Contacts of the helix formed by residues 1475 - 1488 (chain A) in PDB entry 6J8J
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 THR1475 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1305A GLU* 3.4 30.0 - - + +
1306A GLY* 3.4 35.0 - - - +
1309A VAL* 4.7 6.7 - - + -
1474A MET* 1.3 77.1 - - - +
1476A GLU* 1.3 66.3 + - - +
1477A GLU* 4.0 5.9 + - - +
1478A GLN* 2.3 53.6 + - - +
1479A LYS* 3.1 9.0 + - - +
1646A ASN* 4.7 0.4 - - - +
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Residues in contact with GLU1476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1470A GLN* 5.4 1.2 - - - +
1474A MET 3.9 0.4 + - - +
1475A THR* 1.3 71.9 - - - +
1477A GLU* 1.3 63.2 + - - +
1479A LYS* 3.2 46.1 + - - +
1480A LYS* 3.5 20.4 + - - +
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Residues in contact with GLU1477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475A THR* 3.1 6.1 + - - +
1476A GLU* 1.3 79.2 - - - +
1478A GLN* 1.3 62.9 + - - +
1480A LYS* 3.2 34.1 + - - +
1481A TYR* 3.4 35.9 + - + -
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Residues in contact with GLN1478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1305A GLU* 5.4 0.3 - - - +
1474A MET* 3.9 10.8 - - + +
1475A THR* 2.3 51.8 + - - +
1477A GLU* 1.3 78.2 - - - +
1479A LYS* 1.3 58.4 + - - +
1481A TYR* 3.2 9.4 + - + +
1482A TYR* 2.9 28.7 + - - +
1642A PRO* 3.2 33.1 + - + +
1645A PHE* 4.5 8.1 - - - -
1646A ASN* 2.8 37.0 + - - +
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Residues in contact with LYS1479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1467A LEU* 5.5 2.2 - - - +
1470A GLN* 4.1 36.3 - - + +
1471A ASP* 3.8 21.9 + - + +
1474A MET* 3.8 36.4 + - + +
1475A THR 3.1 6.7 + - - +
1476A GLU* 3.4 40.3 + - - +
1477A GLU 3.1 0.2 - - - -
1478A GLN* 1.3 78.2 - - - +
1480A LYS* 1.3 64.1 + - - +
1482A TYR* 3.3 11.0 + - + +
1483A ASN* 3.2 30.1 + - - +
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Residues in contact with LYS1480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476A GLU* 3.7 24.0 + - - +
1477A GLU* 3.2 25.0 + - - +
1479A LYS* 1.3 79.2 - - - +
1481A TYR* 1.3 69.3 + - + +
1483A ASN* 3.3 18.1 + - - +
1484A ALA* 3.4 10.7 + - - +
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Residues in contact with TYR1481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477A GLU* 3.4 35.2 + - + +
1478A GLN* 3.2 12.6 + - + +
1480A LYS* 1.3 81.1 - - + +
1482A TYR* 1.3 64.5 + - - +
1484A ALA* 3.2 17.4 + - + +
1485A MET* 3.3 24.4 + - + +
1642A PRO* 6.1 1.6 - - + -
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Residues in contact with TYR1482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471A ASP* 6.0 2.7 - - + -
1474A MET* 3.2 34.3 - - + -
1478A GLN 2.9 12.7 + - - +
1479A LYS* 3.3 14.6 + - + +
1481A TYR* 1.3 76.0 - - - +
1483A ASN* 1.3 75.0 + - - +
1485A MET* 3.3 13.8 + - - +
1486A LYS* 3.2 41.5 + - + +
1639A MET* 3.6 34.1 - - + +
1642A PRO* 5.1 1.8 - - + -
1760A LEU* 5.7 1.9 - - - +
1761A GLU* 2.8 29.5 + - - -
1764A SER* 4.6 12.0 + - - -
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Residues in contact with ASN1483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479A LYS* 3.2 16.5 + - - +
1480A LYS* 3.5 11.4 + - - +
1481A TYR 3.2 0.4 - - - -
1482A TYR* 1.3 87.6 - - - +
1484A ALA* 1.3 63.1 + - - +
1486A LYS* 3.1 32.3 + - - +
1487A LYS* 3.3 20.7 + - - +
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Residues in contact with ALA1484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1480A LYS 3.4 7.3 + - - +
1481A TYR* 3.2 13.9 + - + +
1483A ASN* 1.3 78.6 - - - +
1485A MET* 1.3 63.2 + - + +
1487A LYS* 3.1 26.0 + - - +
1488A LEU* 3.8 8.4 + - - +
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Residues in contact with MET1485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1481A TYR* 3.3 20.1 + - + +
1482A TYR* 3.6 10.1 - - - +
1483A ASN 3.2 0.2 - - - -
1484A ALA* 1.3 74.6 - - + +
1486A LYS* 1.3 65.3 + - - +
1488A LEU* 3.1 30.7 + - + +
1635A PHE* 3.6 10.4 - - - -
1638A MET* 4.0 22.7 - - + +
1639A MET* 2.8 38.1 - - + +
1641A LEU* 5.9 0.4 - - + -
1642A PRO* 3.5 37.0 - - + -
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Residues in contact with LYS1486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482A TYR* 3.2 35.8 + - + +
1483A ASN* 3.1 28.3 + - - +
1485A MET* 1.3 80.5 - - - +
1487A LYS* 1.3 66.4 + - - +
1489A GLY* 3.2 14.7 + - - -
1490A SER 4.5 0.9 + - - -
1635A PHE* 5.2 2.4 - - - -
1639A MET* 4.2 8.2 - - - -
1764A SER* 5.2 9.0 - - - +
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Residues in contact with LYS1487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1483A ASN* 3.3 23.6 + - - +
1484A ALA* 3.1 16.9 + - - +
1486A LYS* 1.3 88.0 - - - +
1488A LEU* 1.3 63.3 + - + +
1489A GLY 3.0 1.3 + - - -
1490A SER* 3.2 24.8 + - - +
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Residues in contact with LEU1488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1484A ALA 3.8 7.4 + - - +
1485A MET* 3.1 24.4 + - + +
1487A LYS* 1.3 79.6 - - + +
1489A GLY* 1.3 60.1 + - - +
1490A SER 3.2 8.3 + - - +
1635A PHE* 4.0 13.2 - - + -
1638A MET* 4.9 15.7 - - + -
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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