Contacts of the strand formed by residues 1373 - 1381 (chain A) in PDB entry 2Y23
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 ASN1373 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1368A VAL* 3.5 7.4 - - - +
1369A THR* 2.9 39.0 + - - +
1370A GLY* 4.6 3.6 - - - -
1371A GLU* 3.6 20.3 + - - +
1372A CYS* 1.3 78.8 - - - +
1374A VAL* 1.3 62.5 + - - +
1414A LEU* 3.7 25.6 - - + +
1415A ILE 3.3 10.8 - - - +
1416A THR* 3.3 10.8 + - - -
1417A GLU* 2.7 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1366A TRP* 4.3 15.9 - - + -
1367A GLU 3.5 13.7 - - - +
1368A VAL* 4.7 10.1 - - + -
1372A CYS 4.9 0.7 - - - +
1373A ASN* 1.3 76.8 - - - +
1375A LEU* 1.3 66.8 + - - +
1376A LEU* 4.2 15.9 - - + -
1413A LEU 4.0 0.3 - - - +
1414A LEU* 3.7 3.9 - - - +
1415A ILE* 2.7 48.2 + - + +
1418A PHE* 3.5 44.0 - - + -
1443A LEU* 5.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1366A TRP* 3.6 4.3 - - - +
1367A GLU* 3.1 60.0 + - + +
1369A THR* 4.2 18.3 - - + +
1373A ASN 4.2 1.0 + - - -
1374A VAL* 1.3 74.0 - - - +
1376A LEU* 1.3 64.7 + - - +
1377A LYS* 4.1 2.9 + - + -
1412A THR* 3.6 39.3 - - + +
1413A LEU 3.5 13.9 - - - +
1414A LEU* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1364A LEU* 4.6 6.5 - - + -
1365A SER 3.7 6.5 - - - +
1366A TRP* 3.9 24.0 - - + -
1374A VAL* 4.2 11.0 - - + -
1375A LEU* 1.3 76.9 - - - +
1377A LYS* 1.3 60.0 + - - +
1391A TRP* 4.2 26.4 - - + -
1411A CYS 3.5 0.4 - - - +
1412A THR* 2.9 31.1 - - - -
1413A LEU* 2.8 20.8 + - + +
1415A ILE* 4.0 19.3 - - + -
1426A TYR* 4.0 37.0 - - + -
1441A LEU* 4.7 10.3 - - + -
1443A LEU* 4.5 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1363A TYR 3.7 1.0 - - - +
1364A LEU* 3.4 4.5 - - - +
1365A SER* 2.9 57.0 + - - +
1366A TRP 4.7 4.5 - - - -
1367A GLU* 3.2 46.1 + - + +
1375A LEU* 5.1 2.7 - - + -
1376A LEU* 1.3 75.3 - - - +
1378A CYS* 1.3 65.8 + - - +
1410A ILE* 5.2 5.4 - - + -
1411A CYS 3.4 4.7 - - - -
1412A THR* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1360A PHE* 3.9 23.6 - - + -
1362A GLU* 3.4 19.3 - - - +
1363A TYR 4.0 12.3 - - - -
1364A LEU* 4.2 14.1 - - + +
1377A LYS* 1.3 77.5 - - - +
1379A LYS* 1.3 62.7 + - - +
1380A VAL* 4.4 5.2 - - - -
1391A TRP* 5.0 2.5 - - - -
1410A ILE* 3.6 13.2 - - - +
1411A CYS* 3.2 50.4 + - - -
1428A VAL* 5.3 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1360A PHE* 3.6 0.9 - - - -
1361A VAL* 3.0 43.1 + - + -
1362A GLU* 3.1 48.2 + - + +
1378A CYS* 1.3 78.3 - - - +
1380A VAL* 1.3 70.8 + - - +
1409A GLY* 3.0 28.4 - - - +
1410A ILE* 4.2 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1359A HIS 3.4 6.5 - - - +
1360A PHE* 3.9 16.2 - - + -
1361A VAL* 4.5 3.9 - - - +
1378A CYS* 4.4 7.2 - - - -
1379A LYS* 1.3 83.8 + - - +
1381A ALA* 1.3 62.0 + - - +
1383A ILE* 4.0 25.8 - - + +
1389A ILE* 5.6 1.8 - - + -
1409A GLY* 2.6 41.4 + - - +
1411A CYS* 4.3 20.0 - - - -
1430A LEU* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1358A PRO* 3.6 0.5 - - - +
1359A HIS* 2.9 51.1 + - + +
1361A VAL* 3.7 15.3 - - + -
1380A VAL* 1.3 75.5 - - - +
1382A ASN* 1.3 73.2 + - + +
1383A ILE* 3.5 5.0 - - - +
----------------------------------------------------------
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