Contacts of the strand formed by residues 366 - 368 (chain A) in PDB entry 5V8V
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 ILE 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A TYR* 3.5 3.3 - - - -
298A ILE* 3.3 33.0 - - + +
305A ILE* 3.8 24.0 - - + -
308A LEU* 3.9 10.1 - - + -
309A MET* 3.5 32.9 - - + +
312A LEU* 5.4 0.9 - - + -
320A ASP* 5.9 0.2 - - - -
321A TYR* 3.8 8.0 + - - +
334A ILE* 4.0 17.9 - - + -
336A PHE* 6.1 1.3 - - + -
350A TYR* 3.8 39.7 - - + +
364A LEU* 2.9 12.4 + - + +
365A ALA* 1.3 81.8 - - - +
367A HIS* 1.3 69.4 + - - +
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Residues in contact with HIS 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A TYR* 4.1 10.5 - + + -
298A ILE 3.1 9.0 + - - -
299A SER* 3.1 38.0 - - - -
300A GLY 3.3 3.5 + - - -
305A ILE* 3.7 8.7 - - - +
316A LYS* 6.2 0.7 - - - +
319A PHE 5.3 4.9 + - - +
320A ASP* 5.9 0.7 - - - -
321A TYR* 4.2 15.9 - - + +
366A ILE* 1.3 78.5 - - - +
368A ALA* 1.3 62.0 + - - +
369A MET* 4.6 1.2 - - - +
502A 90D 2.4 71.5 + + + -
318B LEU* 3.3 34.7 - - + +
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Residues in contact with ALA 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A GLY 3.2 7.0 - - - +
302A THR* 3.7 38.4 - - + +
305A ILE* 3.8 16.1 - - + +
321A TYR* 4.4 9.1 - - + +
367A HIS* 1.3 76.8 - - - +
369A MET* 1.3 62.2 + - - +
316B LYS* 6.3 2.9 - - - -
317B ARG 5.4 0.2 - - - +
318B LEU* 3.5 23.9 - - - +
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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