Contacts of the helix formed by residues 1181 - 1192 (chain D) 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 SER1181 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179D GLN 3.9 3.2 + - - -
1180D LEU* 1.3 81.2 - - - +
1182D ARG* 1.3 64.4 + - - +
1183D LYS* 4.0 5.4 + - - +
1184D PHE* 3.4 23.0 + - - +
1185D ILE* 3.4 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140B ASP* 4.6 27.3 + - - +
1141B ARG 5.0 0.2 - - - +
1160B ASN* 4.1 19.1 - - - +
1166B PRO* 6.4 0.4 - - + -
1180D LEU 3.7 0.8 + - - -
1181D SER* 1.3 73.8 - - - +
1183D LYS* 1.3 63.3 + - - +
1185D ILE* 3.4 13.4 + - + +
1186D SER* 3.2 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160B ASN* 3.2 42.5 + - + +
1161B ILE* 3.3 21.7 + - - +
1162B ASP 4.7 1.6 - - - +
1163B PRO* 3.8 31.5 - - + +
1166B PRO* 5.7 6.5 - - + -
1219B THR* 5.7 2.6 + - - -
1181D SER* 3.3 6.1 + - - +
1182D ARG* 1.3 76.5 - - - +
1184D PHE* 1.3 66.8 + - - +
1186D SER* 3.0 3.3 + - - -
1187D ASP* 2.6 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175D LEU* 5.3 2.2 - - + -
1180D LEU* 3.9 38.1 - - + -
1181D SER* 3.4 22.2 + - - +
1183D LYS* 1.3 77.9 - - - +
1185D ILE* 1.3 55.2 + - - +
1187D ASP* 3.7 9.0 - - + +
1188D TYR* 2.7 64.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141B ARG* 4.0 19.5 - - + +
1160D VAL* 4.6 10.8 - - + -
1175D LEU* 4.2 19.1 - - + -
1176D ASP 4.8 0.4 - - - -
1177D SER* 3.3 38.1 - - - +
1180D LEU* 3.6 17.3 - - + +
1181D SER 3.4 16.7 + - - +
1182D ARG* 3.4 12.2 + - + +
1183D LYS 3.2 0.4 - - - -
1184D PHE* 1.3 76.2 - - - +
1186D SER* 1.3 64.9 + - - +
1188D TYR* 3.5 4.9 - - - +
1189D LEU* 2.9 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140B ASP 4.2 0.3 + - - -
1141B ARG 2.9 23.4 + - - -
1142B LEU 3.5 14.0 + - - -
1160B ASN* 2.9 33.2 + - - -
1215B ARG* 3.8 17.5 - - - -
1182D ARG 3.2 5.1 + - - -
1183D LYS 3.0 7.7 + - - -
1185D ILE* 1.3 77.6 - - - +
1187D ASP* 1.3 65.8 + - - +
1189D LEU* 3.1 1.8 + - - +
1190D TRP* 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1215B ARG* 2.8 38.7 + - - +
1183D LYS* 2.6 53.8 + - - +
1184D PHE* 3.7 10.2 - - + +
1186D SER* 1.3 71.4 - - - +
1188D TYR* 1.3 63.2 + - - +
1190D TRP* 3.5 1.7 + - - +
1191D SER* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171D GLN* 5.2 6.8 + - - -
1172D PRO* 6.1 0.2 - - - +
1173D ILE* 4.7 16.0 + - + -
1174D HIS 5.3 0.7 + - - -
1175D LEU* 3.3 43.3 - - + +
1184D PHE* 2.7 43.8 + + + +
1185D ILE 3.5 3.1 - - - +
1187D ASP* 1.3 73.7 - - - +
1189D LEU* 1.3 74.3 + - + +
1191D SER* 2.7 24.8 + - - -
1192D LEU* 3.5 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141B ARG* 3.5 46.0 - - + +
1142B LEU* 4.2 16.4 - - + -
1149D ILE* 4.6 7.7 - - + +
1151D TRP* 4.1 12.3 - - + -
1160D VAL* 4.9 3.1 - - + -
1164D HIS* 5.3 0.7 - - - -
1173D ILE* 3.7 34.3 - - + -
1175D LEU* 4.7 5.4 - - + -
1185D ILE* 2.9 26.0 + - + +
1186D SER 3.6 2.7 - - - +
1188D TYR* 1.3 87.9 - - + +
1190D TRP* 1.3 57.5 + - - +
1192D LEU* 2.8 32.0 + - + +
1193D VAL* 3.7 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142B LEU* 3.0 52.1 + - + +
1144B LEU* 4.2 12.1 - - + -
1158B PHE* 3.8 16.7 - + - -
1211B LEU* 3.9 12.3 - - + -
1212B ALA* 3.7 32.2 - - + +
1215B ARG* 3.5 45.0 - - - +
1146D VAL* 3.7 26.9 - - + -
1147D SER* 5.5 0.4 - - - -
1186D SER 2.9 22.4 + - - +
1187D ASP 3.9 0.9 - - - +
1189D LEU* 1.3 77.7 - - - +
1191D SER* 1.3 57.6 + - - +
1193D VAL* 3.0 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216B LYS* 5.7 8.3 - - - +
1187D ASP 3.0 15.5 + - - -
1188D TYR* 2.7 21.9 + - - -
1189D LEU 3.1 0.2 + - - -
1190D TRP* 1.3 76.2 - - - +
1192D LEU* 1.3 66.0 + - - +
1193D VAL 3.2 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1149D ILE* 5.9 1.1 - - + -
1164D HIS* 3.1 48.0 + - + +
1171D GLN* 4.3 28.7 - - + +
1173D ILE* 4.5 16.4 - - + -
1188D TYR* 3.8 38.6 - - + +
1189D LEU* 2.8 14.8 + - - +
1191D SER* 1.3 82.9 + - - +
1193D VAL* 1.3 59.4 + - - +
1194D ASP* 3.4 3.6 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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