Contacts of the strand formed by residues 366 - 371 (chain R) in PDB entry 5A31
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 366 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359R TRP* 3.5 8.6 - - - -
360R SER* 2.9 41.2 + - - -
363R LYS* 3.4 51.7 + - + +
364R ARG 3.4 3.3 - - - +
365R GLY* 1.4 79.3 - - - +
367R LEU* 1.3 63.9 + - - +
380R ILE* 3.7 27.4 - - + -
381R TRP 3.4 4.3 - - - +
382R ASN* 4.9 5.8 - - - +
389R MET* 4.5 11.0 - - + -
403R TRP* 4.8 8.9 + - + -
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Residues in contact with LEU 367 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316R LYS* 5.8 0.7 - - + -
325R ALA* 3.6 26.2 - - + -
333R VAL* 4.2 5.8 - - + -
335R VAL* 4.0 27.6 - - + -
347R PHE* 4.4 1.6 - - + -
357R MET* 4.5 7.9 - - + -
358R ALA 3.5 7.6 - - - +
359R TRP* 3.7 29.8 - - + +
366R VAL* 1.3 76.6 - - - +
368R ALA* 1.3 74.0 + - - +
369R THR* 3.9 15.7 - - + -
380R ILE* 3.4 4.0 - - - +
381R TRP* 2.8 53.3 + - + +
383R VAL* 4.2 7.6 - - + -
403R TRP* 5.2 0.2 - - - -
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Residues in contact with ALA 368 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357R MET* 3.2 4.0 - - - +
358R ALA 2.6 33.3 + - - +
367R LEU* 1.3 75.1 - - - +
369R THR* 1.3 66.3 + - - +
378R LEU* 4.5 0.9 - - + -
379R LYS 3.4 7.0 - - - +
380R ILE* 4.3 7.6 - - + -
401R MET* 3.5 23.6 - - + -
403R TRP* 3.8 17.0 - - + +
410R LEU* 3.8 13.9 - - + -
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Residues in contact with THR 369 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333R VAL* 4.1 7.0 - - + -
350R HIS* 2.7 29.0 + - - -
354R VAL* 4.1 8.5 - - - -
356R ALA 3.5 5.4 - - - -
357R MET* 3.8 24.5 - - + -
367R LEU* 3.9 10.5 - - + -
368R ALA* 1.3 81.0 - - - +
370R GLY* 1.3 59.1 + - - +
377R ARG 3.6 0.9 - - - +
378R LEU* 3.5 3.6 - - - +
379R LYS* 2.8 37.2 + - - +
381R TRP* 2.9 31.5 + - + +
401R MET* 3.7 4.5 - - - -
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Residues in contact with GLY 370 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350R HIS* 3.9 3.4 - - - -
353R ALA 3.8 0.5 - - - +
354R VAL* 3.7 19.2 - - - +
355R LYS 4.0 3.8 + - - -
356R ALA* 2.8 21.4 + - - +
369R THR* 1.3 76.3 - - - +
371R GLY* 1.3 63.7 + - - -
377R ARG 3.3 6.5 - - - -
398R ILE* 3.7 20.7 - - - +
401R MET* 3.6 7.2 - - - +
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Residues in contact with GLY 371 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350R HIS* 3.6 9.5 - - - -
352R ALA* 5.0 0.7 - - - -
353R ALA 3.5 7.2 - - - -
354R VAL* 4.9 0.4 - - - -
370R GLY* 1.3 72.7 - - - -
372R GLY* 1.3 65.3 + - - +
375R ASP* 3.4 20.2 - - - -
376R ARG 3.8 3.6 + - - -
377R ARG 3.1 13.1 + - - -
398R ILE* 2.8 31.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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