Contacts of the helix formed by residues 1483 - 1499 (chain G) in PDB entry 6BAA
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 SER1483 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1481G ASN 4.2 0.4 + - - -
1482G PHE* 1.3 76.3 - - - +
1484G GLN* 1.3 56.0 + - - +
1485G GLY* 3.2 6.1 + - - -
1486G GLN* 2.6 33.5 + - - +
1487G ARG* 2.7 35.0 + - - +
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Residues in contact with GLN1484 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1427G GLN 5.1 0.3 - - - +
1429G PRO* 4.5 6.8 - - + +
1483G SER* 1.3 73.8 - - - +
1485G GLY* 1.3 57.1 + - - +
1487G ARG* 3.5 6.9 + - - +
1488G GLN* 2.9 27.0 + - - +
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Residues in contact with GLY1485 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1483G SER* 3.2 5.8 + - - -
1484G GLN* 1.3 78.4 - - - +
1486G GLN* 1.3 58.8 + - - +
1488G GLN* 3.1 9.2 + - - +
1489G LEU* 2.8 27.2 + - - +
1512G ILE* 5.4 12.9 - - - +
1516G THR* 5.6 7.6 - - - -
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Residues in contact with GLN1486 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482G PHE* 3.7 12.8 - - + -
1483G SER* 2.6 34.6 + - - +
1485G GLY* 1.3 70.6 - - - +
1487G ARG* 1.3 58.5 + - - +
1489G LEU* 3.3 9.6 + - - +
1490G PHE* 2.9 26.2 + - - +
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Residues in contact with ARG1487 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429G PRO* 3.3 27.6 - - + +
1431G LEU* 5.5 9.6 - - + -
1479G GLY* 5.3 4.7 - - - +
1482G PHE* 4.1 8.8 - - + +
1483G SER 2.7 21.8 + - - +
1484G GLN* 3.6 8.3 - - - +
1486G GLN* 1.3 70.7 - - - +
1488G GLN* 1.3 59.1 + - - +
1490G PHE* 3.2 10.2 + - - +
1491G CYS* 2.9 24.3 + - - +
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Residues in contact with GLN1488 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1426G LEU 5.5 0.9 - - - -
1427G GLN* 4.1 19.1 - - - +
1429G PRO* 3.5 9.8 - - - +
1484G GLN 2.9 16.4 + - - +
1485G GLY* 3.1 13.0 + - - +
1487G ARG* 1.3 72.1 - - - +
1489G LEU* 1.3 60.7 + - - +
1491G CYS* 3.3 4.8 + - - +
1492G LEU* 2.8 28.1 + - - +
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Residues in contact with LEU1489 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458G ALA* 3.4 28.5 - - - +
1459G GLN 5.6 0.9 - - - -
1460G LEU* 4.5 11.4 - - + +
1485G GLY 2.8 13.1 + - - +
1486G GLN* 3.4 12.8 - - - +
1488G GLN* 1.3 73.9 - - - +
1490G PHE* 1.3 58.6 + - - +
1492G LEU* 3.2 6.4 + - - -
1493G ALA* 2.9 26.7 + - - +
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Residues in contact with PHE1490 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1439G ASN* 5.7 5.9 - - + +
1460G LEU* 5.3 0.8 - - - +
1486G GLN 2.9 14.2 + - - +
1487G ARG* 3.3 13.0 - - - +
1489G LEU* 1.3 75.1 - - - +
1491G CYS* 1.3 57.7 + - - +
1493G ALA* 3.3 7.8 + - - +
1494G ARG* 2.9 27.9 + - - +
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Residues in contact with CYS1491 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425G ILE* 3.7 16.8 - - + +
1426G LEU 4.6 7.0 - - - +
1429G PRO* 3.7 23.1 - - + -
1487G ARG 2.9 14.0 + - - +
1488G GLN* 3.5 9.0 - - - +
1490G PHE* 1.3 73.2 - - - +
1492G LEU* 1.3 60.7 + - - +
1494G ARG* 3.3 8.8 + - - +
1495G ALA* 2.9 27.9 + - - +
