Contacts of the helix formed by residues 1493 - 1519 (chain A) in PDB entry 2YIN
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 SER1493 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1462A MET 4.2 0.4 - - - -
1463A TRP* 3.5 25.2 - - - -
1492A ILE* 1.3 73.8 - - - +
1494A PRO* 1.3 75.2 - - - +
1495A LEU* 3.6 8.7 + - - +
1496A GLU* 2.6 50.7 + - - +
1497A ASN* 2.9 12.9 + - - +
1555A TYR* 6.0 0.7 - - - -
1562A ASP* 5.5 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459A PHE 3.4 12.6 - - - +
1460A ALA 3.1 28.3 - - - +
1462A MET 2.4 30.3 - - - +
1463A TRP* 3.3 28.5 - - + +
1493A SER* 1.3 84.4 - - - +
1495A LEU* 1.3 62.9 + - - +
1497A ASN* 3.4 6.5 + - + +
1498A ALA* 2.9 24.9 + - - +
1546A TYR* 5.2 1.0 - - - -
1550A PHE* 3.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493A SER* 3.0 9.4 + - - +
1494A PRO* 1.3 81.0 - - - +
1496A GLU* 1.3 63.6 + - + +
1498A ALA* 3.1 5.4 + - - +
1499A ILE* 3.0 29.8 + - + +
1550A PHE* 3.8 24.3 - - + -
1555A TYR* 3.6 24.4 + - - +
1562A ASP* 3.7 20.6 - - + +
1565A LYS* 3.7 31.9 - - + -
1566A LEU* 3.8 19.1 - - + -
1569A LEU* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1491A THR 4.3 3.5 - - - +
1492A ILE* 3.4 22.1 - - + +
1493A SER* 2.6 47.3 + - - +
1495A LEU* 1.3 75.8 - - - +
1497A ASN* 1.3 57.9 + - - +
1499A ILE* 3.3 13.0 + - - +
1500A GLU* 3.2 28.1 + - - +
1565A LYS* 4.1 32.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1462A MET* 5.0 9.7 - - + +
1463A TRP* 4.9 1.6 - - - +
1464A ILE* 2.6 54.2 - - - +
1492A ILE* 3.6 14.3 + - + +
1493A SER 2.9 13.4 + - - +
1494A PRO* 3.5 9.6 - - + +
1496A GLU* 1.3 74.2 - - - +
1498A ALA* 1.3 63.2 + - - +
1499A ILE 3.1 1.1 - - - -
1500A GLU* 3.3 9.1 + - - +
1501A THR* 2.8 36.3 + - - -
33C ILE* 5.0 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1494A PRO 2.9 14.8 + - - +
1495A LEU 3.3 9.0 - - - +
1497A ASN* 1.3 74.7 - - - +
1499A ILE* 1.3 63.6 + - - +
1501A THR* 3.2 3.1 + - - -
1502A MET* 2.9 27.4 + - - +
1546A TYR* 3.4 47.8 - - + -
1550A PHE* 3.9 8.5 - - + -
1569A LEU* 4.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495A LEU* 3.0 19.9 + - + +
1496A GLU* 3.4 11.7 - - - +
1497A ASN 3.1 0.4 - - - -
1498A ALA* 1.3 76.7 - - - +
1500A GLU* 1.3 59.0 + - + +
1502A MET* 3.1 3.3 + - - +
1503A SER* 2.8 37.3 + - - +
1565A LYS* 3.6 38.1 - - + +
1568A HIS* 3.9 33.7 - - + +
1569A LEU* 4.2 21.8 - - + +
1572A LEU* 3.8 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1464A ILE* 5.1 1.7 - - - +
1466A ARG* 2.7 43.4 + - - -
1492A ILE* 3.3 22.9 - - - +
1496A GLU 3.2 10.7 + - - +
1497A ASN* 3.6 13.5 - - - +
1499A ILE* 1.3 76.8 - - + +
1501A THR* 1.3 57.5 + - - +
1503A SER* 3.1 7.6 + - - -
1504A THR* 2.9 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497A ASN* 2.8 21.8 + - - -
