Contacts of the helix formed by residues 1506 - 1511 (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 GLU1506 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1426F GLN* 3.1 33.7 + - - +
1505F ASP* 1.3 66.8 - - - +
1507F ALA* 1.3 65.4 + - - +
1508F THR 3.0 5.0 + - - -
1509F ALA* 3.1 10.5 + - - +
1535F ILE* 3.1 37.8 + - + +
1536F ALA* 4.2 0.4 - - - +
1537F HIS* 3.5 33.4 - - + +
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Residues in contact with ALA1507 (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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1424F ILE* 3.6 20.0 - - + -
1425F LEU 4.9 0.2 - - - -
1426F GLN 5.2 0.9 - - - -
1487F GLN* 3.3 18.9 + - - +
1491F LEU* 3.6 31.4 - - + -
1504F MET* 4.4 15.3 - - + +
1505F ASP 3.1 5.2 + - - +
1506F GLU* 1.3 76.6 - - - +
1508F THR* 1.3 58.7 + - - +
1509F ALA 3.2 1.5 + - - -
1510F SER 4.0 2.1 + - - -
1511F ILE* 3.1 19.0 - - - +
1535F ILE 4.2 2.8 + - - -
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Residues in contact with THR1508 (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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1491F LEU* 6.3 0.4 - - - -
1506F GLU 3.0 1.8 + - - -
1507F ALA* 1.3 74.0 - - - +
1509F ALA* 1.3 66.1 - - - +
1510F SER 3.2 3.4 - - - -
1511F ILE* 2.9 33.9 + - - +
1516F GLU* 4.2 28.4 - - - +
1519F LEU* 6.5 1.1 - - - -
1536F ALA* 6.4 1.8 - - - -
1537F HIS 6.3 0.9 - - - -
1538F ARG* 4.8 10.6 - - - +
1541F THR* 4.9 9.0 - - - -
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Residues in contact with ALA1509 (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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857F SER* 3.6 34.6 + - - +
858F ALA 5.8 0.2 - - - +
888F HIS* 4.4 9.2 - - - +
1426F GLN* 3.6 16.6 - - - +
1506F GLU 3.1 17.1 + - - +
1508F THR* 1.3 78.5 - - - +
1510F SER* 1.3 62.6 + - - +
1511F ILE 3.4 3.6 + - - +
1537F HIS* 4.1 19.3 - - + +
1538F ARG* 5.0 11.2 + - - +
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Residues in contact with SER1510 (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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715F VAL* 5.0 1.2 - - - +
857F SER* 3.6 16.0 + - - -
888F HIS* 3.0 28.7 - - - -
1426F GLN 5.1 2.3 + - - -
1428F PRO* 4.9 6.4 - - - +
1483F GLN* 4.6 10.7 + - - +
1484F GLY* 4.2 19.6 + - - -
1487F GLN* 4.2 31.7 + - - +
1507F ALA 4.0 2.0 + - - -
1508F THR 3.2 0.4 - - - -
1509F ALA* 1.3 79.3 - - - +
1511F ILE* 1.3 58.9 + - - +
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Residues in contact with ILE1511 (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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715F VAL* 5.4 5.2 - - + -
888F HIS* 4.1 7.6 - - - +
1484F GLY* 4.9 1.8 - - - +
1487F GLN* 3.6 20.2 - - + -
1488F LEU* 3.5 28.0 - - + -
1491F LEU* 4.9 8.3 - - + -
1507F ALA 3.1 28.3 - - - +
1508F THR* 2.9 24.4 + - - +
1509F ALA 4.0 3.3 - - - +
1510F SER* 1.3 80.9 - - - +
1512F ASP* 1.3 81.9 + - - +
1515F THR* 3.8 10.3 - - + -
1516F GLU* 3.3 29.8 - - + +
1519F LEU* 5.2 5.2 - - + -
1538F ARG* 5.2 3.6 + - - -
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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