Contacts of the helix formed by residues 1538 - 1543 (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 ARG1538 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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856G PHE* 5.8 4.9 + - - +
861G ILE* 5.3 9.0 - - - +
888G HIS* 3.6 17.4 + - - +
889G LYS* 3.2 58.3 - - - +
891G GLN* 5.4 5.3 - - - +
1508G THR* 4.8 15.3 + - - +
1509G ALA* 5.0 8.4 + - - +
1511G ILE 5.2 4.8 + - - -
1513G MET* 5.0 7.9 - - - +
1516G GLU* 3.1 36.9 + - - +
1536G ALA* 3.0 19.1 - - + +
1537G HIS* 1.3 86.6 + - + +
1539G VAL* 1.3 66.8 + - - +
1540G HIS* 4.2 5.8 - - + +
1541G THR* 3.0 13.5 + - - +
1580G ASP* 5.9 1.6 + - - -
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Residues in contact with VAL1539 (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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861G ILE* 6.2 3.8 - - + -
1377G CYS* 4.8 11.4 - - + -
1378G GLY 6.1 0.4 - - - +
1536G ALA* 5.0 3.8 - - - +
1537G HIS 4.1 1.3 - - - -
1538G ARG* 1.3 67.2 - - - +
1540G HIS* 1.3 59.3 + - + +
1541G THR 2.9 5.6 - - - -
1542G ILE* 2.6 29.9 + - + +
1543G LEU* 3.0 16.0 + - - +
1573G PHE* 3.5 30.7 - - + -
1576G PHE* 4.1 13.7 - - + +
1577G VAL* 4.1 28.3 - - + -
1580G ASP* 3.4 26.5 + - + +
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Residues in contact with HIS1540 (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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928G LYS 4.2 18.1 + - - -
929G THR* 4.3 23.2 + - - -
1516G GLU* 5.2 5.5 + - - +
1517G ASN* 3.6 27.6 + - - -
1538G ARG* 4.9 7.4 - - + -
1539G VAL* 1.3 82.6 - - + +
1541G THR* 1.3 60.6 + - - +
1543G LEU* 4.1 20.7 + - + +
1544G SER* 5.3 0.5 + - - -
1577G VAL* 6.1 0.4 - - - -
1580G ASP* 6.4 1.8 - - + -
1581G LYS 6.3 2.0 - - - -
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Residues in contact with THR1541 (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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1508G THR* 4.9 8.7 - - - -
1516G GLU* 2.4 37.0 + - + +
1520G GLN* 3.2 43.2 + - + +
1524G MET* 5.5 1.0 - - - +
1534G THR* 6.2 2.2 - - - -
1536G ALA* 4.5 9.0 - - + -
1538G ARG* 3.0 12.6 + - - +
1539G VAL 2.9 1.0 - - - -
1540G HIS* 1.3 76.8 + - - +
1542G ILE* 1.3 58.3 + - - +
1543G LEU 3.2 2.1 + - - -
1544G SER* 3.2 22.9 + - - -
1545G ALA* 4.7 0.3 + - - +
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Residues in contact with ILE1542 (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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1375G GLY* 3.5 39.9 - - - -
1376G ILE 3.6 7.4 - - - +
1377G CYS* 3.7 26.9 - - + -
1534G THR* 4.6 6.5 - - - +
1536G ALA* 4.4 10.1 - - + +
1538G ARG 3.6 0.8 + - - -
1539G VAL* 2.6 30.9 + - + +
1541G THR* 1.3 70.5 - - - +
1543G LEU* 1.3 55.7 + - - +
1544G SER 2.9 11.9 + - - -
1545G ALA* 3.3 14.5 + - + +
1548G VAL* 4.0 22.0 - - + +
1562G PRO* 4.3 0.5 - - - +
1573G PHE* 3.4 31.4 - - + -
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Residues in contact with LEU1543 (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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1539G VAL 3.0 34.0 + - - +
1540G HIS* 4.1 16.2 - - + +
1541G THR 3.2 1.2 - - - -
1542G ILE* 1.3 76.7 - - - +
1544G SER* 1.3 57.7 + - - +
1562G PRO* 4.2 19.5 - - + +
1566G LEU* 3.8 28.7 - - + -
1573G PHE* 3.7 24.9 - - + -
1577G VAL* 4.0 22.2 - - + -
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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