Contacts of the helix formed by residues 1525 - 1538 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477B ALA* 3.6 13.9 - - + +
1524B ASP* 1.3 73.6 - - - +
1526B VAL* 1.3 69.3 + - - +
1527B THR* 3.6 11.2 - - - +
1528B GLN* 3.0 20.2 + - - -
1529B VAL* 2.9 20.8 + - - +
1568B ASP* 3.6 31.0 - - + -
1582B LEU* 4.6 9.4 - - + +
1583B ASN 3.9 9.2 - - - +
1584B THR* 4.2 0.7 - - - +
1653B HIS* 2.8 37.5 + - - -
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Residues in contact with VAL1526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524B ASP 3.7 0.6 + - - -
1525B THR* 1.3 75.1 - - - +
1527B THR* 1.3 62.2 + - - +
1529B VAL* 3.6 8.3 + - - +
1530B LYS* 3.2 32.6 + - - +
1554B LEU* 3.9 22.8 - - + +
1566B LEU* 3.2 38.6 - - + +
1567B GLN* 3.6 24.7 - - - +
1568B ASP 3.7 9.6 - - - +
1583B ASN* 3.2 20.5 + - + +
1584B THR 4.3 6.3 - - - +
1588B TYR* 4.9 0.7 - - + -
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Residues in contact with THR1527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1525B THR* 3.0 8.5 - - - +
1526B VAL* 1.3 76.0 - - - +
1528B GLN* 1.3 67.2 + - + +
1530B LYS* 3.2 23.9 + - - +
1531B GLU* 3.1 26.2 + - + +
1549B ALA* 4.9 10.0 - - + +
1550B GLY* 6.5 0.4 - - - -
1568B ASP* 3.7 19.9 + - - +
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Residues in contact with GLN1528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475B ILE* 2.7 46.0 + - - +
1477B ALA* 3.4 24.8 - - + +
1524B ASP* 3.4 19.0 - - + +
1525B THR* 3.0 36.0 + - - +
1527B THR* 1.3 79.8 - - + +
1529B VAL* 1.3 63.0 + - - +
1531B GLU* 3.3 9.7 + - - +
1532B LYS* 3.1 31.1 + - - +
1653B HIS* 3.6 2.6 - - - -
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Residues in contact with VAL1529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1518B VAL* 5.6 0.8 - - + +
1521B LEU 5.6 2.0 - - - +
1524B ASP* 3.5 26.9 - - + +
1525B THR 2.9 17.6 + - - +
1526B VAL* 3.8 7.9 - - - +
1528B GLN* 1.3 77.2 - - - +
1530B LYS* 1.3 56.5 + - - +
1532B LYS* 3.0 11.0 + - + +
1533B LEU* 2.8 28.9 + - + +
1554B LEU* 4.1 22.9 - - + -
1585B LEU* 5.1 8.7 - - + -
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Residues in contact with LYS1530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1526B VAL* 3.2 26.6 + - - +
1527B THR* 3.5 24.5 + - - +
1529B VAL* 1.3 77.4 - - - +
1531B GLU* 1.3 56.4 + - - +
1533B LEU* 3.1 9.0 + - - +
1534B LEU* 2.8 35.8 + - + +
1549B ALA* 3.2 35.4 + - + +
1550B GLY* 4.4 4.8 - - - -
1552B MET* 4.1 17.6 + - + +
1553B ASP* 4.8 1.2 - - - +
1554B LEU* 3.9 38.8 - - + +
1566B LEU 5.7 0.4 + - - -
1567B GLN* 6.2 0.6 - - - +
1568B ASP 6.1 0.4 - - - +
1598B LEU* 6.0 4.0 - - + -
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Residues in contact with GLU1531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1467B LYS* 5.5 0.9 + - - -
1471B GLU* 5.5 3.1 - - - +
1527B THR* 3.1 20.7 + - + +
1528B GLN* 3.5 12.3 - - - +
1530B LYS* 1.3 75.6 - - - +
1532B LYS* 1.3 58.5 + - + +
1534B LEU* 3.3 8.4 + - - +
1535B ASP* 3.0 52.0 + - - +
1543B TYR* 4.8 12.5 + - - -
1549B ALA* 3.8 22.4 + - + +
1762B HIS* 4.0 28.6 + - + +
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Residues in contact with LYS1532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471B GLU* 3.4 61.9 + - - +
