Contacts of the strand formed by residues 1336 - 1341 (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 LYS1336 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1390A LEU* 5.6 1.8 - - - -
1391A ASN* 3.1 16.4 + - + +
1393A TRP* 3.7 21.1 - - + +
1334B ARG 4.1 10.1 + - - +
1335B MET* 1.3 78.8 - - - +
1337B LEU* 1.3 56.0 + - - +
1338B MET* 3.7 33.9 - - + -
1403B SER* 2.7 41.5 + - - -
1408B PHE* 3.8 24.4 - - - +
1409B MET* 3.5 19.1 - - - -
1412B ARG 3.0 12.3 + - - +
1413B ALA* 4.2 0.7 - - + -
1414B LEU* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1376A TRP* 3.9 32.1 - - + -
1390A LEU* 4.2 17.2 - - + +
1391A ASN 2.9 8.1 + - - +
1392A VAL* 3.3 23.6 - - + +
1393A TRP 2.8 31.5 + - - -
1335B MET 4.2 0.4 + - - -
1336B LYS* 1.3 71.8 - - - +
1338B MET* 1.3 55.9 + - - +
1339B ILE* 4.5 9.0 - - + -
1351B LEU* 5.0 1.1 - - + -
1414B LEU* 3.4 40.6 - - + +
1416B LEU* 4.1 32.8 - - + +
1504B ILE* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1393A TRP* 3.5 32.8 - - + -
1395A PHE* 4.1 16.2 - - + -
1401A PHE* 5.4 2.5 - - + -
1336B LYS* 3.7 22.0 - - + -
1337B LEU* 1.3 72.0 - - - +
1339B ILE* 1.3 56.6 + - - +
1340B VAL* 4.0 2.4 + - + -
1409B MET* 3.6 40.2 - - + +
1413B ALA* 3.6 25.1 - - + -
1414B LEU 2.8 10.2 + - - +
1415B TYR* 3.3 31.8 - - + +
1416B LEU* 2.7 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1392A VAL* 3.6 27.1 - - + -
1393A TRP 2.8 15.2 + - - +
1394A ASP* 4.3 8.3 - - + +
1395A PHE* 3.0 31.0 + - - +
1337B LEU* 4.4 4.7 - - + +
1338B MET* 1.3 75.2 - - - +
1340B VAL* 1.3 62.5 + - - +
1347B LYS* 3.7 29.6 - - + +
1350B LEU* 5.3 0.7 - - + -
1351B LEU* 3.8 33.4 - - + +
1416B LEU* 3.5 25.1 - - + +
1418B VAL* 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1395A PHE* 3.8 11.4 - - + -
1401A PHE* 3.8 34.1 - - + -
1339B ILE* 1.3 79.4 - - - +
1341B GLY* 1.3 58.6 + - - +
1347B LYS* 3.5 11.7 - - - +
1415B TYR* 4.3 14.6 - - + -
1416B LEU 2.9 15.8 + - - +
1417B ALA* 4.1 9.4 - - + -
1418B VAL* 2.9 25.5 + - - +
1434B TRP* 3.5 27.1 - - + -
1438B ILE* 4.0 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1397A GLY* 3.4 7.3 - - - -
1340B VAL* 1.3 78.4 - - - +
1342B ASN* 1.3 60.3 + - - -
1347B LYS* 3.1 17.3 - - - -
1418B VAL 3.6 14.8 - - - -
1431B MET* 4.1 6.5 - - - -
1434B TRP* 3.1 34.1 - - - -
----------------------------------------------------------
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