Contacts of the strand formed by residues 1365 - 1371 (chain B) in PDB entry 3KQ4
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 LYS1365 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1309B THR* 4.0 23.8 - - + -
1310B ILE 4.1 1.3 - - - -
1311B ARG* 4.1 24.7 - - + +
1343B GLY* 3.2 42.5 + - - -
1344B PRO* 5.5 2.6 - - - +
1361B THR* 3.6 13.2 - - - +
1363B SER* 3.2 7.4 + - - +
1364B SER* 1.3 81.8 + - - +
1366B LEU* 1.3 61.4 + - - +
1367B GLN* 4.1 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1308B TRP 4.0 0.5 - - - +
1309B THR* 3.3 2.9 - - - +
1310B ILE* 2.9 67.6 + - + +
1318B VAL* 3.9 16.4 - - + -
1320B TYR* 2.7 47.3 - - + +
1340B LEU* 4.9 0.2 - - + -
1341B TYR 3.4 7.2 - - - +
1361B THR* 3.8 10.8 - - + -
1365B LYS* 1.3 78.4 - - - +
1367B GLN* 1.3 72.8 + - - +
1368B VAL* 4.0 13.0 + - + -
1384B MET* 6.1 1.8 - - + -
1386B TRP* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1307B ASN* 4.4 17.7 + - - +
1308B TRP 3.3 6.5 - - - +
1309B THR* 3.1 23.5 - - + +
1339B GLU 4.0 0.2 - - - +
1340B LEU* 3.6 4.3 - - - -
1341B TYR* 2.9 56.2 + - + +
1343B GLY 3.7 19.5 + - - +
1344B PRO* 5.6 0.2 - - - +
1365B LYS* 4.1 23.3 - - + +
1366B LEU* 1.3 75.9 - - - +
1368B VAL* 1.3 61.9 + - - +
1369B LEU* 4.2 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1291B LEU* 3.5 14.8 - - + -
1306B CYS 3.5 0.9 - - - +
1307B ASN* 3.4 5.4 - - - -
1308B TRP* 2.8 72.2 + - + +
1310B ILE* 6.0 0.9 - - + +
1338B LEU* 5.5 7.2 - - + -
1339B GLU 3.6 2.7 - - - +
1340B LEU* 3.2 27.8 - - + -
1366B LEU* 4.6 12.1 - - + +
1367B GLN* 1.3 73.4 - - - +
1369B LEU* 1.3 63.4 + - - +
1382B PHE* 5.8 1.1 - - + -
1384B MET* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305B HIS 5.8 0.4 - - - -
1306B CYS 3.2 15.0 - - - +
1307B ASN* 3.4 30.7 - - + +
1308B TRP* 5.2 0.2 - - - -
1337B TYR* 4.8 1.4 - - + -
1338B LEU* 3.0 6.4 - - - +
1339B GLU* 2.5 55.7 + - + +
1341B TYR* 3.5 34.1 - - + +
1367B GLN* 4.2 9.6 - - - +
1368B VAL* 1.3 75.3 - - - +
1370B LEU* 1.3 59.5 + - - +
1371B LEU* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1293B SER* 4.1 25.6 - - - -
1300B TYR* 5.3 7.4 - - + -
1304B GLN* 3.4 17.1 - - - +
1306B CYS* 3.1 43.8 + - + +
1308B TRP* 4.2 15.5 - - + -
1327B LEU* 3.8 28.0 - - + -
1336B ASP* 6.1 0.2 - - + -
1337B TYR 3.1 22.7 - - - +
1338B LEU* 4.1 13.2 - - + +
1368B VAL 4.2 0.6 + - - -
1369B LEU* 1.3 73.2 - - - +
1371B LEU* 1.3 66.8 + - - +
1372B THR* 3.9 8.5 + - + +
1382B PHE* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A VAL* 4.6 16.4 - - + -
1304B GLN 3.4 7.0 - - - +
1305B HIS* 4.3 24.5 - - + +
1306B CYS 4.4 3.1 - - - +
1335B THR 4.6 0.2 - - - +
1336B ASP* 3.5 3.3 - - - +
1337B TYR* 2.8 80.1 + - + +
1339B GLU* 6.0 0.2 - - - +
1369B LEU* 4.0 18.1 - - + -
1370B LEU* 1.3 87.5 - - - +
1372B THR* 1.3 59.1 + - - +
----------------------------------------------------------
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