1473B GLY 5.6 0.6 + - - -
1475B ILE* 6.2 1.1 - - - -
1518B VAL* 3.3 25.2 - - + +
1519B LYS 4.2 12.8 - - - +
1520B GLY* 4.1 13.1 - - - -
1521B LEU* 4.2 2.8 - - - +
1524B ASP* 2.7 35.4 + - - +
1528B GLN* 3.1 18.1 + - - +
1529B VAL* 3.0 12.4 + - + +
1531B GLU* 1.3 76.5 - - + +
1533B LEU* 1.3 61.2 + - - +
1535B ASP* 3.9 5.9 + - - +
1536B ALA* 3.3 15.1 + - - +
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Residues in contact with LEU1533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505B CYS* 4.6 20.6 - - + -
1518B VAL* 4.3 11.2 - - + +
1529B VAL* 2.8 15.7 + - + +
1530B LYS* 3.1 12.3 + - - +
1532B LYS* 1.3 76.5 - - - +
1534B LEU* 1.3 56.3 + - + +
1536B ALA* 3.7 0.6 - - - +
1537B VAL* 2.8 41.3 + - - +
1554B LEU* 5.9 6.1 - - + -
1598B LEU* 6.0 5.8 - - + -
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Residues in contact with LEU1534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1530B LYS* 2.8 16.8 + - + +
1531B GLU* 3.8 9.9 - - - +
1533B LEU* 1.3 74.3 - - + +
1535B ASP* 1.3 63.4 + - - +
1536B ALA 3.1 4.5 - - - -
1537B VAL* 5.9 0.2 - - + -
1538B TYR* 2.8 65.9 + - + +
1543B TYR* 6.2 4.0 - - + -
1546B ARG* 4.1 13.2 - - + -
1547B PRO* 3.4 29.8 - - + +
1548B LYS* 4.4 0.7 - - - +
1549B ALA* 3.7 31.0 - - + +
1552B MET* 5.1 12.3 - - + -
1598B LEU* 6.1 4.3 - - + -
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Residues in contact with ASP1535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1308B LEU* 4.3 11.0 - - + +
1467B LYS* 3.4 32.2 + - - -
1468B GLN* 5.9 2.9 - - - +
1471B GLU* 4.2 7.8 - - - +
1531B GLU* 3.0 33.1 + - - +
1532B LYS* 4.3 4.4 - - - +
1533B LEU 3.4 0.2 - - - -
1534B LEU* 1.3 80.1 - - - +
1536B ALA* 1.3 58.5 + - - +
1539B LYS* 3.6 18.5 - - - +
1543B TYR* 5.5 1.4 - - - -
1546B ARG* 3.8 24.9 + - - +
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Residues in contact with ALA1536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1308B LEU* 6.0 0.4 - - - -
1516B VAL* 5.3 6.0 - - + +
1517B PRO 4.8 3.4 - - - +
1518B VAL* 3.4 31.4 - - + -
1532B LYS 3.3 17.8 + - - +
1533B LEU 3.3 1.2 + - - +
1534B LEU 3.1 0.2 - - - -
1535B ASP* 1.3 80.5 - - - +
1537B VAL* 1.3 65.1 + - - +
1538B TYR 3.4 0.2 - - - -
1539B LYS* 3.6 16.0 + - - +
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Residues in contact with VAL1537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505B CYS* 3.5 32.1 - - + -
1506B VAL 4.3 0.7 - - - +
1507B ASN* 4.5 7.4 - - + -
1508B PRO* 3.5 28.5 - - + -
1516B VAL* 4.1 19.5 - - + -
1518B VAL* 5.1 0.2 - - + -
1533B LEU* 2.8 25.7 + - - +
1536B ALA* 1.3 75.2 - - + +
1538B TYR* 1.3 74.9 + - + +
1539B LYS* 3.3 2.8 + - - +
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Residues in contact with TYR1538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508B PRO* 4.1 26.7 + - + +
1534B LEU* 2.8 46.9 + - + +
1535B ASP 4.3 0.4 - - - -
1537B VAL* 1.3 93.7 - - + +
1539B LYS* 1.3 64.3 + - - +
1540B GLY 3.3 3.4 - - - +
1541B VAL* 3.2 33.0 - - + +
1545B GLN 5.6 0.9 - - - -
1546B ARG* 3.0 40.6 + - + +
1547B PRO* 4.0 28.0 - - + +
1552B MET* 5.9 3.3 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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