Contacts of the helix formed by residues 2595 - 2603 (chain F) in PDB entry 1CVU
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 THR2595 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2565B GLN* 4.7 17.6 - - - +
2566B SER* 5.4 3.4 + - - -
2596F LYS* 1.3 90.2 + - - +
2597F THR* 3.2 3.1 - - - +
2598F ALA* 2.9 11.9 + - - +
2599F THR* 2.9 32.1 + - - +
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Residues in contact with LYS2596 (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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2561B THR* 4.3 20.6 + - - -
2566B SER* 4.0 16.0 + - - -
2595F THR* 1.3 90.3 - - - +
2597F THR* 1.3 81.1 + - - +
2599F THR* 3.5 7.9 + - - -
2600F ILE* 3.4 30.6 + - + +
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Residues in contact with THR2597 (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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2566B SER* 4.9 9.8 + - - -
2569B CYS* 3.5 16.2 - - + -
2570B ASN* 3.7 21.8 + - - +
2595F THR 3.2 2.4 - - - -
2596F LYS* 1.3 94.0 + - - +
2598F ALA* 1.3 66.3 + - - +
2600F ILE* 3.4 2.2 + - - -
2601F ASN* 2.5 67.0 + - - +
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Residues in contact with ALA2598 (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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2565B GLN* 4.2 27.5 - - + +
2569B CYS* 3.8 0.8 - - - +
2575B CYS* 3.4 22.2 - - - +
2577B PHE* 6.0 3.6 - - + -
2595F THR* 2.9 14.3 + - - +
2597F THR* 1.3 77.8 - - - +
2599F THR* 1.3 58.2 + - - +
2602F ALA* 2.9 37.1 + - + +
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Residues in contact with THR2599 (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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2595F THR* 2.9 20.8 + - - +
2596F LYS* 3.7 11.8 - - - -
2598F ALA* 1.3 79.4 - - - +
2600F ILE* 1.3 66.8 + - + +
2602F ALA* 4.3 2.5 - - - +
2603F SER* 3.3 19.2 + - - -
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Residues in contact with ILE2600 (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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2596F LYS* 3.4 19.6 + - + +
2597F THR* 4.3 2.0 - - - +
2599F THR* 1.3 81.3 - - + +
2601F ASN* 1.3 68.8 + - - +
2603F SER* 2.6 22.4 + - - +
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Residues in contact with ASN2601 (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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2569B CYS* 3.3 18.2 + - - +
2570B ASN* 4.5 3.8 + - - +
2574B GLY* 4.6 4.3 - - - +
2575B CYS* 3.8 9.1 - - + +
2597F THR* 2.5 54.4 + - - +
2600F ILE* 1.3 80.9 - - - +
2602F ALA* 1.3 63.8 + - - +
2603F SER 3.6 1.9 + - - +
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Residues in contact with ALA2602 (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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2574B GLY 4.2 10.8 - - - +
2575B CYS* 4.3 13.6 - - - +
2598F ALA 2.9 22.1 + - - +
2599F THR* 4.3 2.9 - - - +
2601F ASN* 1.3 79.6 - - - +
2603F SER* 1.3 65.2 + - - +
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Residues in contact with SER2603 (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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2599F THR 3.3 10.8 + - - -
2600F ILE* 2.6 31.6 + - - +
2601F ASN 3.3 3.0 - - - +
2602F ALA* 1.3 79.9 - - - +
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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