Contacts of the helix formed by residues 1482 - 1496 (chain G) in PDB entry 6C3P
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 SER1482 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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716G GLY* 3.8 4.0 - - - -
774G GLN* 5.2 1.8 - - - -
1481G PHE* 1.3 78.0 - - - +
1483G GLN* 1.3 68.4 + - - +
1484G GLY 3.3 0.2 - - - -
1485G GLN* 3.1 15.9 + - - +
1486G ARG* 2.9 24.5 + - - +
2002G MG 4.5 0.2 - - - -
2004G ATP 2.3 70.5 + - - -
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Residues in contact with GLN1483 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774G GLN* 3.4 42.8 - - + +
775G LYS* 3.1 42.9 - - - +
854G ASP* 5.4 0.2 - - - +
888G HIS* 6.0 1.3 - - - +
1428G PRO* 4.0 18.3 - - - +
1482G SER* 1.3 75.2 - - - +
1484G GLY* 1.3 59.6 + - - +
1486G ARG* 2.9 35.0 + - - +
1487G GLN* 2.9 27.5 + - - +
1510G SER* 4.6 12.6 + - - +
2004G ATP 4.0 1.7 + - - +
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Residues in contact with GLY1484 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715G VAL* 3.5 23.5 - - - +
1482G SER 3.3 0.2 - - - -
1483G GLN* 1.3 76.0 - - - +
1485G GLN* 1.3 59.8 + - - +
1487G GLN* 3.3 6.4 + - - +
1488G LEU* 2.9 37.5 + - - +
1510G SER* 4.2 17.2 - - - -
2004G ATP 3.6 7.9 + - - -
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Residues in contact with GLN1485 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715G VAL* 3.3 34.4 + - - +
716G GLY* 3.4 10.3 - - - -
1459G LEU* 4.4 15.3 - - - +
1462G VAL* 4.4 21.9 - - - +
1481G PHE* 3.5 23.7 - - + -
1482G SER* 3.1 36.0 + - - +
1484G GLY* 1.3 75.3 - - - +
1486G ARG* 1.3 58.1 + - - +
1488G LEU* 3.1 9.5 + - - +
1489G PHE* 2.9 36.3 + - + -
2004G ATP 5.1 5.5 + - - +
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Residues in contact with ARG1486 (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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775G LYS* 5.0 5.8 - - - +
1428G PRO* 3.6 15.9 + - + +
1430G LEU* 3.5 24.1 - - + +
1477G GLY 3.5 20.8 + - - -
1478G GLY* 2.5 31.3 + - - +
1479G GLU* 4.5 7.5 + - - +
1481G PHE* 2.3 41.2 + - + +
1482G SER 2.9 11.8 + - - +
1483G GLN* 2.9 49.0 + - - +
1485G GLN* 1.3 72.3 - - - +
1487G GLN* 1.3 66.5 + - - +
1489G PHE* 3.2 11.2 + - + +
1490G CYS* 3.0 26.3 + - - -
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Residues in contact with GLN1487 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424G ILE* 3.6 7.1 - - - +
1425G LEU 3.3 20.4 + - - -
1426G GLN 2.9 19.9 + - - +
1428G PRO* 3.2 26.9 - - + +
1483G GLN 2.9 12.8 + - - +
1484G GLY* 3.6 7.9 - - - +
1485G GLN 3.3 0.2 - - - -
1486G ARG* 1.3 75.8 - - - +
1488G LEU* 1.3 57.1 + - - +
1490G CYS* 3.1 6.1 + - - +
1491G LEU* 2.9 54.1 + - + +
1507G ALA* 3.3 28.2 + - - +
1510G SER* 4.2 15.6 + - - -
1511G ILE* 3.6 11.0 - - + -
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Residues in contact with LEU1488 (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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715G VAL* 5.1 7.6 - - + -
1457G ALA* 2.9 31.6 - - + +
1458G GLN 5.7 0.9 - - - +
1459G LEU* 3.4 22.5 - - + +
1484G GLY* 2.9 27.6 + - - +
1485G GLN* 3.3 11.9 - - - +
1487G GLN* 1.3 76.6 - - - +
1489G PHE* 1.3 63.5 + - - +
1491G LEU* 3.2 7.4 + - + +
1492G ALA* 2.9 24.8 + - - +
1511G ILE* 3.5 31.4 - - + -
1515G THR* 4.9 10.5 - - + -
1519G LEU* 3.4 22.4 - - + -
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Residues in contact with PHE1489 (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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1430G LEU* 4.3 19.5 - - + -
1435G ILE* 4.1 24.9 - - + -
1438G ASN* 6.5 0.2 - - + -
1439G LEU* 4.3 8.8 - - + +
1454G LEU* 5.3 7.2 - - + -
1459G LEU* 4.1 23.3 - - + -
1462G VAL* 6.4 1.6 - - + -
1463G VAL* 5.2 9.9 - - + -
1466G LEU* 6.0 0.9 - - + -
1474G ILE* 4.9 4.9 - - + -
1481G PHE* 3.8 46.2 - + + -
1485G GLN* 2.9 40.4 + - + -
1486G ARG* 3.2 12.3 + - - +
