Contacts of the helix formed by residues 1320 - 1338 (chain A) in PDB entry 5OA1
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 GLN1320 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1315A ASN* 5.8 2.2 - - - +
1316A VAL* 2.8 32.8 + - + +
1319A ASN* 1.3 75.4 - - + +
1321A PHE* 1.4 60.1 + - - +
1322A ILE 3.4 0.4 - - - -
1323A HIS* 3.2 7.2 + - - +
1324A LEU* 3.0 47.4 + - + +
1496A SER* 4.9 1.4 - - - +
1497A ILE* 3.5 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1263A LEU* 3.7 18.8 - - + -
1294A MET* 3.7 22.7 - - + -
1316A VAL* 3.1 7.3 + - - +
1317A ILE* 3.8 27.1 - - + -
1320A GLN* 1.4 75.5 - - - +
1322A ILE* 1.4 55.9 + - + +
1324A LEU* 3.3 4.0 + - - +
1325A LEU* 2.8 53.9 + - + +
1472A PHE* 3.6 31.4 - + - -
1489A VAL* 4.0 8.7 - - + -
1492A ILE* 3.7 18.8 - - + -
1493A CYS* 3.6 26.7 - - - -
1496A SER* 3.5 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1317A ILE* 3.3 25.5 + - + +
1318A SER* 4.0 3.1 - - - +
1320A GLN 3.4 0.4 - - - -
1321A PHE* 1.4 79.2 - - + +
1323A HIS* 1.4 57.5 + - + +
1325A LEU* 3.2 7.2 + - + +
1326A GLU* 2.9 43.0 + - + +
1454A HIS* 2.5 63.3 - - + +
1457A ILE* 4.1 18.6 - - + -
1460A TYR* 3.8 29.6 - - + -
1472A PHE* 5.0 7.9 - - + -
1474A LEU* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1318A SER 5.2 3.4 - - - -
1319A ASN* 3.2 24.6 + - - +
1320A GLN* 3.2 9.4 + - - +
1322A ILE* 1.4 76.6 - - - +
1324A LEU* 1.3 61.5 + - + +
1326A GLU* 4.0 17.4 + - - +
1327A ALA* 3.3 23.9 + - - +
1453A HIS* 5.1 12.8 + - - -
1454A HIS* 5.8 5.4 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1320A GLN* 3.0 44.5 + - + +
1321A PHE 3.6 4.3 - - - +
1322A ILE 3.3 0.2 - - - -
1323A HIS* 1.3 74.6 - - + +
1325A LEU* 1.3 63.1 + - - +
1327A ALA* 3.7 6.6 + - + +
1328A ALA* 3.2 22.5 + - - +
1492A ILE* 3.8 21.8 - - + +
1495A LYS* 5.4 7.6 - - + +
1496A SER* 4.0 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1292A ILE* 4.7 2.9 - - + -
1321A PHE* 2.8 31.7 + - + +
1322A ILE* 3.6 7.4 - - + +
1324A LEU* 1.3 74.1 - - - +
1326A GLU* 1.4 59.3 + - + +
1328A ALA* 3.2 6.3 + - - +
1329A ILE* 3.0 44.4 + - + +
1472A PHE* 3.9 21.3 - - + -
1474A LEU* 3.9 28.5 - - + -
1485A MET* 5.3 0.2 - - - -
1488A ILE* 4.4 11.4 - - + -
1489A VAL* 3.8 39.9 - - + -
1492A ILE* 4.2 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1322A ILE* 2.9 34.7 + - + +
1323A HIS* 4.0 21.1 + - - +
1325A LEU* 1.4 74.8 - - + +
1327A ALA* 1.3 57.2 + - - +
1329A ILE* 3.5 8.5 + - - +
1330A VAL* 3.1 36.5 + - + +
1453A HIS 5.1 1.7 - - - +
1454A HIS* 4.2 6.2 - - - +
1455A ARG* 3.3 40.5 + - - +
1456A PHE* 4.0 12.2 + - + -
1457A ILE* 5.4 1.0 + - - +
1474A LEU* 5.2 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1323A HIS 3.3 16.9 + - - +
1324A LEU* 3.8 7.6 - - + +
1326A GLU* 1.3 78.7 - - - +
1328A ALA* 1.3 56.4 + - - +
1330A VAL* 3.8 5.9 + - - +
1331A LYS* 3.2 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1324A LEU 3.2 13.5 + - - +
