Contacts of the helix formed by residues 1136 - 1148 (chain C) 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 ALA1136 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128A LEU* 4.9 13.5 - - + -
1131A LEU* 3.8 25.9 - - + +
1132A GLN* 6.1 1.8 - - + -
1133C ILE* 3.3 12.6 + - - +
1135C SER* 1.3 78.4 - - - +
1137C VAL* 1.3 64.6 + - + +
1138C TYR 3.6 0.2 - - - -
1139C VAL* 3.9 5.7 + - - +
1140C ALA* 3.4 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127A ARG* 5.3 8.1 - - - +
1131A LEU* 4.8 14.1 - - + -
1133C ILE* 3.3 38.2 + - + +
1134C PRO* 5.6 0.7 - - + -
1136C ALA* 1.3 74.3 - - + +
1138C TYR* 1.3 61.8 + - + +
1139C VAL 3.1 1.6 - - - -
1140C ALA* 3.2 6.4 + - - +
1141C GLN* 3.0 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133C ILE 4.9 0.4 + - - -
1134C PRO 5.7 4.9 - - - +
1135C SER* 4.7 6.5 + - - +
1136C ALA 4.7 0.2 - - - +
1137C VAL* 1.3 81.3 - - - +
1139C VAL* 1.3 60.6 + - + +
1141C GLN* 4.0 12.6 - - + +
1142C LEU* 3.3 58.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135A ALA* 5.9 4.3 - - + -
1146A ILE* 3.6 32.2 - - + +
1147A ARG* 5.1 11.4 - - - +
1135C SER 3.3 22.2 - - - +
1136C ALA* 3.9 6.4 + - - +
1137C VAL 3.1 0.6 - - - -
1138C TYR* 1.3 83.0 - - + +
1140C ALA* 1.3 58.0 - - + +
1141C GLN 3.2 1.8 + - - -
1142C LEU* 3.7 11.9 + - - +
1143C TYR* 3.3 28.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131A LEU* 4.3 28.5 - - + +
1134A SER* 6.3 0.9 - - - -
1135A ALA* 4.9 8.1 - - + +
1138A TYR* 5.2 4.9 - - - -
1136C ALA 3.4 16.6 + - - +
1137C VAL* 3.2 5.2 + - - +
1139C VAL* 1.3 79.3 - - - +
1141C GLN* 1.3 59.3 + - - +
1142C LEU 3.6 0.2 - - - -
1143C TYR* 4.2 14.1 - - - +
1144C HIS* 4.1 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137C VAL* 3.0 37.4 + - - +
1138C TYR* 4.3 11.8 - - - +
1139C VAL 3.2 0.2 - - - -
1140C ALA* 1.3 76.2 - - - +
1142C LEU* 1.3 65.9 + - + +
1143C TYR 3.3 1.3 - - - -
1144C HIS* 3.4 11.7 + - + +
1145C GLN* 3.1 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1146A ILE* 4.2 21.8 - - + -
1138C TYR* 3.3 63.0 + - + +
1139C VAL* 4.0 7.0 - - - +
1140C ALA 3.6 0.2 - - - -
1141C GLN* 1.3 80.7 - - + +
1143C TYR* 1.3 64.4 + - - +
1145C GLN* 4.5 13.2 - - - +
1146C VAL* 3.1 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135A ALA* 4.3 23.5 + - + -
1138A TYR* 3.6 44.8 - + + -
1139A LYS* 4.3 5.8 - - - +
1142A LEU* 4.7 8.7 - - + -
1144A LEU* 3.0 41.3 + - + -
1145A GLU* 3.7 2.3 - - - +
1146A ILE* 3.4 39.3 + - + +
1139C VAL* 3.3 32.3 - - + -
1140C ALA* 4.2 11.4 - - - +
1141C GLN 3.3 0.2 - - - -
1142C LEU* 1.3 80.5 - - - +
1144C HIS* 1.3 55.2 + - - +
1146C VAL* 5.6 0.2 - - - -
1147C SER* 2.6 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138A TYR* 3.9 17.8 + - + +
1140C ALA 4.1 10.0 + - - +
1141C GLN* 3.4 14.9 + - + +
1142C LEU 3.3 0.2 - - - -
1143C TYR* 1.3 80.6 - - - +
1145C GLN* 1.3 61.7 + - + +
1147C SER* 3.8 1.2 + - - -
1148C LYS* 3.2 25.6 + - - -
1149C ILE 3.6 14.2 + - - -
1150C GLU* 3.0 35.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141C GLN* 3.1 18.6 + - + +
1142C LEU* 4.1 14.6 - - - +
1143C TYR 3.3 0.2 - - - -
1144C HIS* 1.3 82.4 - - + +
1146C VAL* 1.3 72.1 + - + +
1148C LYS* 3.4 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142C LEU* 3.1 26.6 + - + +
1143C TYR 4.9 0.2 - - - +
1145C GLN* 1.3 84.4 - - + +
1147C SER* 1.3 60.2 + - - +
1148C LYS* 4.4 4.2 - - - +
1190C TRP* 4.9 18.3 - - + -
1193C VAL* 3.4 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138A TYR* 3.8 4.3 - - - -
1142A LEU* 3.8 24.5 - - - -
1143C TYR 2.6 25.4 + - - -
1144C HIS 3.8 0.7 + - - -
1146C VAL* 1.3 78.1 - - - +
1148C LYS* 1.3 70.4 + - - +
1149C ILE* 3.2 30.2 + - - +
1164C HIS* 3.6 14.0 + - - -
1189C LEU 5.6 1.4 - - - +
1190C TRP* 5.4 8.0 - - - -
1193C VAL* 4.4 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144C HIS* 3.2 15.0 + - - -
1145C GLN 3.4 15.9 - - - +
1146C VAL 3.5 5.4 - - - +
1147C SER* 1.3 83.0 + - - +
1149C ILE* 1.3 58.2 + - - +
1164C HIS* 3.2 41.1 - - + +
1193C VAL* 5.5 10.0 + - + +
----------------------------------------------------------
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