1498A ALA 3.2 7.8 + - - -
1500A GLU* 1.3 76.4 - - - +
1502A MET* 1.3 63.4 - - - +
1504A THR* 3.8 5.8 - - - -
1505A ALA* 3.2 22.0 + - - +
1546A TYR* 3.6 22.7 + - + +
33C ILE* 5.9 1.9 - - - +
35C THR* 4.0 25.4 - - - +
36C VAL 4.5 5.8 - - - +
37C PHE* 4.7 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1498A ALA 2.9 12.4 + - - +
1499A ILE* 3.6 4.0 - - - +
1501A THR* 1.3 76.7 - - - +
1503A SER* 1.3 65.4 + - - +
1505A ALA* 3.2 3.9 + - - +
1506A ASN* 3.0 29.7 + - - +
1543A PHE* 3.9 17.0 - - + -
1546A TYR* 3.0 46.2 - - + -
1569A LEU* 4.8 10.1 - - + -
1572A LEU* 3.7 34.8 - - + -
1573A ILE* 4.6 6.7 - - - +
1576A GLN* 3.4 24.9 - - - +
37C PHE* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499A ILE* 2.8 29.3 + - - +
1500A GLU* 3.6 8.7 - - - -
1502A MET* 1.3 72.6 - - - +
1504A THR* 1.3 58.3 + - - +
1506A ASN* 3.3 3.9 + - - +
1507A GLU* 2.8 46.8 + - - +
1568A HIS* 5.3 2.1 + - - -
1572A LEU* 4.1 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1500A GLU* 2.9 20.6 + - - +
1501A THR* 3.8 6.7 - - - -
1503A SER* 1.3 77.2 - - - +
1505A ALA* 1.3 58.0 + - - +
1507A GLU* 3.4 13.6 + - + +
1508A LYS* 2.8 54.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1501A THR 3.2 15.1 + - - +
1502A MET* 3.2 6.7 + - - +
1504A THR* 1.3 80.8 - - - +
1506A ASN* 1.3 63.1 + - - +
1508A LYS* 3.4 9.7 + - - +
1509A ILE* 3.0 32.9 + - - +
1534A ILE* 4.5 12.4 - - + +
1576A GLN* 4.7 1.8 - - - +
37C PHE* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1502A MET* 3.0 17.3 + - - +
1503A SER* 3.8 4.3 - - - +
1505A ALA* 1.3 75.0 - - - +
1507A GLU* 1.3 66.0 + - - +
1509A ILE* 3.1 10.8 + - - +
1510A LEU* 2.9 26.2 + - - +
1572A LEU* 3.4 34.8 - - + +
1575A TRP* 4.0 17.9 - - + -
1576A GLN* 3.2 47.5 + - - +
1579A PHE* 3.9 9.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1503A SER* 2.8 37.2 + - - +
1504A THR* 3.6 12.9 + - + +
1506A ASN* 1.3 73.1 - - - +
1508A LYS* 1.3 57.8 + - - +
1510A LEU* 3.5 5.4 + - - +
1511A MET* 2.9 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1504A THR* 2.8 39.2 + - + +
1505A ALA* 3.5 8.4 - - - +
1507A GLU* 1.3 73.6 - - - +
1509A ILE* 1.3 66.8 + - - +
1511A MET* 3.6 8.9 + - - +
1512A MET* 3.0 27.5 + - + +
1515A GLN* 5.1 0.2 + - - -
1530A LEU* 4.0 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505A ALA 3.0 17.3 + - - +
1506A ASN* 3.1 23.3 + - - +
1508A LYS* 1.3 73.5 - - - +
1510A LEU* 1.3 66.6 + - - +
1512A MET* 2.9 6.6 + - + +
1513A ILE* 2.9 29.9 + - + +
1530A LEU* 4.0 12.1 - - + -
1531A LEU* 4.5 15.3 - - + -
1534A ILE* 4.0 20.6 - - + -
1576A GLN* 4.3 5.8 - - + -
1579A PHE* 3.6 38.6 - - + +
1580A LEU* 3.9 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1506A ASN 2.9 15.1 + - - +
1507A GLU* 3.7 6.1 - - - +
