Contacts of the helix formed by residues 1538 - 1543 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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856F PHE* 5.8 4.8 + - - +
861F ILE* 5.3 8.4 - - - +
888F HIS* 3.6 16.9 + - - +
889F LYS* 3.2 57.9 - - - +
891F GLN* 5.4 5.3 - - - +
1508F THR* 4.8 16.3 + - - +
1509F ALA* 5.0 8.4 + - - +
1511F ILE 5.2 4.6 + - - -
1513F MET* 5.0 8.5 - - - +
1516F GLU* 3.1 36.2 + - - +
1536F ALA* 3.0 19.3 - - + +
1537F HIS* 1.3 85.8 + - + +
1539F VAL* 1.3 66.5 + - - +
1540F HIS* 3.1 6.5 - - + +
1541F THR* 3.0 12.7 + - - +
1580F ASP* 5.9 1.2 + - - -
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Residues in contact with VAL1539 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861F ILE* 6.2 3.4 - - + -
1377F CYS* 4.8 11.4 - - + -
1536F ALA* 5.0 3.1 - - - +
1537F HIS 4.4 1.3 + - - -
1538F ARG* 1.3 67.9 - - - +
1540F HIS* 1.3 59.2 + - + +
1541F THR 2.9 5.6 - - - -
1542F ILE* 2.6 30.9 + - + +
1543F LEU* 3.0 15.7 + - - +
1573F PHE* 3.5 31.2 - - + -
1576F PHE* 4.1 14.1 - - + +
1577F VAL* 4.1 28.5 - - + -
1580F ASP* 3.4 26.5 + - + +
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Residues in contact with HIS1540 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928F LYS 4.2 18.2 + - - -
929F THR* 4.3 23.9 + - - -
1516F GLU* 5.2 5.5 + - - +
1517F ASN* 3.6 27.5 + - - -
1538F ARG* 3.1 7.4 - - + -
1539F VAL* 1.3 83.8 - - + +
1541F THR* 1.3 58.0 + - - +
1543F LEU* 4.1 20.2 + - + +
1544F SER* 5.3 0.9 + - - -
1577F VAL* 6.1 0.4 - - - -
1580F ASP* 6.4 1.3 - - + -
1581F LYS 6.3 1.8 - - - -
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Residues in contact with THR1541 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508F THR* 4.9 8.6 - - - -
1516F GLU* 2.4 37.4 + - + +
1520F GLN* 3.2 42.8 + - + +
1524F MET* 5.5 0.9 - - - +
1534F THR* 6.3 2.2 - - - -
1536F ALA* 4.5 9.0 - - + -
1538F ARG* 3.0 12.2 + - - +
1539F VAL 2.9 0.8 - - - -
1540F HIS* 1.3 77.5 + - - +
1542F ILE* 1.3 59.4 + - - +
1543F LEU 3.2 2.4 + - - -
1544F SER* 3.2 22.7 + - - -
1545F ALA* 4.7 0.5 + - - +
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Residues in contact with ILE1542 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375F GLY* 3.5 40.4 - - - -
1376F ILE 3.6 7.6 - - - +
1377F CYS* 3.7 27.8 - - + -
1534F THR* 4.6 5.4 - - - +
1536F ALA* 4.4 9.2 - - + -
1538F ARG 3.6 0.6 + - - -
1539F VAL* 2.6 29.9 + - + +
1541F THR* 1.3 70.9 - - - +
1543F LEU* 1.3 56.0 + - - +
1544F SER 2.9 11.7 + - - -
1545F ALA* 3.3 14.5 + - + +
1548F VAL* 4.0 21.9 - - + +
1562F PRO* 4.3 0.2 - - - +
1573F PHE* 3.4 31.6 - - + -
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Residues in contact with LEU1543 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539F VAL 3.0 33.5 + - - +
1540F HIS* 4.1 18.2 - - + +
1541F THR 3.2 1.6 - - - -
1542F ILE* 1.3 76.7 - - - +
1544F SER* 1.3 56.9 + - - +
1562F PRO* 4.2 19.8 - - + +
1566F LEU* 3.8 28.7 - - + -
1573F PHE* 3.7 24.5 - - + -
1577F VAL* 4.0 21.3 - - + -
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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