* 1.3 57.5 + - + +
1224B GLN* 2.6 24.9 + - - +
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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
------------------------------------------------------------
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