1325A LEU* 3.2 9.5 + - - +
1327A ALA* 1.3 75.7 - - - +
1329A ILE* 1.4 58.9 + - - +
1331A LYS* 3.6 7.7 + - - +
1332A GLU* 3.1 26.2 + - - +
1488A ILE* 4.4 13.1 - - + +
1492A ILE* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1325A LEU* 3.0 35.2 + - + +
1326A GLU* 3.5 6.7 + - + +
1328A ALA* 1.4 74.2 - - - +
1330A VAL* 1.4 60.7 + - + +
1332A GLU* 3.1 8.6 + - - +
1333A ILE* 3.0 45.2 + - + +
1474A LEU* 3.9 25.1 - - + -
1476A LEU* 3.8 20.2 - - + -
1483A LEU* 4.0 12.3 - - + -
1485A MET* 3.8 32.1 - - + -
1488A ILE* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1326A GLU* 3.1 20.5 + - + +
1327A ALA* 4.0 7.0 - - - +
1329A ILE* 1.4 74.6 - - + +
1331A LYS* 1.3 62.5 + - - +
1333A ILE* 3.2 15.5 + - + +
1334A LYS* 3.1 23.1 + - + +
1456A PHE* 6.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1327A ALA 3.2 20.0 + - - +
1328A ALA* 3.7 8.3 - - - +
1329A ILE 3.3 0.2 - - - -
1330A VAL* 1.3 76.3 - - - +
1332A GLU* 1.3 58.1 + - - +
1334A LYS* 3.6 11.1 + - + +
1335A LYS* 3.1 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1328A ALA 3.1 16.1 + - - +
1329A ILE* 3.1 7.2 + - - +
1331A LYS* 1.3 73.7 - - - +
1333A ILE* 1.4 65.4 + - - +
1335A LYS* 3.9 20.5 + - - +
1336A GLN* 3.2 28.2 + - - +
1483A LEU* 3.8 22.9 - - + +
1488A ILE* 3.9 23.7 - - + +
255B ASP* 5.2 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1329A ILE* 3.0 39.2 + - + +
1330A VAL* 3.2 14.6 + - + +
1332A GLU* 1.4 74.2 - - - +
1334A LYS* 1.4 64.5 + - - +
1336A GLN* 3.3 10.5 + - - +
1337A LYS* 3.2 48.7 + - + +
1476A LEU* 4.3 4.3 - - + -
1480A THR* 4.1 36.3 - - + +
1483A LEU* 4.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1330A VAL* 3.1 14.1 + - + +
1331A LYS* 3.7 13.2 - - + +
1332A GLU 3.4 0.2 - - - -
1333A ILE* 1.4 76.6 - - - +
1335A LYS* 1.4 51.5 - - + +
1337A LYS* 3.2 7.2 + - - +
1338A ARG* 2.8 80.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331A LYS* 3.1 57.7 + - + +
1332A GLU* 3.9 23.9 + - - +
1333A ILE 3.4 0.2 - - - -
1334A LYS* 1.4 76.1 - - + +
1336A GLN* 1.3 60.6 + - - +
1338A ARG* 3.9 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332A GLU* 3.2 18.5 + - - +
1333A ILE* 3.4 13.4 - - - +
1334A LYS 3.2 0.4 - - - -
1335A LYS* 1.3 79.5 - - - +
1337A LYS* 1.4 82.8 + - - +
1338A ARG 3.8 1.4 + - - -
1479A ASP 5.3 1.4 - - - +
1480A THR* 5.0 2.8 - - - +
1481A GLU* 3.1 36.8 + - - +
1482A LYS 5.7 1.6 - - - +
1483A LEU* 5.8 5.4 - - + -
315B LYS* 3.5 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1333A ILE* 3.2 33.2 + - + +
1334A LYS* 3.9 6.3 - - - +
1336A GLN* 1.4 90.2 - - - +
1338A ARG* 1.4 65.9 + - - +
1479A ASP* 3.1 34.3 + - - +
1480A THR* 6.0 0.4 - - - +
315B LYS* 5.6 1.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1334A LYS* 2.8 57.3 + - + +
1335A LYS* 4.1 18.6 - - - +
1336A GLN 3.5 3.4 - - - -
1337A LYS* 1.4 81.0 - - - +
----------------------------------------------------------
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