Contacts of the strand formed by residues 354 - 359 (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 354 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313R CYS* 3.8 2.9 - - - -
314R GLY 4.0 0.7 + - - -
327R GLY* 3.2 31.0 - - - +
328R GLY 3.2 8.7 + - - +
331R ASN 3.9 9.4 - - - +
332R VAL 4.6 0.4 - - - +
333R VAL* 3.6 27.8 - - + -
350R HIS* 3.6 41.1 - - + +
352R ALA 3.8 2.7 - - - +
353R ALA* 1.3 75.1 - - - +
355R LYS* 1.3 59.1 + - - +
356R ALA 4.3 4.9 - - - +
357R MET* 3.8 16.6 - - + -
369R THR* 4.1 11.4 - - - -
370R GLY 3.7 11.4 - - - +
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Residues in contact with LYS 355 (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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188R PHE* 2.8 55.0 + - + +
189R TYR* 4.3 7.0 - - - -
190R TYR 2.9 24.8 + - - -
191R SER* 3.9 16.2 - - - -
313R CYS* 3.4 27.8 - - - +
314R GLY* 3.6 15.2 - - - -
353R ALA 3.8 2.8 + - - -
354R VAL* 1.3 74.7 - - - +
356R ALA* 1.3 66.0 + - - +
357R MET* 3.3 6.9 + - - +
370R GLY 4.0 1.4 + - - -
399R CYS* 2.9 26.0 + - - +
400R ASN* 4.0 4.0 - - - +
443R LEU* 3.1 17.6 + - - +
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Residues in contact with ALA 356 (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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354R VAL* 4.3 1.6 - - - +
355R LYS* 1.3 76.8 - - - +
357R MET* 1.3 61.1 + - - +
369R THR* 3.5 0.9 - - - -
370R GLY 2.8 34.8 + - - +
398R ILE* 3.7 19.9 + - + +
399R CYS 4.0 1.8 - - - -
400R ASN* 3.5 47.6 - - - +
401R MET* 3.6 7.5 - - + +
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Residues in contact with MET 357 (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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314R GLY* 4.3 8.5 - - - -
315R LEU 4.5 0.9 - - - -
316R LYS* 3.1 42.0 + - + +
325R ALA* 3.7 34.8 - - + +
326R SER 3.7 16.4 - - - +
327R GLY* 4.0 3.1 - - - +
333R VAL* 3.6 31.0 - - + -
354R VAL* 3.8 15.0 - - + -
355R LYS 3.3 13.1 + - - +
356R ALA* 1.3 75.0 - - - +
358R ALA* 1.3 61.9 + - - +
367R LEU* 4.5 3.6 - - + -
368R ALA 3.2 13.5 - - - +
369R THR* 3.8 11.7 - - + -
401R MET* 3.8 7.2 - - - +
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Residues in contact with ALA 358 (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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316R LYS* 4.9 7.4 - - - +
357R MET* 1.3 75.0 - - - +
359R TRP* 1.3 64.2 + - - +
367R LEU* 3.5 2.3 - - - -
368R ALA* 2.6 40.6 + - - +
401R MET* 3.7 20.2 - - + +
402R VAL* 4.6 3.8 - - - -
403R TRP* 3.6 33.0 - - + +
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Residues in contact with TRP 359 (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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316R LYS* 3.1 31.7 + - + +
317R TRP 3.7 22.6 - - - +
318R ASN* 3.2 35.4 - - - +
323R LYS* 4.0 30.5 - - + -
324R LEU 4.3 1.6 - - - -
325R ALA* 4.0 16.9 - - + +
335R VAL* 4.0 7.2 - - + -
358R ALA* 1.3 74.8 - - - +
360R SER* 1.3 65.2 + - - +
361R PRO* 3.3 10.0 - - - +
365R GLY* 4.0 23.8 - - - -
366R VAL 3.5 22.2 - - - -
367R LEU* 3.7 26.6 - - + +
383R VAL* 4.0 19.3 - - + -
403R TRP* 3.5 11.3 - - - +
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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