Contacts of the helix formed by residues 1538 - 1543 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856H PHE* 5.8 4.9 + - - +
861H ILE* 5.3 8.1 - - - +
888H HIS* 3.6 16.9 + - - +
889H LYS* 3.2 58.1 - - - +
891H GLN* 5.4 5.1 - - - +
1508H THR* 4.8 15.9 + - - +
1509H ALA* 5.0 8.0 + - - +
1511H ILE 5.2 5.1 + - - -
1513H MET* 5.0 7.5 - - - +
1516H GLU* 3.1 36.9 + - - +
1536H ALA* 3.0 18.7 - - - +
1537H HIS* 1.3 87.1 + - + +
1539H VAL* 1.3 65.7 + - - +
1540H HIS* 4.2 5.6 - - + +
1541H THR* 3.0 13.2 + - - +
1580H ASP* 5.9 2.1 + - - -
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Residues in contact with VAL1539 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861H ILE* 6.2 3.6 - - + -
1377H CYS* 4.8 12.1 - - + -
1536H ALA* 5.0 3.4 - - - +
1537H HIS 4.1 1.5 - - - -
1538H ARG* 1.3 66.8 - - - +
1540H HIS* 1.3 60.3 + - + +
1541H THR 2.9 4.7 - - - -
1542H ILE* 2.6 30.0 + - + +
1543H LEU* 3.0 16.7 + - - +
1573H PHE* 3.5 31.2 - - + -
1576H PHE* 4.1 13.2 - - + +
1577H VAL* 4.1 27.6 - - + -
1580H ASP* 3.4 26.8 + - + +
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Residues in contact with HIS1540 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928H LYS 4.2 18.8 + - - -
929H THR* 4.3 24.5 + - - -
1516H GLU* 5.2 5.8 + - - +
1517H ASN* 3.6 26.9 + - - -
1538H ARG* 3.1 7.6 - - + -
1539H VAL* 1.3 82.0 - - + +
1541H THR* 1.3 58.8 + - - +
1543H LEU* 4.1 20.4 + - + +
1544H SER* 5.3 0.7 + - - -
1577H VAL* 6.1 0.2 - - - -
1580H ASP* 6.1 1.8 - - + +
1581H LYS 6.3 1.6 - - - -
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Residues in contact with THR1541 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508H THR* 4.9 8.0 - - - -
1516H GLU* 2.4 37.8 + - + +
1520H GLN* 3.2 43.2 + - + +
1524H MET* 5.5 0.9 - - - +
1534H THR* 6.2 2.7 - - - -
1536H ALA* 4.5 9.0 - - + -
1538H ARG* 3.0 11.4 + - - +
1539H VAL 2.9 0.6 - - - -
1540H HIS* 1.3 76.6 + - - +
1542H ILE* 1.3 58.7 + - - +
1543H LEU 3.2 2.6 + - - -
1544H SER* 3.2 23.3 + - - -
1545H ALA* 4.7 0.3 + - - +
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Residues in contact with ILE1542 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375H GLY* 3.5 39.9 - - - -
1376H ILE 3.6 7.2 - - - +
1377H CYS* 3.7 27.4 - - + -
1534H THR* 4.6 5.8 - - - +
1536H ALA* 4.4 10.5 - - + +
1538H ARG 3.6 1.0 + - - -
1539H VAL* 2.6 30.9 + - + +
1541H THR* 1.3 70.5 - - - +
1543H LEU* 1.3 56.9 + - - +
1544H SER 2.9 11.4 + - - -
1545H ALA* 3.3 15.1 + - + +
1548H VAL* 4.0 21.7 - - + +
1573H PHE* 3.4 31.0 - - + -
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Residues in contact with LEU1543 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539H VAL 3.0 34.2 + - - +
1540H HIS* 4.1 17.9 - - + +
1541H THR 3.2 1.8 - - - -
1542H ILE* 1.3 75.3 - - - +
1544H SER* 1.3 58.4 + - - +
1562H PRO* 4.2 20.8 - - + +
1566H LEU* 3.8 29.4 - - + -
1573H PHE* 3.7 24.2 - - + -
1577H VAL* 4.0 21.5 - - + -
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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