Contacts of the strand formed by residues 1257 - 1263 (chain A) in PDB entry 3CMT
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 GLN1257 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046A SER 4.7 1.2 - - - +
1050A ALA* 3.9 9.0 - - - +
1243A ARG* 3.3 34.7 + - + +
1244A VAL 3.3 13.0 - - - +
1245A LYS* 3.4 38.3 - - + +
1255A PHE 5.2 4.3 + - - +
1256A LYS* 1.3 77.4 - - - +
1258A ALA* 1.3 63.1 + - - +
1259A GLU* 4.3 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046A SER* 3.4 26.9 - - - +
1047A LEU* 3.5 32.8 - - + +
1050A ALA* 4.2 2.4 - - + +
1242A THR 3.9 0.3 - - - +
1243A ARG* 3.3 3.0 - - - +
1244A VAL* 2.8 39.3 + - + +
1257A GLN* 1.3 75.8 - - - +
1259A GLU* 1.3 62.2 + - - +
1260A PHE* 4.3 6.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046A SER* 3.5 12.0 + - - -
1228A ILE* 4.0 12.5 - - + +
1241A GLU* 5.6 2.9 - - + +
1242A THR 3.2 7.2 - - - +
1243A ARG* 2.4 50.8 + - + +
1257A GLN* 4.3 5.7 - - + +
1258A ALA* 1.3 77.3 - - - +
1260A PHE* 1.3 64.2 + - - +
1273A GLU* 4.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044A SER* 3.3 25.4 - - - -
1046A SER* 4.1 3.4 - - - -
1047A LEU* 4.8 2.2 - - + -
1075A LEU* 3.9 17.5 - - + -
1225A ILE* 4.7 0.4 - - + -
1241A GLU* 3.7 6.6 + - - +
1242A THR* 2.7 62.5 + - + +
1244A VAL* 3.7 26.9 - - + -
1258A ALA* 4.3 8.1 - - + -
1259A GLU* 1.3 78.6 - - - +
1261A GLN* 1.3 73.3 + - - +
1262A ILE* 3.8 17.0 - - + -
1268A ILE* 3.8 19.7 - - + -
1269A ASN 5.1 0.4 - - - +
1273A GLU* 3.5 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1231A VAL* 3.5 26.2 - - + +
1240A SER 3.6 3.4 - - - -
1241A GLU* 3.2 34.7 + - - +
1260A PHE* 1.3 78.2 - - - +
1262A ILE* 1.3 61.0 + - - +
1263A LEU* 3.8 15.0 - - + +
1268A ILE* 3.3 4.3 - - - -
1269A ASN* 2.7 64.9 + - + +
1302A LYS* 5.4 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070A SER 4.3 2.5 - - - +
1071A GLY* 4.0 28.7 - - - +
1074A THR* 3.8 28.9 - - + +
1075A LEU* 5.4 1.1 - - + +
1103A TYR* 4.9 2.9 - - - +
1225A ILE* 4.8 2.0 - - + -
1239A GLY* 3.1 2.3 - - - -
1240A SER* 2.7 46.8 + - - +
1242A THR* 3.7 20.2 - - + +
1260A PHE* 3.8 20.0 - - + -
1261A GLN* 1.3 72.6 - - - +
1263A LEU* 1.3 68.3 + - - +
1264A TYR* 3.6 5.0 + - + -
1267A GLY* 3.5 9.0 - - - +
1268A ILE* 4.5 7.0 - - + -
1502A ADP 4.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103A TYR* 4.7 0.3 + - - -
1231A VAL* 4.0 26.7 - - + -
1238A VAL* 3.8 16.8 - - + +
1239A GLY* 4.5 1.6 - - - -
1261A GLN* 4.0 12.3 - - + +
1262A ILE* 1.3 76.7 - - - +
1264A TYR* 1.3 65.6 + - - +
1266A GLU* 3.0 34.3 + - + +
1267A GLY* 2.8 41.9 + - - +
1269A ASN* 4.1 33.0 - - + +
----------------------------------------------------------
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