Contacts of the helix formed by residues 1375 - 1389 (chain A) in PDB entry 2XBA
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 ASN1375 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241A GLU* 3.6 20.3 + - - +
1309A LYS* 3.4 15.8 - - - +
1312A THR* 4.5 0.9 - - - -
1373A ARG 3.8 0.2 + - - -
1374A PRO* 1.3 77.0 - - - +
1376A PHE* 1.3 62.7 + - - +
1377A ALA* 3.2 12.7 + - - +
1378A ILE* 2.9 32.9 + - - +
1379A ILE* 3.0 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234A ALA* 4.0 11.0 - - + +
1237A CYS* 3.4 41.7 - - + -
1238A GLN* 3.7 23.1 - - + -
1241A GLU* 3.1 33.0 + - + +
1308A SER* 4.5 2.7 - - - -
1311A ASP* 3.7 31.9 - - + -
1312A THR* 3.7 24.2 - - - -
1315A PHE* 3.7 26.9 - + + -
1375A ASN* 1.3 74.2 - - - +
1377A ALA* 1.3 60.3 + - - +
1379A ILE* 3.8 16.6 - - + +
1380A LEU* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238A GLN* 3.5 25.3 - - + +
1241A GLU* 4.6 3.3 + - - +
1375A ASN* 3.2 13.7 + - - +
1376A PHE* 1.3 78.1 - - - +
1378A ILE* 1.3 61.8 + - + +
1380A LEU* 3.5 3.5 + - - +
1381A GLU* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1374A PRO* 3.8 13.2 - - + -
1375A ASN* 2.9 28.3 + - - +
1377A ALA* 1.3 78.1 - - + +
1379A ILE* 1.3 65.6 + - - +
1381A GLU* 3.1 29.2 + - - +
1382A ARG* 3.0 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234A ALA* 4.3 5.8 - - + -
1312A THR* 3.9 17.5 - - + +
1315A PHE* 3.5 30.3 - - + -
1361A ILE* 4.4 9.8 - - + +
1365A CYS* 3.7 24.2 - - - -
1374A PRO* 3.7 17.0 - - + +
1375A ASN 3.0 16.0 + - - +
1376A PHE* 3.3 32.1 + - + +
1378A ILE* 1.3 77.0 - - - +
1380A LEU* 1.3 63.3 + - - +
1382A ARG* 3.1 9.1 + - - +
1383A ILE* 2.9 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1231A ARG* 3.7 40.4 - - + +
1234A ALA* 3.9 17.5 - - + +
1235A CYS* 4.0 10.3 - - + +
1238A GLN* 3.2 48.2 - - + +
1376A PHE 2.9 16.5 + - - +
1377A ALA 3.7 4.3 - - - +
1379A ILE* 1.3 77.7 - - - +
1381A GLU* 1.3 56.2 + - - +
1383A ILE* 3.4 6.1 + - + +
1384A GLU* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1377A ALA 3.0 14.8 + - - +
1378A ILE* 3.1 35.7 + - - +
1380A LEU* 1.3 76.3 - - - +
1382A ARG* 1.3 59.9 + - + +
1384A GLU* 3.4 6.2 + - - +
1385A TYR* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361A ILE* 3.8 29.8 - - + +
1364A GLN* 3.3 45.0 + - - +
1374A PRO* 3.9 11.1 - - - +
1378A ILE* 3.0 41.6 + - + +
1379A ILE* 3.1 8.7 + - - +
1381A GLU* 1.3 76.7 - - + +
1383A ILE* 1.3 65.8 + - - +
1385A TYR* 3.3 8.1 + - - +
1386A CYS* 2.9 27.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227A LEU* 3.9 30.7 - - + +
1230A ALA* 3.9 13.7 - - + +
1231A ARG* 3.9 16.2 - - + +
1234A ALA* 3.8 20.6 - - + -
1315A PHE* 3.9 13.7 - - + -
1319A LEU* 5.3 2.5 - - + -
1361A ILE* 3.8 17.0 - - + +
1379A ILE* 2.9 39.6 + - + +
1380A LEU* 3.7 5.6 - - - +
1382A ARG* 1.3 75.5 - - - +
1384A GLU* 1.3 65.3 + - - +
1386A CYS* 3.1 6.9 + - - +
1387A THR* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1231A ARG* 4.2 21.2 + - - +
1380A LEU 2.9 17.8 + - - +
1381A GLU* 3.7 6.7 - - - +
1383A ILE* 1.3 77.9 - - - +
1385A TYR* 1.3 63.3 + - - +
1387A THR* 3.1 19.3 + - - +
1388A GLN* 2.8 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357A PRO* 6.4 1.8 - - + -
1381A GLU 3.0 15.2 + - - +
1382A ARG* 3.4 12.8 - - - +
1384A GLU* 1.3 77.2 - - - +
1386A CYS* 1.3 64.8 + - - +
1388A GLN* 3.2 15.7 + - + +
1389A ASP* 3.3 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227A LEU* 4.1 18.2 - - + -
1357A PRO* 3.8 34.3 - - - -
1358A VAL* 4.0 5.4 - - - -
1361A ILE* 3.8 19.3 - - - -
1382A ARG* 2.9 21.0 + - - -
1383A ILE* 3.5 7.6 - - - +
1385A TYR* 1.3 74.4 - - - +
1387A THR* 1.3 63.1 + - - +
1389A ASP* 3.2 16.7 + - - +
1392A VAL* 3.5 26.8 - - + +
1393A ILE* 3.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224A LEU* 3.7 20.1 - - + +
1227A LEU* 3.7 29.4 - - - +
1228A HIS* 4.7 9.8 - - + +
1231A ARG* 5.9 1.9 - - - +
1383A ILE* 2.9 19.5 + - - +
1384A GLU* 3.2 23.3 + - - +
1385A TYR 3.1 0.2 - - - -
1386A CYS* 1.3 78.1 - - - +
1388A GLN* 1.3 77.0 + - - +
1393A ILE* 3.5 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1384A GLU* 2.8 36.6 + - + +
1385A TYR* 3.2 8.5 + - + +
1387A THR* 1.3 98.8 + - - +
1389A ASP* 1.3 58.7 - - - +
1390A PRO* 3.2 14.9 - - - +
1393A ILE* 4.9 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357A PRO* 4.4 9.0 - - - +
1385A TYR* 3.3 20.2 + - + +
1386A CYS* 3.2 12.3 + - - +
1388A GLN* 1.3 74.7 - - - +
1390A PRO* 1.4 70.7 - - - +
1391A ASP* 2.9 24.4 + - - +
1392A VAL* 3.0 31.7 + - + +
1393A ILE* 3.2 13.9 + - - +
----------------------------------------------------------
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