Contacts of the helix formed by residues 1120 - 1126 (chain B) in PDB entry 1BRW
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 THR1120 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089B ASP 5.1 4.5 + - - -
1092B THR* 3.9 21.3 - - + -
1093B LEU* 4.6 8.7 - - + +
1110B SER* 3.8 23.1 - - - +
1111B GLY 3.3 2.6 + - - +
1119B GLY* 1.3 71.6 - - - -
1121B ILE* 1.3 58.5 + - - +
1123B LYS* 3.7 15.1 - - - +
1124B LEU* 2.9 49.8 + - + +
1150B ILE* 4.3 0.9 - - + -
2002B PO4 2.6 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1110B SER* 3.4 26.7 - - - +
1111B GLY* 3.0 26.8 + - - +
1112B ARG* 3.7 31.2 - - + +
1120B THR* 1.3 76.9 - - - +
1122B ASP* 1.3 60.3 + - - +
1124B LEU* 3.6 10.1 + - + +
1125B GLU* 3.2 23.7 + - - +
1132B VAL* 3.8 27.0 - - + +
1151B ILE* 3.4 35.0 - - - +
1152B GLY* 3.7 7.0 - - - +
1153B GLN* 5.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112B ARG* 2.9 30.7 + - - -
1113B GLY* 3.2 15.1 + - - +
1119B GLY* 2.9 10.7 + - - +
1121B ILE* 1.3 76.8 - - - +
1123B LYS* 1.3 63.1 + - - +
1125B GLU* 3.1 15.6 + - - +
1126B SER 3.5 0.9 + - - -
1249B ASN* 3.1 22.8 + - - +
1363B ALA 4.8 3.2 - - - +
1365B ARG* 3.0 29.8 + - - -
1372B ILE* 3.5 19.1 - - + +
1374B LEU* 3.5 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086B GLY 5.8 0.6 + - - -
1088B GLY 5.1 0.6 - - - +
1089B ASP* 3.1 28.3 + - - +
1093B LEU* 4.3 25.4 - - + -
1118B GLY* 4.2 10.4 - - - -
1119B GLY 3.1 29.6 + - - +
1120B THR* 3.4 15.0 + - - +
1122B ASP* 1.3 77.1 - - - +
1124B LEU* 1.3 57.5 + - - +
1126B SER* 3.1 24.8 - - - -
1127B VAL 4.4 0.3 + - - -
1248B GLY 3.7 10.5 - - - +
1249B ASN* 3.4 25.1 - - - +
1252B GLU* 2.9 41.7 + - + +
1253B VAL* 3.4 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093B LEU* 3.5 26.9 - - + -
1120B THR* 2.9 35.2 + - + +
1121B ILE* 3.9 6.7 - - + +
1123B LYS* 1.3 71.4 - - - +
1125B GLU* 1.3 61.4 + - - +
1126B SER 3.1 6.6 + - - -
1127B VAL* 3.3 16.5 + - + +
1130B PHE* 3.5 52.9 - - + +
1132B VAL* 4.3 5.4 - - + -
1150B ILE* 3.9 24.2 - - + +
1253B VAL* 6.0 0.2 - - + -
1309B PHE* 5.7 0.9 - - + -
1312B PHE* 3.9 21.5 - - + -
1313B LEU* 4.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112B ARG* 2.7 43.2 + - - -
1121B ILE 3.2 12.0 + - - +
1122B ASP* 3.1 14.0 + - - +
1124B LEU* 1.3 72.0 - - - +
1126B SER* 1.3 62.8 + - - +
1127B VAL 3.1 11.1 + - - +
1130B PHE 4.7 10.8 - - - +
1132B VAL* 3.6 24.3 - - + +
1374B LEU* 3.4 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122B ASP 3.5 3.7 + - - -
1123B LYS 3.1 19.0 + - - -
1124B LEU 3.1 0.2 - - - -
1125B GLU* 1.3 78.9 - - - +
1127B VAL* 1.3 60.5 + - - +
1128B PRO* 3.4 4.3 - - - +
1249B ASN 4.3 0.2 - - - -
1250B ALA* 3.0 44.0 - - - +
1253B VAL* 4.4 3.0 - - - +
1329B LEU* 3.7 9.6 - - - +
1330B PRO* 3.4 22.6 - - - +
1374B LEU* 3.7 18.2 - - - -
----------------------------------------------------------
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