Contacts of the helix formed by residues 1255 - 1264 (chain B) in PDB entry 1RQQ
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 THR1255 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124B ASN* 5.6 6.3 - - - +
1188B THR* 5.6 7.0 - - + -
1192B MET* 3.4 4.5 - - - -
1253B ARG 5.3 2.0 - - - +
1254B PRO* 1.3 76.0 - - - +
1256B PHE* 1.3 59.5 + - - +
1257B LEU* 3.7 8.1 + - - +
1258B GLU* 2.9 44.0 + - - +
1259B ILE* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117B ALA* 3.5 27.2 - - + +
1120B MET* 3.5 43.7 - - + -
1121B ALA* 3.7 13.0 - - - +
1124B ASN* 5.2 2.2 + - + +
1133B LEU* 4.3 0.7 - - + -
1188B THR* 3.8 26.6 - - + +
1191B ASP* 3.8 28.0 - - + -
1192B MET* 3.3 38.0 - - + +
1195B PHE* 3.7 24.2 - + + -
1255B THR* 1.3 73.6 - - - +
1257B LEU* 1.3 64.0 + - - +
1259B ILE* 3.1 4.7 + - + +
1260B VAL* 3.0 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121B ALA* 4.0 21.7 - - + +
1124B ASN* 6.1 2.0 - - - +
1125B ALA* 6.4 0.7 - - + -
1255B THR* 3.2 8.1 - - - +
1256B PHE* 1.3 76.5 - - - +
1258B GLU* 1.3 58.5 + - + +
1260B VAL* 3.2 6.8 + - - +
1261B ASN* 2.8 29.8 + - - +
1276B PHE* 4.2 11.0 - - + -
1277B PHE* 3.6 18.7 - - + -
1282B ASN* 3.7 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253B ARG 4.8 0.2 - - - +
1254B PRO* 3.2 18.2 - - + +
1255B THR* 2.9 45.4 + - - +
1257B LEU* 1.3 78.1 - - + +
1259B ILE* 1.3 58.8 + - - +
1261B ASN* 3.3 7.6 + - - +
1262B LEU* 2.7 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117B ALA* 3.8 19.3 - - + -
1192B MET* 3.7 20.9 - - + -
1195B PHE* 3.9 20.6 - - + -
1241B LEU* 4.0 26.7 - - + -
1244B MET* 5.1 0.2 - - - -
1245B CYS* 5.1 3.4 - - - -
1254B PRO* 3.7 26.9 - - + -
1255B THR 2.9 18.9 + - - +
1256B PHE* 3.1 7.2 + - - +
1258B GLU* 1.3 77.7 - - - +
1260B VAL* 1.3 64.3 + - - +
1262B LEU* 3.1 16.8 + - + +
1263B LEU* 3.3 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1114B ALA* 4.2 4.9 - - + +
1117B ALA* 3.9 5.4 - - + +
1118B ASP* 3.8 33.7 - - + +
1121B ALA* 5.2 1.8 - - + -
1256B PHE 3.0 16.1 + - - +
1257B LEU* 3.6 2.9 - - - +
1259B ILE* 1.3 75.2 - - - +
1261B ASN* 1.3 51.4 + - - +
1263B LEU* 2.7 12.2 + - - -
1264B LYS* 2.7 34.6 + - + +
1267B LEU* 5.2 1.3 - - + -
1271B PHE* 3.9 24.2 - - + -
1277B PHE* 3.4 41.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1257B LEU 2.8 16.4 + - - +
1258B GLU* 3.6 9.5 - - - +
1259B ILE 3.3 0.2 - - - -
1260B VAL* 1.3 76.4 - - - +
1262B LEU* 1.3 69.4 + - - +
1264B LYS* 2.9 59.2 + - - +
1277B PHE* 3.6 21.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1237B ARG* 3.5 17.7 + - - -
1241B LEU* 4.0 25.4 - - + -
1244B MET* 4.1 22.7 - - + -
1258B GLU* 2.7 37.2 + - + +
1259B ILE* 3.4 12.8 - - + +
1260B VAL 3.1 0.6 - - - -
1261B ASN* 1.3 86.8 - - - +
1263B LEU* 1.3 64.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1110B ILE* 3.9 33.7 - - + +
1113B ALA* 4.3 7.9 - - + -
1114B ALA* 3.9 37.0 - - + +
1237B ARG* 3.9 21.8 - - - +
1241B LEU* 4.4 17.7 - - + -
1259B ILE* 3.4 27.4 - - + +
1260B VAL 2.7 6.5 + - - +
1262B LEU* 1.3 89.0 - - + +
1264B LYS* 1.3 62.4 + - - +
1265B ASP 3.0 4.7 + - - -
1266B ASP* 3.2 10.3 + - - +
1267B LEU* 3.0 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1260B VAL* 2.7 18.3 + - + +
1261B ASN* 2.9 49.6 + - - +
1263B LEU* 1.3 72.1 - - - +
1265B ASP* 1.3 84.2 + - - +
1267B LEU* 3.8 22.3 - - - +
1271B PHE* 5.4 0.7 - - - +
1272B PRO* 5.8 2.8 - - - +
1277B PHE* 4.2 15.5 - - + -
1278B HIS* 4.4 23.2 + - + +
----------------------------------------------------------
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