Contacts of the helix formed by residues 1525 - 1538 (chain A) in PDB entry 3RYT
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 THR1525 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477A ALA* 3.5 12.6 - - + +
1523A CYS 3.5 1.6 + - - -
1524A ASP* 1.3 75.6 - - - +
1526A VAL* 1.3 69.0 + - - +
1527A THR* 3.4 21.5 - - - +
1528A GLN* 2.9 37.2 + - - -
1529A VAL* 3.0 12.9 + - - +
1568A ASP* 4.2 10.8 - - + -
1582A LEU* 4.6 10.8 - - + +
1583A ASN 3.9 14.4 - - - +
1584A THR* 4.6 0.2 - - - -
1653A HIS* 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524A ASP 3.8 0.6 + - - -
1525A THR* 1.3 75.3 - - - +
1527A THR* 1.3 56.6 + - - +
1529A VAL* 3.8 6.7 + - - +
1530A LYS* 3.1 37.2 + - - +
1554A LEU* 4.0 23.7 - - + +
1566A LEU* 3.2 29.6 - - + +
1567A GLN 4.0 16.2 - - - +
1568A ASP* 3.8 16.6 - - + +
1583A ASN 3.6 13.8 + - - +
1584A THR* 5.1 2.9 - - - +
1588A TYR* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1525A THR* 3.0 10.5 - - - +
1526A VAL* 1.3 77.6 - - - +
1528A GLN* 1.3 64.2 + - - +
1530A LYS* 3.6 20.3 + - - +
1531A GLU* 3.4 24.5 + - + +
1549A ALA* 4.7 10.0 - - + +
1568A ASP* 3.6 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475A ILE* 2.8 39.8 + - - +
1477A ALA* 3.3 12.5 - - + +
1524A ASP* 3.1 23.3 - - + +
1525A THR* 2.9 29.4 + - - +
1527A THR* 1.3 78.2 - - - +
1529A VAL* 1.3 61.5 + - - +
1531A GLU* 3.0 19.2 + - - +
1532A LYS* 3.0 22.8 + - - +
1653A HIS* 2.9 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1503A LEU* 5.1 10.5 - - + -
1521A LEU 5.1 5.4 - - - +
1524A ASP* 3.6 27.8 - - + +
1525A THR 3.0 14.5 + - - +
1526A VAL* 4.1 4.9 - - - +
1528A GLN* 1.3 71.9 - - - +
1530A LYS* 1.3 57.5 + - - +
1531A GLU 2.9 4.9 - - - -
1532A LYS* 2.8 30.5 + - + +
1533A LEU* 2.8 40.1 + - + +
1554A LEU* 4.1 17.7 - - + -
1585A LEU* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1526A VAL* 3.1 33.1 + - + +
1527A THR* 3.7 24.6 + - - +
1528A GLN 3.4 0.2 - - - -
1529A VAL* 1.3 77.2 - - - +
1531A GLU* 1.3 56.8 + - - +
1533A LEU* 4.5 1.9 - - - +
1534A LEU* 3.2 35.7 + - + +
1549A ALA* 3.6 20.7 + - + +
1550A GLY* 5.1 3.6 + - - -
1552A MET* 3.3 29.7 + - + +
1553A ASP* 4.6 4.9 + - - +
1554A LEU* 3.9 31.4 - - + +
1567A GLN* 5.1 5.9 - - - +
1568A ASP* 5.5 3.6 - - - +
1598A LEU* 4.2 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1471A GLU* 6.1 0.9 - - - +
1527A THR* 3.4 15.7 + - + +
1528A GLN* 3.0 15.0 + - - +
1529A VAL 2.9 0.8 - - - -
1530A LYS* 1.3 76.1 - - - +
1532A LYS* 1.3 64.7 + - + +
1534A LEU* 3.3 6.5 + - - +
1535A ASP* 3.0 43.9 + - - +
1543A TYR* 4.7 15.0 + - - -
