Contacts of the helix formed by residues 1487 - 1496 (chain B) in PDB entry 6PUO
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 ASN1487 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241B ASN* 5.0 8.3 - - + +
1429B MET* 4.3 19.4 - - + +
1430B ASP* 2.8 33.6 + - + +
1431B ASP* 3.8 18.6 + - - +
1432B PRO* 5.2 1.2 - - - +
1485B TYR* 3.2 16.4 - - - -
1486B ALA* 1.3 74.8 - - + +
1488B HIS* 1.3 81.5 + - - +
1489B LYS 3.2 0.4 - - - -
1490B THR* 2.3 37.7 + - + +
1491B LEU* 3.5 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1349B TYR* 4.2 29.8 + + - -
1386B ALA* 3.9 16.5 - - + -
1387B LEU* 3.1 55.5 + - + +
1429B MET* 5.9 0.7 - - + -
1484B LEU* 3.9 16.1 - - + +
1485B TYR* 3.8 23.7 - + + +
1486B ALA 3.2 0.8 - - - -
1487B ASN* 1.3 105.1 + - - +
1489B LYS* 1.3 61.8 + - - +
1491B LEU* 3.1 23.5 + - + +
1492B LEU* 3.3 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ASP* 5.8 3.4 - - - +
1479B ASP 5.0 1.1 - - - -
1480B ARG* 2.5 31.0 + - - +
1481B ARG* 4.3 2.6 - - - +
1482B ILE* 3.4 25.7 + - + +
1484B LEU* 4.1 16.6 - - + +
1485B TYR 3.4 19.1 - - - +
1486B ALA* 3.7 12.1 - - - +
1487B ASN 3.2 0.8 - - - -
1488B HIS* 1.3 74.6 - - - +
1490B THR* 1.3 62.1 + - + +
1492B LEU* 3.3 8.6 + - + +
1493B GLN* 2.9 29.6 + - - +
1503B TYR* 5.6 8.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429B MET* 5.9 0.9 - - - +
1486B ALA 4.7 2.9 - - - +
1487B ASN* 2.3 39.8 + - + +
1489B LYS* 1.3 78.7 - - + +
1491B LEU* 1.3 64.5 + - - +
1493B GLN* 3.8 6.6 + - - +
1494B LYS* 3.4 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1349B TYR* 4.1 30.5 - - + -
1351B MET* 3.9 26.3 - - + +
1387B LEU* 4.4 8.3 - - + -
1424B VAL* 4.9 2.3 - - - +
1425B TYR* 5.5 13.2 - - + -
1429B MET* 4.3 22.0 - - + -
1442B THR* 5.4 4.0 - - + -
1444B ALA* 4.2 15.7 - - + -
1487B ASN 3.5 17.7 - - - +
1488B HIS* 3.1 14.5 + - + +
1490B THR* 1.3 85.4 + - - +
1492B LEU* 1.3 60.4 + - + +
1494B LYS* 3.2 7.9 + - - +
1495B ALA* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1351B MET* 4.6 10.5 - - + -
1374B VAL* 4.4 26.0 - - + -
1387B LEU* 4.2 27.6 - - + -
1478B VAL* 4.6 25.3 - - + +
1484B LEU* 4.7 10.5 - - + -
1488B HIS 3.5 14.6 - - - +
1489B LYS* 3.3 11.0 + - - +
1491B LEU* 1.3 78.9 - - + +
1493B GLN* 1.3 61.0 + - - +
1495B ALA* 3.5 13.6 - - + +
1496B ALA* 2.9 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1489B LYS 2.9 17.4 + - - +
1490B THR* 4.1 7.9 - - - +
1491B LEU 3.3 0.2 - - - -
1492B LEU* 1.3 76.3 - - - +
1494B LYS* 1.3 58.4 + - - +
1496B ALA* 4.4 4.7 - - - +
1497B ALA* 4.3 12.6 + - - +
1503B TYR* 4.5 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424B VAL* 3.5 21.4 - - + +
1425B TYR* 5.4 7.9 - - + -
1490B THR 3.4 11.5 + - - +
1491B LEU* 3.2 10.2 + - - +
1492B LEU 3.2 0.4 - - - -
1493B GLN* 1.3 76.5 - - - +
1495B ALA* 1.3 60.8 + - - +
1496B ALA 3.5 0.2 - - - -
1497B ALA* 3.9 15.2 + - - +
1498B GLU* 4.2 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1351B MET* 3.7 27.4 - - - -
1424B VAL* 4.2 12.6 - - + -
1446B SER* 5.9 0.7 - - - -
1491B LEU 2.8 15.3 + - - +
1492B LEU* 3.0 16.9 + - + +
1494B LYS* 1.3 76.9 - - - +
1496B ALA* 1.3 62.9 + - - +
1497B ALA 3.2 1.8 - - - -
1498B GLU* 3.2 18.2 + - - +
1499B PHE* 3.8 13.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372B LEU* 6.2 1.6 - - - -
1478B VAL* 5.7 7.6 - - + -
1492B LEU* 2.9 14.8 + - + +
1493B GLN* 4.3 5.4 + - - +
1494B LYS 3.5 0.2 - - - -
1495B ALA* 1.3 75.3 - - - +
1497B ALA* 1.3 55.9 + - - +
1498B GLU 3.2 0.2 - - - -
1499B PHE* 3.2 3.4 + - - +
1500B GLY* 2.7 33.8 + - - -
1501B ALA* 3.2 33.3 + - + +
1502B HIS 4.9 5.8 - - - +
1503B TYR* 6.2 3.6 - - + -
----------------------------------------------------------
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