Contacts of the strand formed by residues 377 - 382 (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 ARG 377 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350R HIS* 3.5 3.5 - - - -
370R GLY* 3.3 3.1 - - - -
371R GLY 3.1 23.3 + - - +
375R ASP* 3.1 39.0 + - - +
376R ARG* 1.3 77.3 - - - +
378R LEU* 1.3 58.7 + - - +
379R LYS* 3.9 14.5 - - - +
391R ASP* 3.1 45.8 + - - +
392R ILE 3.4 2.0 - - - -
393R ASP* 3.8 39.3 + - - +
398R ILE* 3.3 4.5 - - - +
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Residues in contact with LEU 378 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368R ALA* 4.5 0.9 - - + -
369R THR 3.5 5.2 - - - +
376R ARG 3.9 0.2 + - - -
377R ARG* 1.3 70.9 - - - +
379R LYS* 1.3 63.5 + - - +
380R ILE* 3.8 12.4 + - + +
390R SER 4.1 0.5 - - - +
391R ASP* 3.3 3.6 + - - -
392R ILE* 2.8 45.4 + - + +
394R SER* 5.1 5.2 - - - -
398R ILE* 3.9 10.0 - - + +
401R MET* 3.7 30.1 - - + -
410R LEU* 3.8 17.7 - - + -
412R THR* 4.4 4.5 - - + -
424R TRP* 3.7 44.2 - - + +
429R MET* 3.9 18.4 - - + -
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Residues in contact with LYS 379 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349R GLU* 3.4 30.9 + - - +
350R HIS* 3.5 35.7 - - + +
367R LEU 3.7 0.7 - - - +
368R ALA* 3.4 3.1 - - - -
369R THR* 2.8 49.9 + - - +
375R ASP* 4.9 0.8 + - - -
377R ARG* 4.0 14.6 - - + +
378R LEU* 1.3 74.7 - - - +
380R ILE* 1.3 65.0 + - - +
381R TRP* 3.4 31.1 - - + +
388R LYS* 4.4 1.6 - - + -
390R SER 3.4 6.3 - - - +
391R ASP* 2.9 44.6 + - - +
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Residues in contact with ILE 380 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366R VAL* 3.7 26.9 - - + -
367R LEU 3.4 5.8 - - - +
368R ALA* 4.3 8.5 - - + -
378R LEU* 3.8 20.9 - - + +
379R LYS* 1.3 80.2 - - - +
381R TRP* 1.3 57.3 + - - +
388R LYS* 3.5 3.8 - - - -
389R MET* 2.7 51.5 + - + -
390R SER* 2.9 22.9 + - - +
403R TRP* 5.2 9.0 - - + -
410R LEU* 4.5 6.5 - - + -
429R MET* 3.3 37.9 - - + -
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Residues in contact with TRP 381 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333R VAL* 5.3 0.4 - - - +
347R PHE* 3.6 73.3 - + + +
349R GLU* 3.7 34.3 - - + -
350R HIS* 4.6 5.3 + + - -
366R VAL* 3.4 3.8 - - - +
367R LEU* 2.8 51.2 + - + +
369R THR* 2.9 37.4 + - + +
379R LYS* 3.4 26.6 - - + +
380R ILE* 1.3 76.6 - - - +
382R ASN* 1.3 60.4 + - - +
383R VAL 3.2 5.8 + - - +
387R ILE 3.4 4.9 - - - +
388R LYS* 3.7 35.2 - - + -
389R MET* 4.4 3.4 - - - -
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Residues in contact with ASN 382 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351J ASP* 5.2 8.3 - - - +
347R PHE* 5.3 0.8 - - - -
363R LYS* 5.2 8.5 - - - +
364R ARG 5.2 2.1 - - - +
365R GLY 3.8 7.4 - - - +
366R VAL* 4.8 5.8 - - - +
381R TRP* 1.3 68.9 - - - +
383R VAL* 1.3 85.6 + - - +
384R ASN* 4.0 3.1 - - - +
385R THR* 3.2 31.0 + - - +
386R SER* 2.9 19.8 + - - -
387R ILE* 2.7 21.9 + - + +
389R MET* 3.8 30.4 - - + +
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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