Contacts of the strand formed by residues 1346 - 1355 (chain D) 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 HIS1346 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1309D ASP* 3.9 21.7 + - + -
1311D ARG* 2.6 32.7 + - - -
1313D PHE* 3.3 28.7 - + + -
1344D PRO* 3.6 14.5 - - + +
1345D ASN* 1.3 71.2 - - - +
1347D THR* 1.3 61.6 + - - +
1391D SER* 4.9 0.9 - - - -
1392D ARG* 3.4 27.6 + - + +
1441D GLU* 3.2 37.4 - - - +
1443D VAL* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345D ASN 4.5 1.6 - - - -
1346D HIS* 1.3 75.8 - - - +
1348D LEU* 1.3 62.3 + - - +
1349D TYR* 4.3 18.8 + - + +
1390D GLY 2.3 33.9 + - - -
1391D SER* 3.4 8.0 - - - -
1392D ARG* 3.7 9.6 - - - +
1440D ILE* 4.0 17.3 - - + -
1441D GLU 3.0 13.6 + - - +
1442D THR* 3.3 18.2 - - - +
1443D VAL* 3.2 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347D THR* 1.3 82.1 + - - +
1349D TYR* 1.3 80.3 + - - +
1350D PRO* 3.6 11.3 - - + +
1389D GLY* 3.4 9.5 - - - -
1390D GLY 3.3 14.2 + - - +
1392D ARG* 4.2 11.9 - - + +
1395D GLY 5.0 3.1 - - - +
1398D LEU* 4.2 10.0 - - + +
1399D PRO* 3.9 35.7 - - + -
1442D THR* 4.1 0.2 - - - -
1443D VAL* 3.6 30.3 - - + +
1445D VAL* 4.5 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347D THR* 4.3 13.4 + - + +
1348D LEU* 1.3 83.4 - - - +
1350D PRO* 1.3 62.6 - - - +
1351D MET* 4.8 2.1 - - + +
1387D LEU* 4.9 13.0 - - + -
1389D GLY* 3.2 33.5 + - - -
1390D GLY* 4.4 1.3 - - - -
1429D MET* 3.6 35.6 - - + +
1440D ILE* 6.0 0.2 - - - +
1442D THR* 3.4 19.0 + - - +
1443D VAL 2.8 21.8 + - - +
1444D ALA* 3.4 4.2 - - - +
1445D VAL 3.4 13.7 + - - +
1488D HIS* 4.2 25.6 + + - -
1491D LEU* 4.1 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1348D LEU* 3.6 18.6 - - + +
1349D TYR* 1.3 88.8 - - - +
1351D MET* 1.3 62.6 + - - +
1352D VAL* 5.8 4.5 - - + -
1387D LEU* 4.4 7.6 - - - +
1388D PRO* 3.5 42.9 - - + +
1389D GLY* 3.8 2.7 - - - -
1399D PRO* 5.9 8.5 - - + -
1402D LEU* 5.6 2.2 - - + -
1445D VAL* 3.6 23.8 - - + +
1447D VAL* 6.1 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1349D TYR 4.8 3.4 - - - +
1350D PRO* 1.3 74.6 - - - +
1352D VAL* 1.3 63.2 + - - +
1353D THR* 4.0 10.7 - - + +
1374D VAL* 5.5 4.7 - - + -
1387D LEU* 4.6 16.8 - - + -
1388D PRO* 5.9 0.9 - - - -
1424D VAL* 4.6 4.5 - - + -
1444D ALA* 4.5 12.8 - - + -
1445D VAL 3.1 14.0 + - - +
1446D SER* 3.6 16.5 - - - -
1447D VAL* 3.2 29.0 + - - +
1491D LEU* 3.9 40.6 - - + +
1492D LEU* 4.6 14.6 - - + -
1495D ALA* 3.7 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1350D PRO* 5.8 3.8 - - + -
1351D MET* 1.3 73.0 - - - +
1353D THR* 1.3 59.8 + - - +
1373D GLU 3.5 0.7 - - - +
1374D VAL* 3.3 25.8 - - + +
1375D LEU* 3.6 42.5 + - + +
1388D PRO* 5.4 7.9 - - + -
1447D VAL* 3.6 25.8 - - + -
1449D PHE* 6.0 7.4 - - + -
1475D TRP* 3.9 11.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1351D MET* 4.3 21.3 - - + +
1352D VAL* 1.3 78.2 - - - +
1354D ARG* 1.3 62.0 + - - +
1372D LEU* 4.0 13.7 - - + -
1373D GLU 3.5 4.3 - - - -
1374D VAL* 4.4 11.2 - - + -
1446D SER* 5.1 6.1 - - - -
1447D VAL 3.2 9.5 + - - +
1448D HIS* 2.4 41.6 + - - +
1449D PHE* 2.9 26.1 + - - +
1475D TRP* 4.9 0.7 - - - -
1492D LEU* 5.8 2.2 - - + -
1495D ALA* 5.9 3.4 - - + -
1499D PHE* 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1353D THR* 1.3 75.8 - - - +
1355D TRP* 1.3 61.9 + - - +
1372D LEU* 3.3 10.0 - - - +
1373D GLU* 2.5 70.9 + - + +
1448D HIS* 4.5 0.7 - - - -
1449D PHE* 3.9 13.5 - - + -
1452D GLN* 3.3 29.5 + - - +
1457D LEU* 6.1 5.0 - - - +
1475D TRP* 3.2 60.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1354D ARG* 1.3 79.0 + - - +
1356D ARG* 1.3 61.3 + - - +
1357D ARG* 3.8 4.4 + - - +
1363D ILE* 3.8 30.5 - - + -
1370D LYS* 3.6 38.8 - - + -
1371D MET 3.4 17.0 - - - -
1372D LEU* 3.6 22.9 - - + -
1373D GLU* 3.1 15.7 - - - +
1448D HIS* 3.1 21.3 + + - -
1449D PHE 3.7 3.8 - - - -
1450D GLN* 3.1 50.4 - - - +
1452D GLN* 3.1 25.8 - - + +
1499D PHE* 4.4 25.6 - + + -
1500D GLY 6.0 0.9 - - - -
1501D ALA* 6.0 0.4 - - - -
----------------------------------------------------------
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