Contacts of the helix formed by residues 1132 - 1143 (chain A) in PDB entry 3B8R
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 THR1132 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002A LEU* 3.9 35.7 - - + -
1006A ILE* 5.3 8.8 - - + +
1099A PHE* 4.8 3.6 - - + -
1131A THR* 1.3 94.0 + - - +
1133A PRO* 1.3 75.9 - - - +
1134A GLU* 3.8 11.9 + - - +
1135A MET* 3.3 27.2 + - + +
1136A TYR* 3.2 8.3 + - - +
1163A LEU* 5.6 0.2 - - - +
1167A ASN* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131A THR* 4.8 0.9 - - + +
1132A THR* 1.3 89.5 - - - +
1134A GLU* 1.3 77.1 + - - +
1136A TYR* 3.3 6.9 + - + +
1137A GLN* 3.3 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132A THR* 3.4 11.8 + - - +
1133A PRO* 1.3 96.6 - - - +
1135A MET* 1.3 58.6 + - - +
1137A GLN* 3.1 9.5 + - - +
1138A THR* 2.9 30.1 + - - -
1159A HIS* 4.5 7.6 + - + +
1163A LEU* 3.9 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006A ILE* 3.7 31.0 - - + -
1009A SER* 5.1 0.7 - - - +
1095A LEU* 4.8 8.2 - - + +
1099A PHE* 3.4 48.2 - - + -
1131A THR* 3.6 8.7 - - - +
1132A THR* 3.3 23.2 + - - +
1134A GLU* 1.3 79.2 - - - +
1136A TYR* 1.3 58.3 + - - +
1138A THR* 3.1 10.6 + - - -
1139A MET* 3.0 33.0 + - + +
1160A LEU* 3.8 23.8 - - + -
1163A LEU* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124A ARG* 5.3 0.3 - - - +
1125A MET 2.8 23.5 + - - -
1126A ARG* 3.6 9.4 - - - -
1127A ALA* 3.2 44.9 - - + -
1128A PRO* 4.1 0.7 - - + -
1131A THR* 3.5 9.1 + - + +
1132A THR 3.2 9.7 + - - +
1133A PRO* 3.8 9.9 - - + +
1134A GLU 3.3 0.2 - - - -
1135A MET* 1.3 79.5 - - - +
1137A GLN* 1.3 58.8 + - - +
1139A MET* 3.4 19.4 - - - +
1140A LEU* 3.1 57.6 + - + +
1143A TRP* 4.7 4.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133A PRO 3.3 10.0 + - - +
1134A GLU* 3.1 12.4 + - - +
1136A TYR* 1.3 77.8 - - - +
1138A THR* 1.3 61.6 + - - +
1139A MET 3.1 0.2 - - - -
1140A LEU* 3.2 23.4 + - - +
1141A ASP* 2.8 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095A LEU* 3.6 22.9 - - + -
1134A GLU 2.9 11.5 + - - -
1135A MET* 3.1 14.8 + - - -
1137A GLN* 1.3 74.9 - - - +
1139A MET* 1.3 65.4 + - - +
1141A ASP* 3.3 10.4 + - + +
1142A CYS* 3.0 21.8 + - - -
1156A LEU* 3.7 26.5 - - + -
1159A HIS* 2.9 35.6 + - + -
1160A LEU* 4.6 7.8 - - + +
1163A LEU* 4.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092A GLY* 3.8 7.4 - - - +
1095A LEU* 3.7 37.2 - - + +
1096A TRP* 3.9 25.8 - - - -
1099A PHE* 4.2 2.7 - - + -
1128A PRO* 4.0 11.2 - - + -
1131A THR* 3.4 25.4 - - - +
1135A MET* 3.0 29.9 + - + +
1136A TYR* 3.4 24.5 - - + +
1137A GLN 3.1 0.2 - - - -
1138A THR* 1.3 76.5 - - - +
1140A LEU* 1.3 64.4 + - - +
1142A CYS* 2.8 19.4 + - - +
1143A TRP* 3.0 31.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124A ARG* 4.3 15.6 + - + -
1136A TYR* 3.1 54.3 + - + +
1137A GLN* 3.2 28.7 + - - +
1139A MET* 1.3 79.3 - - - +
1141A ASP* 1.3 63.9 + - - +
1143A TRP* 3.0 33.1 + - + +
1144A HIS* 3.3 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137A GLN* 2.8 48.2 + - - +
1138A THR* 3.5 10.1 + - + +
1140A LEU* 1.3 75.9 - - - +
1142A CYS* 1.3 62.5 + - - +
1144A HIS* 3.1 23.8 + - - +
1149A GLN 4.8 0.7 - - - +
1150A ARG* 3.9 0.7 - - - +
1151A PRO* 3.5 25.2 - - + +
1156A LEU* 6.2 0.2 - - + -
1159A HIS* 5.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088A VAL* 3.6 30.5 - - - +
1089A TRP* 3.5 12.0 + - - -
1091A PHE* 4.1 14.1 - - - -
1092A GLY* 3.8 13.9 - - - -
1095A LEU* 4.6 0.2 - - - -
1138A THR* 3.0 24.5 + - - +
1139A MET 2.8 9.4 + - - +
1141A ASP* 1.3 75.8 - - - +
1143A TRP* 1.3 58.4 + - - +
1144A HIS 3.2 0.4 - - - -
1150A ARG* 3.4 22.7 + - - -
1151A PRO* 4.0 7.9 - - - -
1156A LEU* 3.9 25.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089A TRP* 3.1 46.0 + + + -
1092A GLY* 3.2 40.9 - - - -
1093A VAL* 3.3 14.4 - - + +
1096A TRP* 4.0 12.6 - + + -
1106A TYR* 5.4 4.5 - - - -
1124A ARG* 3.0 48.7 + - + +
1125A MET* 4.0 52.3 - - + -
1136A TYR* 4.7 2.5 - + - -
1139A MET* 3.0 29.3 + - + -
1140A LEU* 3.0 21.7 + - + +
1142A CYS* 1.3 78.9 - - - +
1144A HIS* 1.3 65.8 + - - +
----------------------------------------------------------
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