Contacts of the strand formed by residues 1311 - 1318 (chain A) in PDB entry 3PTA
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 ARG1311 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A GLU* 4.4 9.7 + - - -
707A ASP* 2.6 39.5 + - - +
1269A ARG* 3.6 47.0 + - + +
1298A VAL* 4.2 8.5 - - + -
1299A LEU 3.2 9.6 - - - +
1300A GLN* 3.0 23.3 - - + +
1309A THR* 4.0 6.6 - - + +
1310A ARG* 1.3 72.3 - - - +
1312A ARG* 1.3 68.1 + - - +
1338A ALA* 4.0 17.0 - - - +
1339A CYS* 4.9 0.9 - - - +
1340A GLN* 3.2 48.6 + - - +
1341A LEU* 5.1 2.5 - - + +
1525A THR* 5.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A ASP* 5.2 2.4 + - - -
1266A GLU* 3.4 23.3 + - + +
1267A ASN* 3.3 8.7 - - - +
1268A VAL* 3.6 37.8 - - - +
1269A ARG* 3.9 3.8 - - - +
1298A VAL* 3.4 7.2 - - - -
1299A LEU* 3.0 32.6 + - + +
1310A ARG* 3.3 64.9 - - - +
1311A ARG* 1.3 83.1 + - - +
1313A ALA* 1.3 65.1 + - - +
1314A ILE* 4.4 7.0 - - + +
1525A THR* 5.2 5.5 - - - +
1578A ASN 5.3 2.0 + - - -
1580A VAL* 5.0 4.9 - - - +
1581A PRO* 4.8 2.9 - - - -
1584A LEU* 4.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266A GLU* 3.4 0.5 - - - -
1267A ASN 2.7 31.9 + - - +
1268A VAL 3.1 20.6 + - - +
1269A ARG* 3.9 3.8 - - - +
1271A PHE* 4.0 21.1 - - + -
1272A VAL* 4.0 20.9 - - + -
1297A GLY 3.6 5.4 - - - -
1298A VAL* 4.7 2.5 - - + +
1312A ARG* 1.3 74.3 - - - +
1314A ILE* 1.3 70.1 + - - +
1315A ILE* 4.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151A LEU* 6.5 0.2 - - + -
1264A LEU* 3.6 20.2 - - + -
1265A LEU 3.7 1.1 - - - -
1266A GLU* 3.6 24.9 - - + -
1296A PHE* 3.1 8.8 - - - +
1297A GLY 2.9 33.0 + - - +
1299A LEU* 4.3 15.9 - - + -
1312A ARG* 4.4 10.8 - - + +
1313A ALA* 1.3 84.2 - - - +
1315A ILE* 1.3 66.3 + - - +
1316A LEU* 3.8 9.1 + - + -
1327A PHE* 3.6 27.0 - - + -
1584A LEU* 5.8 4.9 - - + -
1588A ILE* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1263A PHE* 3.5 13.2 - - + +
1264A LEU* 3.5 2.2 - - - -
1265A LEU* 3.0 55.0 + - + +
1266A GLU 5.7 0.4 - - - -
1267A ASN* 5.8 0.2 - - + -
1271A PHE* 3.8 35.0 - - + -
1272A VAL* 6.0 0.2 - - + -
1280A LEU* 4.4 13.7 - - + -
1283A THR* 4.9 6.3 - - - +
1284A LEU* 4.4 9.9 - - + -
1287A LEU* 3.8 28.7 - - + -
1295A THR 3.6 8.7 - - - +
1296A PHE* 4.5 6.1 - - + -
1313A ALA* 4.4 3.6 - - + -
1314A ILE* 1.3 84.9 - - - +
1316A LEU* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1263A PHE 3.7 1.8 - - - +
1264A LEU* 3.3 34.3 - - + -
1294A CYS* 3.0 7.5 - - - +
1295A THR* 2.9 43.4 + - + -
1314A ILE* 3.8 10.9 - - + -
1315A ILE* 1.3 72.3 - - - +
1317A ALA* 1.3 60.7 + - - +
1324A LEU* 3.9 7.5 - - + +
1325A PRO* 4.0 33.2 - - + +
1326A LEU 4.5 4.5 - - - +
1327A PHE* 3.7 29.2 - - + -
1588A ILE* 5.0 9.4 - - + +
1592A ILE* 4.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262A PHE* 3.5 7.3 - - - +
1263A PHE* 2.9 59.6 + - + +
1287A LEU* 3.9 15.3 - - + -
1292A TYR* 4.0 14.6 - - + -
1293A GLN 2.9 9.2 - - - +
1294A CYS* 4.2 0.4 - - + -
1316A LEU* 1.3 76.2 - - - +
1318A ALA* 1.3 61.7 + - - +
1324A LEU* 4.3 2.2 - - - -
1325A PRO* 5.3 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261A ARG 3.2 5.4 - - - -
1262A PHE* 3.7 23.3 - - + -
1292A TYR* 3.2 7.5 - - - -
1293A GLN* 2.6 36.2 + - + +
1317A ALA* 1.3 75.4 - - - +
1319A ALA* 1.3 71.9 + - - +
1322A GLU* 4.3 3.4 - - + -
1323A LYS 4.1 2.0 - - - +
1324A LEU* 4.1 26.9 - - + +
1325A PRO* 4.2 0.2 - - + -
----------------------------------------------------------
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