Contacts of the strand formed by residues 362 - 367 (chain A) in PDB entry 5NV6
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 GLY 362 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLN* 4.3 6.7 - - - +
243A ILE* 3.9 5.4 - - - -
274A GLN* 4.7 0.7 - - - -
275A TYR 3.1 13.7 - - - -
315A ALA* 4.4 6.7 - - - -
358A LEU* 3.9 1.0 - - - -
359A ALA* 2.8 41.1 + - - +
360A THR 3.5 0.8 + - - -
361A ASN* 1.3 82.7 + - - +
363A VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLN* 5.2 0.2 - - - +
203A HIS* 4.9 5.4 - - + -
214A CYS* 3.9 21.5 - - - -
243A ILE* 4.6 0.9 - - - +
275A TYR 3.0 6.5 + - - +
276A THR* 3.3 6.5 - - + +
277A LEU 2.9 24.6 + - - -
315A ALA* 3.8 19.5 - - + -
316A MET 4.0 15.0 - - - +
317A CYS* 4.5 2.7 - - - -
356A ASP* 3.9 18.6 - - - +
357A ILE 3.8 5.4 - - - +
358A LEU* 4.9 5.2 - - + +
362A GLY* 1.3 78.2 - - - +
364A ILE* 1.3 66.2 - - - +
365A HIS* 3.7 31.2 - - + +
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Residues in contact with ILE 364 (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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243A ILE* 3.8 35.4 - - + +
246A ILE* 3.8 41.5 - - + -
247A ILE* 4.7 4.5 - - + -
253A PHE* 4.7 4.5 - - + -
277A LEU* 3.4 12.6 - - + +
279A ALA* 3.8 26.5 - - + -
356A ASP 3.8 0.7 + - - -
357A ILE* 2.9 46.2 + - + +
359A ALA* 4.5 0.7 - - + -
363A VAL* 1.3 77.7 - - - +
365A HIS* 1.3 66.4 + - - +
366A TYR* 4.2 20.2 - - + -
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Residues in contact with HIS 365 (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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276A THR* 3.8 25.6 - - + -
277A LEU 2.9 6.2 + - - -
278A LEU* 3.3 23.3 - - + +
279A ALA 3.0 22.7 + - - -
316A MET 3.1 22.1 + - - -
318A ALA* 4.0 2.2 + - + -
344A LEU* 4.0 26.4 - - + +
352A ILE* 4.0 11.4 - - + -
354A ASN 3.4 6.3 - - - +
355A LYS* 3.6 7.8 - - - -
356A ASP* 3.2 46.8 + - - -
363A VAL* 3.7 8.1 - - + +
364A ILE* 1.3 72.1 + - - +
366A TYR* 1.3 64.6 + - - +
367A ILE* 4.5 0.2 - - - +
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Residues in contact with TYR 366 (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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246A ILE* 5.2 0.2 - - - +
250A GLU* 3.3 31.9 + - - +
252A THR* 3.7 17.0 - - + -
253A PHE* 3.6 32.5 - + - -
279A ALA 3.5 6.3 - - - +
281A THR* 4.4 10.1 - - + -
352A ILE* 3.3 7.7 - - - +
353A SER* 3.0 40.6 + - - +
354A ASN* 3.0 43.0 + - + -
357A ILE* 3.5 35.0 - - + +
364A ILE* 4.2 8.1 - - + -
365A HIS* 1.3 70.9 - - - +
367A ILE* 1.3 59.2 + - - +
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Residues in contact with ILE 367 (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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278A LEU* 3.4 30.7 - - + +
279A ALA 2.9 7.1 + - - -
280A PRO* 3.4 15.2 - - + +
281A THR* 3.2 25.3 + - - +
284A ALA* 4.0 0.2 - - - +
310A HIS* 4.1 4.3 - - + -
346A ILE* 3.9 9.2 - - + -
351A ILE* 3.3 34.8 - - + +
352A ILE* 3.8 21.3 - - + -
365A HIS 3.4 0.2 + - - -
366A TYR* 1.3 73.0 - - - +
368A ASP* 1.4 62.2 + - - +
369A GLU 3.4 19.3 - - - +
371A LEU* 3.8 27.1 - - + -
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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