Contacts of the helix formed by residues 438 - 448 (chain F) in PDB entry 5ZRV
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 VAL 438 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434F GLY 3.2 9.4 + - - -
435F CYS* 4.9 0.8 - - - +
436F ARG 3.0 0.8 + - - -
437F LEU* 1.3 79.3 - - - +
439F MET* 1.3 57.3 + - - +
441F ALA* 3.1 3.5 + - - +
442F ALA* 2.8 23.2 + - - -
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Residues in contact with MET 439 (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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59F GLY* 6.0 6.5 - - - +
435F CYS 5.9 0.2 - - - -
436F ARG 3.3 6.5 + - - -
438F VAL* 1.3 76.0 - - - +
440F ALA* 1.3 57.1 + - - +
441F ALA 3.1 0.2 - - - -
442F ALA* 3.0 3.7 + - - +
443F ASN* 2.9 29.6 + - - +
444F ARG 4.2 0.2 + - - -
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Residues in contact with ALA 440 (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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436F ARG 3.4 9.2 + - - -
437F LEU* 3.3 9.3 + - - +
438F VAL 3.2 0.4 - - - -
439F MET* 1.3 75.8 - - - +
441F ALA* 1.3 59.0 + - - +
444F ARG* 4.3 11.0 + - - +
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Residues in contact with ALA 441 (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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437F LEU 2.9 14.2 + - - -
438F VAL* 3.1 4.6 + - - +
440F ALA* 1.3 80.1 - - - +
442F ALA* 1.3 57.4 + - - +
443F ASN 3.6 0.4 - - - -
444F ARG* 3.5 0.7 + - - -
445F LEU* 2.9 27.2 + - - -
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Residues in contact with ALA 442 (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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334F LYS 5.6 7.9 - - - +
438F VAL 2.8 14.5 + - - -
439F MET* 3.0 3.5 + - - +
441F ALA* 1.3 73.6 - - - +
443F ASN* 1.3 65.3 + - - +
445F LEU* 3.3 1.4 + - - -
446F ARG* 3.0 20.6 + - - -
470F GLU 6.0 1.6 - - - -
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Residues in contact with ASN 443 (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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439F MET* 2.9 15.8 + - - +
442F ALA* 1.3 70.6 - - - +
444F ARG* 1.3 57.6 + - - +
446F ARG* 3.8 1.6 - - - +
447F LYS* 3.0 24.8 + - - -
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Residues in contact with ARG 444 (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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439F MET 4.2 2.4 + - - -
440F ALA* 4.3 10.9 + - - +
441F ALA 3.5 6.1 + - - -
442F ALA 3.1 1.0 - - - -
443F ASN* 1.3 75.8 - - - +
445F LEU* 1.3 58.0 + - - +
447F LYS* 2.9 16.7 + - - +
448F GLU* 3.3 9.5 + - - -
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Residues in contact with LEU 445 (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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441F ALA 2.9 18.6 + - - -
442F ALA 3.9 0.7 - - - -
444F ARG* 1.3 70.3 - - - +
446F ARG* 1.3 61.4 + - - +
448F GLU 2.9 16.6 - - - +
449F GLY 3.1 17.7 - - - +
450F GLY 4.0 7.8 - - - +
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Residues in contact with ARG 446 (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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442F ALA 3.0 16.9 + - - -
443F ASN* 3.8 2.5 - - - +
445F LEU* 1.3 78.5 - - - +
447F LYS* 1.3 59.6 + - - +
448F GLU 2.8 11.3 - - - +
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Residues in contact with LYS 447 (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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443F ASN 3.0 11.5 + - - -
444F ARG* 2.9 9.4 + - - +
446F ARG* 1.3 77.2 - - - +
448F GLU* 1.3 58.5 + - - +
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Residues in contact with GLU 448 (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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444F ARG 3.3 9.6 + - - -
445F LEU 2.9 9.1 - - - +
446F ARG 2.8 17.3 - - - +
447F LYS* 1.3 74.3 - - - +
449F GLY* 1.3 64.2 + - - +
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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