Contacts of the helix formed by residues 1446 - 1457 (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 SER1446 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1445G CYS* 1.3 74.8 - - - +
1447G ASP* 1.3 66.7 + - - +
1448G SER* 3.3 17.8 + - - -
1449G THR* 2.5 39.6 + - - +
1450G LEU* 3.0 13.0 + - - +
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Residues in contact with ASP1447 (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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1436G ARG* 2.7 48.6 + - - -
1445G CYS 4.4 0.2 + - - -
1446G SER* 1.3 71.7 + - - +
1448G SER* 1.3 65.5 + - - +
1450G LEU* 3.4 13.6 - - + +
1451G TRP* 2.8 46.9 + - + +
1470G LEU* 5.2 1.6 - - + -
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Residues in contact with SER1448 (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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1446G SER* 3.1 13.6 + - - -
1447G ASP* 1.3 77.9 - - - +
1449G THR* 1.3 60.4 + - - +
1451G TRP* 3.4 6.6 + - - +
1452G GLU* 2.9 29.5 + - - +
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Residues in contact with THR1449 (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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1445G CYS* 4.2 8.0 - - - +
1446G SER* 2.5 38.6 + - - +
1448G SER* 1.3 78.6 - - - +
1450G LEU* 1.3 58.0 + - - +
1452G GLU* 3.2 20.1 + - - +
1453G ALA* 2.9 29.8 + - - +
1496G VAL* 5.7 7.9 - - - +
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Residues in contact with LEU1450 (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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1436G ARG* 3.8 21.8 - - - +
1439G LEU* 3.9 25.2 - - + +
1440G ASP* 3.2 36.8 - - - +
1445G CYS* 4.5 4.9 - - + -
1446G SER 3.0 18.3 + - - +
1447G ASP* 3.1 32.3 + - - +
1449G THR* 1.3 77.7 - - - +
1451G TRP* 1.3 57.8 + - - +
1453G ALA* 3.2 7.5 + - - +
1454G LEU* 2.9 33.1 + - - +
1470G LEU* 4.5 15.0 - - + -
1496G VAL* 4.7 9.0 - - + -
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Residues in contact with TRP1451 (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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1447G ASP* 2.8 46.0 + - + +
1448G SER* 3.7 6.3 - - - +
1450G LEU* 1.3 72.0 - - - +
1452G GLU* 1.3 56.4 + - - +
1454G LEU* 3.4 14.3 + - + +
1455G GLU* 2.8 30.7 + - - +
1460G LYS* 3.3 54.5 - - + +
1463G VAL* 3.8 33.9 - - + -
1464G LYS* 4.8 8.5 - - + -
1469G GLY* 4.6 10.5 - - - -
1470G LEU* 3.3 29.3 - - + +
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Residues in contact with GLU1452 (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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1448G SER* 2.9 15.5 + - - +
1449G THR* 3.3 26.8 - - - +
1450G LEU 3.1 0.2 - - - -
1451G TRP* 1.3 76.5 - - - +
1453G ALA* 1.3 58.0 + - - +
1455G GLU* 3.2 6.2 + - - +
1456G ILE* 2.9 44.0 + - + +
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Residues in contact with ALA1453 (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* 5.5 2.0 - - + -
1449G THR 2.9 16.0 + - - +
1450G LEU* 3.7 4.0 - - - +
1452G GLU* 1.3 76.5 - - - +
1454G LEU* 1.3 62.9 + - - +
1456G ILE* 3.3 12.1 - - - +
1457G ALA* 3.2 26.0 + - - +
1492G ALA* 3.9 26.7 - - + +
1495G PHE* 4.4 6.5 - - + +
1496G VAL* 4.2 20.6 - - + +
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Residues in contact with LEU1454 (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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1435G ILE* 4.7 14.4 - - + -
1439G LEU* 4.7 9.2 - - + -
1450G LEU 2.9 17.2 + - - +
1451G TRP* 3.5 23.1 - - + +
1453G ALA* 1.3 77.7 - - - +
1455G GLU* 1.3 54.9 + - - +
1457G ALA* 3.3 2.8 + - - -
1458G GLN 2.9 7.1 + - - -
1459G LEU* 2.5 51.4 + - + +
1460G LYS* 3.4 12.8 - - - +
1463G VAL* 4.1 22.0 - - + -
1470G LEU* 3.7 31.4 - - + -
1489G PHE* 5.3 7.6 - - + -
1492G ALA* 4.8 8.1 - - + -
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Residues in contact with GLU1455 (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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1451G TRP 2.8 18.1 + - - +
1452G GLU* 3.2 6.7 + - - +
1454G LEU* 1.3 70.9 - - - +
1456G ILE* 1.3 61.5 + - + +
1457G ALA 3.0 4.3 - - - -
1458G GLN* 2.5 33.0 + - - +
1459G LEU 4.5 0.2 - - - +
1460G LYS* 3.2 27.3 - - + +
1461G LEU* 3.2 34.5 - - - +
1464G LYS* 4.2 1.2 + - - -
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Residues in contact with ILE1456 (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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1452G GLU* 2.9 31.7 + - + +
1453G ALA* 3.3 16.2 - - - +
1455G GLU* 1.3 77.3 - - + +
1457G ALA* 1.3 56.8 + - - +
1458G GLN* 3.1 13.7 + - - +
1495G PHE* 3.4 39.2 - - + -
1519G LEU* 4.7 4.9 - - - +
1522G VAL* 3.4 32.4 - - + +
1523G VAL* 5.1 6.6 + - + +
1526G ALA* 4.6 17.3 - - + -
1527G PHE* 5.5 7.0 - - + -
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Residues in contact with ALA1457 (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 ALA 3.2 18.6 + - - +
1454G LEU 3.8 0.2 - - - +
1455G GLU 3.0 0.8 - - - -
1456G ILE* 1.3 75.2 - - - +
1458G GLN* 1.3 74.8 + - - +
1459G LEU* 3.2 16.3 - - + +
1488G LEU* 2.9 31.9 - - + +
1492G ALA* 3.9 15.5 - - + +
1495G PHE* 4.2 16.4 - - + -
1519G LEU* 4.6 3.4 - - - -
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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