1509A ILE* 1.3 76.3 - - - +
1511A MET* 1.3 64.8 + - + +
1513A ILE* 2.8 53.6 + - + +
1514A ASN* 3.0 22.9 + - - +
1575A TRP* 5.8 2.0 - - + +
1579A PHE* 3.6 29.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1428A ASP* 4.0 35.3 - - + +
1432A ASN* 4.2 26.9 - - - +
1435A LYS* 4.5 9.4 - - - +
1507A GLU* 2.9 47.4 + - + +
1508A LYS* 4.0 7.9 - - - +
1510A LEU* 1.3 74.4 - - + +
1512A MET* 1.3 63.7 + - - +
1514A ASN* 3.4 3.3 + - - +
1515A GLN* 3.0 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508A LYS* 3.0 15.8 + - + +
1509A ILE 2.9 13.1 + - - +
1511A MET* 1.3 74.7 - - - +
1513A ILE* 1.3 63.2 + - + -
1515A GLN* 3.3 30.7 + - - +
1516A TYR* 3.1 45.4 + - + -
1526A PRO* 3.7 28.7 - - + +
1527A LEU* 3.4 27.8 - - + -
1530A LEU* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509A ILE* 2.9 27.7 + - + +
1510A LEU* 2.8 46.0 + - + +
1512A MET* 1.3 70.6 - - + +
1514A ASN* 1.3 72.8 + - - +
1516A TYR* 3.2 2.1 + - - +
1517A GLN* 2.7 48.8 + - - +
1527A LEU* 5.9 2.2 - - + -
1579A PHE* 4.5 5.4 - - + +
1582A ALA* 4.6 13.0 - - + -
1583A GLY* 4.2 27.4 - - - +
1586A ILE* 3.9 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1428A ASP* 3.7 21.1 + - - +
1510A LEU* 3.0 30.8 + - - +
1511A MET 3.5 7.4 - - - +
1513A ILE* 1.3 86.6 - - - +
1515A GLN* 1.3 63.2 - - + +
1517A GLN* 3.4 20.0 + - - +
1518A SER* 3.0 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1511A MET* 3.0 37.1 + - + +
1512A MET* 3.3 33.1 + - - +
1514A ASN* 1.3 75.5 - - + +
1516A TYR* 1.3 65.5 + - + +
1518A SER* 3.7 5.0 - - - -
1519A ASP* 3.0 24.4 + - - +
1522A LEU* 3.3 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1512A MET* 3.1 51.1 + - + +
1513A ILE 3.9 1.6 - - - +
1515A GLN* 1.3 89.0 - - + +
1517A GLN* 1.3 63.4 + - - +
1519A ASP 2.8 20.8 - - - +
1520A GLU* 4.6 4.7 - - - +
1522A LEU* 3.5 35.8 - - + +
1523A PRO 2.4 34.8 + - - -
1524A ILE* 4.2 8.5 - - + -
1526A PRO* 3.5 19.9 - - + +
1527A LEU* 3.7 26.9 + - + -
1586A ILE* 4.2 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1513A ILE* 2.7 31.8 + - - +
1514A ASN* 3.4 26.9 + - - +
1516A TYR* 1.3 74.3 - - - +
1518A SER* 1.3 60.9 + - - +
1519A ASP 4.9 0.7 - - - -
1520A GLU* 4.9 6.2 - - - +
1586A ILE* 4.0 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1514A ASN 3.0 19.3 + - - -
1515A GLN* 3.7 5.9 + - - -
1517A GLN* 1.3 79.6 - - - +
1519A ASP* 1.3 58.9 + - - +
1520A GLU* 4.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1515A GLN 3.0 13.6 + - - +
1516A TYR* 2.8 27.1 - - - +
1517A GLN 3.4 0.2 - - - -
1518A SER* 1.3 81.2 - - - +
1520A GLU* 1.3 62.9 + - - +
1521A THR* 2.5 55.2 + - - +
1522A LEU* 3.8 26.9 - - + +
----------------------------------------------------------
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