1549A ALA* 4.2 18.9 + - + +
1762A HIS* 4.6 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1471A GLU* 3.7 50.9 + - + +
1518A VAL* 4.1 16.4 - - + +
1519A LYS 4.5 13.5 - - - +
1520A GLY* 4.4 4.5 - - - -
1521A LEU* 4.4 17.8 - - - +
1524A ASP* 3.7 27.1 - - - +
1528A GLN* 3.0 19.1 + - - +
1529A VAL* 2.8 15.3 + - + +
1531A GLU* 1.3 75.6 - - - +
1533A LEU* 1.3 64.5 + - + +
1535A ASP* 3.0 10.0 + - - +
1536A ALA* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1503A LEU* 5.2 11.0 - - + -
1505A CYS* 4.5 11.7 - - + -
1518A VAL* 3.7 37.0 - - + -
1529A VAL* 2.8 36.3 + - + +
1530A LYS 4.5 1.3 - - - +
1532A LYS* 1.3 72.1 - - + +
1534A LEU* 1.3 55.9 + - - +
1537A VAL* 2.7 45.6 + - + +
1554A LEU* 3.6 31.4 - - + -
1596A VAL* 3.8 14.8 - - + -
1598A LEU* 4.2 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1530A LYS* 3.2 24.2 + - + +
1531A GLU* 3.3 9.7 + - - +
1533A LEU* 1.3 78.8 - - - +
1535A ASP* 1.3 60.7 + - - +
1538A TYR* 3.3 49.2 + - + +
1546A ARG* 3.3 22.6 - - + -
1547A PRO* 3.1 37.0 - - + +
1548A LYS 4.0 0.9 - - - +
1549A ALA* 3.6 25.1 - - + +
1552A MET* 4.5 8.7 - - + -
1598A LEU* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467A LYS* 3.4 32.2 + - - -
1468A GLN* 5.8 3.6 - - - +
1471A GLU* 4.6 6.9 - - - +
1531A GLU* 3.0 31.5 + - - +
1532A LYS* 3.0 9.6 + - - +
1534A LEU* 1.3 80.4 - - - +
1536A ALA* 1.3 61.6 + - - +
1538A TYR 3.8 1.0 - - - +
1539A LYS* 3.5 23.4 + - - +
1543A TYR* 5.3 1.6 - - - -
1546A ARG* 3.3 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1516A VAL* 4.2 12.4 - - + +
1517A PRO 4.7 2.2 - - - +
1518A VAL* 3.6 35.7 - - + -
1532A LYS 3.0 11.1 + - - +
1533A LEU 3.9 0.4 - - - +
1535A ASP* 1.3 76.4 - - - +
1537A VAL* 1.3 64.2 + - - +
1539A LYS* 3.1 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505A CYS* 3.8 21.1 - - + -
1507A ASN* 3.4 26.0 + - - +
1508A PRO* 3.4 26.9 - - + -
1509A GLU* 5.6 0.2 - - + -
1516A VAL* 3.8 28.3 - - + -
1518A VAL* 5.3 0.2 - - + -
1533A LEU* 2.7 27.9 + - + +
1534A LEU* 4.8 0.4 - - - -
1536A ALA* 1.3 75.2 - - + +
1538A TYR* 1.3 75.8 - - + +
1539A LYS 3.5 3.1 + - - -
1598A LEU* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508A PRO* 4.3 11.9 - - + +
1509A GLU* 4.1 33.3 + - + +
1534A LEU* 3.3 38.9 + - + +
1535A ASP 3.8 4.7 - - - -
1537A VAL* 1.3 93.4 - - + +
1539A LYS* 1.3 61.9 + - - +
1540A GLY 3.5 1.8 - - - +
1541A VAL* 3.1 37.0 - - + +
1546A ARG* 2.9 41.2 + - + +
1547A PRO* 3.8 25.7 - - + +
1552A MET* 5.8 1.6 - - + +
----------------------------------------------------------
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