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Residues in contact with LEU1492 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425G ILE* 4.7 4.5 - - - +
1458G ALA* 3.7 13.7 - - + -
1488G GLN 2.8 14.1 + - - +
1489G LEU* 3.2 11.9 + - - +
1491G CYS* 1.3 77.2 - - - +
1493G ALA* 1.3 56.6 + - - +
1495G ALA* 3.3 8.2 + - - +
1496G PHE* 2.8 28.4 + - - +
1523G VAL* 5.7 9.6 - - + -
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Residues in contact with ALA1493 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1440G LEU* 6.3 3.1 - - + -
1451G LEU 5.3 0.7 - - - +
1454G ALA* 3.3 42.1 - - + +
1455G LEU* 3.8 10.1 - - + +
1458G ALA* 3.4 5.0 - - + +
1460G LEU* 5.7 1.6 - - + -
1489G LEU 2.9 13.8 + - - +
1490G PHE* 3.6 10.3 - - - +
1492G LEU* 1.3 77.1 - - - +
1494G ARG* 1.3 57.9 + - - +
1496G PHE* 3.3 1.3 + - - -
1497G VAL* 2.8 28.1 + - - +
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Residues in contact with ARG1494 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1439G ASN 5.2 3.6 - - - +
1440G LEU* 5.8 5.6 - - - +
1442G PRO* 4.3 28.0 - - + +
1490G PHE 2.9 14.4 + - - +
1491G CYS* 3.5 12.3 - - - +
1493G ALA* 1.3 75.5 - - - +
1495G ALA* 1.3 57.0 + - - +
1497G VAL* 3.6 6.7 + - - +
1498G ARG* 3.0 28.2 + - - +
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Residues in contact with ALA1495 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1423G SER* 4.8 9.0 - - - -
1424G ILE 5.3 2.5 - - - -
1425G ILE* 3.7 24.5 - - + +
1491G CYS 2.9 14.4 + - - +
1492G LEU* 3.5 8.7 - - - +
1494G ARG* 1.3 74.4 - - - +
1496G PHE* 1.3 60.3 + - - +
1498G ARG* 3.1 7.7 + - - +
1499G LYS* 2.9 24.3 + - - -
1500G THR* 4.0 7.0 + - - -
1531G ARG* 5.6 0.7 + - - -
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Residues in contact with PHE1496 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453G GLU* 4.5 7.0 - - + -
1454G ALA* 3.6 25.1 - - + -
1457G ILE* 3.6 29.6 - - + -
1458G ALA* 5.7 0.7 - - + +
1492G LEU 2.8 19.9 + - - +
1493G ALA* 3.3 8.0 + - - +
1495G ALA* 1.3 72.6 - - - +
1497G VAL* 1.3 62.8 + - - +
1499G LYS* 3.1 18.7 + - - +
1531G ARG* 4.7 20.3 + - - +
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Residues in contact with VAL1497 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1440G LEU* 5.4 7.2 - - + +
1443G GLU* 5.9 4.1 - - + +
1450G THR* 4.7 11.0 - - - +
1451G LEU* 5.3 3.4 - - - -
1454G ALA* 3.7 16.3 - - + +
1493G ALA 2.8 17.5 + - - +
1494G ARG* 3.9 6.7 - - - +
1496G PHE* 1.3 76.6 - - - +
1498G ARG* 1.3 61.5 + - - +
1499G LYS* 3.4 4.0 + - - +
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Residues in contact with ARG1498 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1423G SER* 3.7 24.5 - - - -
1443G GLU* 5.7 10.5 - - + -
1494G ARG 3.0 19.0 + - - +
1495G ALA 3.1 5.5 + - - +
1497G VAL* 1.3 78.1 - - - +
1499G LYS* 1.3 68.0 + - - +
1500G THR* 3.3 2.7 + - - -
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Residues in contact with LYS1499 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1495G ALA 2.9 6.7 + - - -
1496G PHE 3.1 14.5 + - - +
1497G VAL 4.3 4.0 - - - +
1498G ARG* 1.3 78.4 - - - +
1500G THR* 1.3 66.9 + - - +
1501G SER 3.7 0.3 + - - -
1531G ARG* 3.5 20.8 + - - +
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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