Contacts of the strand formed by residues 1339 - 1347 (chain A) in PDB entry 2VK7
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 ARG1339 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1333A GLN* 3.3 1.6 - - - +
1334A ASP 2.9 27.1 + - - -
1337A THR* 3.2 20.1 + - - +
1338A GLY* 1.3 76.4 - - - +
1340A ILE* 1.3 63.1 + - - +
1341A PHE* 3.5 30.2 - - + -
1435A TYR* 3.4 52.7 + - + -
1436A SER 3.5 5.6 - - - +
1437A ASP* 2.9 39.7 + - - +
1503A SER 4.9 6.1 + - - -
1504A GLY 6.4 0.2 - - - -
1289B GLY* 5.6 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271A PHE* 5.2 5.6 - - + -
1273A THR* 3.6 22.7 - - + -
1279A ILE* 3.7 10.3 - - + -
1331A LEU* 4.6 6.5 - - + -
1332A ILE 3.6 12.1 - - - +
1333A GLN* 3.7 26.0 - - + +
1338A GLY 4.3 1.3 - - - +
1339A ARG* 1.3 72.8 - - - +
1341A PHE* 1.3 65.8 + - - +
1435A TYR* 3.0 8.0 - - - +
1436A SER* 2.9 39.1 + - - +
1439A ASP* 3.6 39.7 - - - +
1440A GLY 3.6 4.0 - - - +
1443A TRP* 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1330A THR 3.8 0.2 - - - +
1331A LEU* 3.4 8.5 - - - +
1332A ILE* 2.8 57.1 + - + +
1334A ASP* 4.1 9.9 - - + -
1339A ARG* 3.5 45.1 - - + -
1340A ILE* 1.3 76.9 - - - +
1342A LEU* 1.3 59.8 + - - +
1343A LEU* 4.1 5.8 - - + -
1433A LEU* 3.4 33.4 - - + -
1434A VAL 3.5 1.8 - - - -
1435A TYR* 4.0 11.7 - + + -
1443A TRP* 4.5 0.2 - - - -
1447A GLN* 6.1 0.7 - - - -
1480A ILE* 4.0 22.7 - - + -
1503A SER 3.3 22.9 - - - -
1504A GLY* 3.9 16.4 - - - -
1507A TRP* 4.8 3.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281A SER* 3.8 30.1 - - - +
1299A THR* 4.3 2.9 - - + -
1301A VAL* 4.1 5.6 - - + -
1317A ILE* 3.8 19.1 - - + -
1318A MET* 3.7 28.6 - - + +
1329A THR* 4.1 14.1 - - + -
1330A THR 3.2 10.8 - - - +
1331A LEU* 4.0 10.8 - - + -
1341A PHE* 1.3 75.1 - - - +
1343A LEU* 1.3 73.9 + - - +
1432A ASN 4.1 0.2 - - - +
1433A LEU* 3.4 0.9 - - - +
1434A VAL* 2.9 36.7 + - + +
1443A TRP* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1328A ASP 3.8 0.3 - - - +
1329A THR* 3.2 5.9 - - - -
1330A THR* 3.0 43.5 + - + +
1332A ILE* 4.8 2.7 - - + -
1341A PHE* 4.1 13.5 - - + +
1342A LEU* 1.3 77.3 - - - +
1344A VAL* 1.3 62.1 + - - +
1431A ILE* 4.2 10.8 - - + -
1432A ASN 3.2 8.1 - - - +
1433A LEU* 3.7 39.5 - - + -
1449A ILE* 4.2 3.1 - - + -
1463A ILE* 3.6 18.8 - - + -
1482A VAL* 4.2 16.8 - - + -
1498A ILE* 4.0 26.5 - - + -
1507A TRP* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299A THR* 4.0 1.6 - - - +
1318A MET* 3.6 27.1 - - + -
1326A VAL* 3.8 23.6 - - + -
1327A ILE 3.4 30.7 - - - +
1328A ASP 3.3 11.2 - - - +
1329A THR* 3.7 20.2 - - + -
1342A LEU* 4.4 0.2 - - + -
1343A LEU* 1.3 76.7 - - - +
1345A THR* 1.3 62.4 + - - +
1431A ILE* 3.7 3.1 - - - -
1432A ASN* 2.9 43.8 + - + +
1463A ILE* 3.7 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1326A VAL* 3.2 4.7 - - - -
1327A ILE* 2.8 48.8 + - - +
1328A ASP* 3.7 2.1 + - - +
1344A VAL* 1.3 74.2 - - - +
1346A HIS* 1.3 61.3 - - - +
1347A PHE* 3.8 23.6 - - + -
1429A SER* 4.0 17.0 - - - -
1430A TYR 3.5 9.0 - - - +
1431A ILE* 4.9 1.1 - - - +
1460A PHE* 4.1 5.4 - - + -
1461A LEU 4.1 0.7 - - - +
1462A GLY* 3.3 13.2 - - - -
1463A ILE* 2.9 31.1 + - - +
2693A FSI 5.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1320A TYR* 3.4 37.8 + + - -
1324A SER* 2.9 21.5 + - - -
1325A SER 3.3 17.9 - - - -
1326A VAL* 4.0 2.5 - - + -
1345A THR* 1.3 75.0 - - - +
1347A PHE* 1.3 70.4 + - - +
1348A PRO* 4.4 1.6 - - + -
1417A ASN* 3.2 30.3 - - - -
1429A SER* 3.5 4.5 - - - -
1430A TYR* 2.8 60.1 + + + +
1432A ASN* 3.6 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1292A ALA* 4.1 7.4 - - + -
1324A SER* 2.7 18.0 + - - -
1325A SER 2.9 21.2 + - - +
1327A ILE* 3.7 31.0 - - + -
1345A THR* 3.8 7.9 - - + -
1346A HIS* 1.3 76.5 - - - +
1348A PRO* 1.3 69.5 - - + +
1351A TYR* 3.2 21.8 - - + +
1352A GLY* 3.3 46.0 - - - -
1353A PHE 3.6 3.1 - - - -
1356A ALA* 4.3 3.8 - - + -
1428A THR 3.7 15.5 - - - -
1429A SER* 3.6 23.6 - - - -
1460A PHE* 3.8 21.8 - + - -
2693A FSI 4.2 7.9 - - + -
----------------------------------------------------------
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