Contacts of the helix formed by residues 1346 - 1355 (chain B) in PDB entry 6XAF
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 GLY1346 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1344B GLY 3.3 1.6 + - - -
1345B SER* 1.3 80.1 - - - +
1347B LYS* 1.3 59.5 + - - +
1348B THR 3.4 2.5 - - - -
1349B THR* 3.8 0.7 - - - -
1350B LEU* 2.9 33.4 + - - +
1418B VAL* 4.3 4.5 - - - -
1452B THR* 4.5 3.3 - - - +
1490B ALA* 4.5 0.3 - - - +
1602B GDP 3.0 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394A ASP* 3.6 13.0 - - - +
1395A PHE 3.0 22.0 + - - +
1396A ALA* 2.9 22.1 + - - +
1339B ILE* 3.7 21.3 - - + +
1340B VAL 3.5 22.9 - - - +
1341B GLY 3.1 33.7 - - - +
1342B ASN 3.5 6.7 + - - -
1345B SER* 3.6 9.2 - - - +
1346B GLY* 1.3 72.4 - - - +
1348B THR* 1.3 61.8 + - - +
1350B LEU* 3.3 2.9 + - - +
1351B LEU* 3.0 23.7 + - - +
1418B VAL* 3.8 16.8 - - + -
1601B MG 4.5 0.2 - - - -
1602B GDP 2.8 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372A ASP* 5.7 3.1 - - - +
1394A ASP* 2.8 24.4 + - - +
1347B LYS* 1.3 76.3 - - - +
1349B THR* 1.3 57.7 + - - +
1351B LEU* 3.4 3.2 + - + +
1352B GLN* 3.0 54.3 + - + +
1601B MG 2.0 32.4 - - - -
1602B GDP 3.0 11.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1346B GLY 3.8 4.5 - - - -
1347B LYS 3.3 0.2 - - - -
1348B THR* 1.3 75.8 - - - +
1350B LEU* 1.3 65.2 + - - +
1352B GLN* 3.4 14.7 + - - +
1353B GLN* 3.1 18.8 + - - +
1490B ALA 3.5 24.0 - - - +
1491B THR* 4.0 13.2 - - + -
1602B GDP 2.7 60.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339B ILE* 5.3 1.8 - - + -
1346B GLY 2.9 18.7 + - - +
1347B LYS 3.7 3.1 - - - +
1349B THR* 1.3 77.4 - - - +
1351B LEU* 1.3 57.3 + - - +
1353B GLN* 3.2 2.9 + - - +
1354B LEU* 2.8 40.1 + - + +
1416B LEU* 4.0 19.1 - - + -
1418B VAL* 3.9 28.3 - - + -
1450B VAL* 4.0 17.5 - - + -
1452B THR* 4.8 2.5 - - + -
1488B VAL* 4.1 13.9 - - + -
1490B ALA* 3.8 15.0 - - + +
1497B LEU* 3.6 30.5 - - + -
1500B LEU* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372A ASP* 5.8 1.1 - - - +
1374A LYS* 4.6 15.3 - - + +
1376A TRP* 4.4 15.5 - - + -
1392A VAL* 3.6 30.7 - - + -
1394A ASP* 4.4 16.8 - - + +
1337B LEU* 5.0 0.9 - - + -
1339B ILE* 3.8 22.0 - - + +
1347B LYS 3.0 16.7 + - - +
1348B THR* 3.8 5.4 - - + +
1350B LEU* 1.3 74.5 - - - +
1352B GLN* 1.3 67.2 + - - +
1354B LEU* 3.1 9.0 + - + -
1355B MET* 2.9 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1374A LYS* 5.8 5.2 - - - +
1348B THR* 3.0 39.5 + - + +
1349B THR* 3.6 13.4 + - - +
1351B LEU* 1.3 77.5 - - + +
1353B GLN* 1.3 63.4 + - - +
1355B MET* 3.3 6.7 + - - +
1356B LYS* 3.2 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1349B THR 3.1 9.3 + - - +
1350B LEU* 3.6 3.4 - - - +
1352B GLN* 1.3 74.3 - - - +
1354B LEU* 1.3 58.0 + - - +
1356B LYS* 3.2 44.4 + - - +
1490B ALA 3.3 22.6 - - - +
1491B THR* 3.2 16.8 - - - +
1492B GLU* 3.5 25.4 - - - +
1493B GLU* 3.4 28.9 + - - +
1497B LEU* 3.5 13.2 - - + -
1501B ARG* 2.5 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1376A TRP* 3.6 26.2 + - + -
1350B LEU* 2.8 44.6 + - + +
1351B LEU* 3.6 11.2 - - + +
1353B GLN* 1.3 72.3 - - - +
1355B MET* 1.3 60.1 + - - +
1356B LYS 3.2 1.1 + - - +
1416B LEU* 4.0 11.7 - - + -
1497B LEU* 4.0 20.9 - - + -
1500B LEU* 4.1 11.9 - - + -
1501B ARG* 2.7 55.0 + - + +
1504B ILE* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1374A LYS* 3.7 31.2 - - + +
1375A ASP 3.8 22.2 - - - +
1376A TRP* 3.6 44.8 + - + +
1377A PRO* 5.2 2.0 - - + -
1351B LEU* 2.9 39.0 + - + +
1352B GLN* 3.7 6.1 - - - +
1354B LEU* 1.3 73.5 - - - +
1356B LYS* 1.3 63.2 + - - +
----------------------------------------------------------
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