Contacts of the strand formed by residues 1293 - 1300 (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 GLN1293 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A LEU* 4.4 4.7 - - + -
876A PHE 2.9 13.9 - - - +
877A GLU* 3.1 12.6 - - - +
878A SER* 2.8 47.5 + - - +
1291A GLY 5.3 0.4 - - - +
1292A TYR* 1.3 74.3 - - - +
1294A CYS* 1.3 58.4 + - - +
1317A ALA* 2.9 5.2 - - - +
1318A ALA* 2.6 50.0 + - + +
1319A ALA 3.0 18.3 + - - +
1320A PRO* 3.9 5.1 + - + -
1322A GLU 2.7 32.1 + - - +
1323A LYS* 5.1 0.2 - - - -
1324A LEU* 3.4 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A PHE* 2.8 58.4 + - - -
1284A LEU* 4.1 24.7 - - + -
1287A LEU* 3.9 38.6 - - + -
1288A VAL* 4.5 4.5 - - - -
1292A TYR 3.8 5.6 + - - -
1293A GLN* 1.3 75.7 - - - +
1295A THR* 1.3 60.7 + - - +
1316A LEU 3.0 12.6 - - - +
1317A ALA* 4.2 1.1 - - + -
1324A LEU* 3.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A TYR 3.7 4.9 + - - -
874A ALA 3.3 11.2 + - - -
875A ARG* 3.3 48.1 + - - +
876A PHE* 5.4 0.2 - - - -
1284A LEU* 4.5 4.1 - - - +
1294A CYS* 1.3 76.2 - - - +
1296A PHE* 1.3 74.3 + - - +
1315A ILE* 3.6 6.4 - - - +
1316A LEU* 2.9 49.3 + - + +
1324A LEU* 4.0 8.5 - - + -
1327A PHE* 4.4 13.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A VAL* 3.9 19.7 - - + -
873A TYR 4.4 3.6 - - - +
874A ALA* 3.5 31.0 - - + -
1272A VAL* 4.6 8.3 - - + -
1280A LEU* 4.3 25.4 - - + -
1284A LEU* 3.6 21.5 - - + -
1295A THR* 1.3 86.6 + - - +
1297A GLY* 1.3 64.0 + - - +
1314A ILE 3.1 13.2 - - - +
1315A ILE* 4.5 11.4 - - + -
1327A PHE* 3.5 13.1 - - - -
1343A VAL* 4.5 21.8 - - + -
1345A VAL* 5.0 2.9 - - + -
1350A PHE* 4.1 25.6 - + + -
1351A VAL 4.2 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1272A VAL* 5.0 1.0 - - - +
1296A PHE* 1.3 84.6 - - - +
1298A VAL* 1.3 68.1 + - - +
1299A LEU* 5.5 0.2 - - - -
1313A ALA* 3.6 1.9 - - - +
1314A ILE* 2.9 32.5 + - - -
1327A PHE* 3.2 20.1 - - - -
1343A VAL* 5.6 1.3 - - - -
1351A VAL 5.1 2.5 - - - -
1352A SER* 5.0 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269A ARG* 3.7 30.7 - - + +
1272A VAL* 4.5 12.6 - - + -
1297A GLY* 1.3 78.8 - - - +
1299A LEU* 1.3 77.6 + - - +
1311A ARG* 4.2 7.9 - - + -
1312A ARG 3.4 17.9 - - - +
1313A ALA* 4.8 1.6 - - - -
1340A GLN 5.4 0.4 - - - +
1341A LEU* 3.5 39.3 + - + +
1343A VAL* 3.3 32.9 - - + +
1352A SER* 5.3 3.9 + - - -
1354A ILE* 4.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1298A VAL* 1.3 84.8 - - - +
1300A GLN* 1.3 59.5 + - - +
1301A ALA 3.7 0.4 + - - -
1304A TYR* 3.3 29.4 - - + +
1310A ARG 3.6 2.1 - - - +
1311A ARG* 3.2 4.5 - - - -
1312A ARG* 3.0 35.3 + - + +
1314A ILE* 4.3 21.3 - - + -
1327A PHE* 4.5 12.8 - - + -
1328A PRO* 3.9 28.0 - - + -
1341A LEU* 4.2 4.3 - - - -
1354A ILE* 3.7 17.9 - - + -
1584A LEU* 3.8 31.5 - - + +
1588A ILE* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299A LEU* 1.3 71.8 - - - +
1301A ALA* 1.3 54.7 + - - +
1302A GLY* 2.6 28.0 + - - +
1303A GLN* 2.6 38.2 + - + +
1304A TYR* 3.5 13.3 - - - -
1308A GLN 3.0 27.7 + - - -
1309A THR* 3.2 8.6 - - - +
1310A ARG 3.2 9.2 + - - +
1311A ARG* 3.0 34.0 + - + +
1334A PHE* 3.8 10.7 - - + -
1338A ALA* 3.3 22.9 - - - +
1339A CYS* 4.1 9.9 - - - -
1341A LEU* 4.0 12.4 - - + +
----------------------------------------------------------
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