1488G LEU* 1.3 76.3 - - - +
1490G CYS* 1.3 57.9 + - - +
1492G ALA* 3.3 6.3 + - + +
1493G ARG* 2.9 32.3 + - - +
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Residues in contact with CYS1490 (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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512G TYR* 4.7 3.0 + - - +
1424G ILE* 4.5 7.4 - - + +
1425G LEU* 5.7 2.9 - - + +
1427G ASP 4.8 2.5 - - - +
1428G PRO* 3.6 8.1 - - + -
1429G VAL 3.4 41.3 - - - -
1430G LEU* 4.1 3.1 - - - -
1486G ARG 3.0 18.1 + - - -
1487G GLN* 3.4 15.5 - - - +
1489G PHE* 1.3 73.4 - - - +
1491G LEU* 1.3 66.0 + - - +
1493G ARG* 3.2 26.6 + - - +
1494G ALA* 3.0 23.6 + - - +
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Residues in contact with LEU1491 (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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1424G ILE* 3.6 22.0 - - + -
1457G ALA* 5.1 0.4 - - + -
1487G GLN* 2.9 56.3 + - + +
1488G LEU* 3.4 12.6 - - + +
1490G CYS* 1.3 77.2 - - - +
1492G ALA* 1.3 57.4 + - - +
1494G ALA* 3.2 2.6 + - - +
1495G PHE* 2.9 46.2 + - + -
1504G MET* 5.7 2.2 - - - -
1507G ALA* 3.6 18.8 - - + +
1508G THR* 6.3 0.2 - - - -
1511G ILE* 4.9 7.2 - - + -
1519G LEU* 3.6 42.4 - - + -
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Residues in contact with ALA1492 (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 LEU* 4.6 8.3 - - + -
1453G ALA* 3.9 24.0 - - + +
1454G LEU* 4.7 9.9 - - + +
1457G ALA* 3.9 7.2 - - + +
1459G LEU* 5.0 2.7 - - + -
1488G LEU 2.9 16.9 + - - +
1489G PHE* 3.6 7.4 - - + +
1491G LEU* 1.3 76.2 - - - +
1493G ARG* 1.3 58.0 + - - +
1495G PHE* 2.8 30.6 + - - +
1496G VAL* 2.8 18.5 + - - +
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Residues in contact with ARG1493 (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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508G LEU* 3.2 32.1 - - - +
512G TYR* 3.9 22.7 + - + -
514G TRP* 3.4 36.7 - - + -
1425G LEU* 6.4 0.4 - - - +
1429G VAL 3.6 14.1 + - - -
1430G LEU* 4.9 4.8 - - - +
1431G PHE* 4.4 9.2 - - - -
1438G ASN* 3.4 26.0 + - - +
1439G LEU* 3.5 22.3 - - + +
1489G PHE* 2.9 19.1 + - - +
1490G CYS* 3.2 34.7 + - - +
1492G ALA* 1.3 75.4 - - - +
1494G ALA* 1.3 62.1 + - - +
1496G VAL* 3.1 18.6 + - - +
1497G ARG* 4.2 5.2 + - - +
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Residues in contact with ALA1494 (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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512G TYR* 4.4 11.6 - - + +
1422G SER* 4.2 13.2 + - - -
1423G ILE 3.9 14.8 - - - +
1424G ILE* 3.5 28.9 - - + -
1490G CYS 3.0 9.0 + - - +
1491G LEU 3.4 8.3 - - - +
1493G ARG* 1.3 75.9 - - - +
1495G PHE* 1.3 65.2 + - + +
1496G VAL 3.1 1.4 + - - -
1497G ARG* 3.1 23.5 + - - +
1499G THR* 5.1 0.5 + - - -
1502G PHE* 5.7 5.3 - - + -
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Residues in contact with PHE1495 (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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1424G ILE* 3.8 7.4 - - + -
1453G ALA* 4.4 7.0 - - + +
1456G ILE* 3.4 35.7 - - + -
1457G ALA* 4.2 9.4 - - + -
1491G LEU* 2.9 52.4 + - + -
1492G ALA* 2.8 18.7 + - - +
1494G ALA* 1.3 71.9 - - + +
1496G VAL* 1.3 64.2 + - - +
1497G ARG 3.1 9.7 + - - +
1502G PHE* 4.3 6.1 - + - -
1504G MET* 3.6 32.5 - - + -
1519G LEU* 5.0 5.8 - - + -
1523G VAL* 4.3 10.5 - - + -
1527G PHE* 3.9 31.6 - + + -
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Residues in contact with VAL1496 (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 LEU* 4.0 27.8 - - + +
1440G ASP* 3.8 20.4 - - - +
1445G CYS* 4.1 15.7 - - - -
1449G THR* 5.7 6.8 - - - +
1450G LEU* 4.7 8.1 - - + -
1453G ALA* 4.2 15.7 - - + -
1492G ALA 2.8 18.1 + - - +
1493G ARG* 3.3 18.8 - - - +
1494G ALA 3.1 1.0 - - - -
1495G PHE* 1.3 76.4 - - - +
1497G ARG* 1.3 63.8 + - + +
1498G LYS* 3.5 2.4 + - - +
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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