Contacts of the strand formed by residues 344 - 350 (chain A) in PDB entry 2NUP
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 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A ALA 3.2 17.5 + - - +
285A ARG* 4.1 16.2 - - - +
286A ILE* 2.9 31.9 + - - +
342A GLY 5.3 0.4 - - - +
343A HIS* 1.3 73.6 - - - +
345A ILE* 1.3 64.0 + - - +
346A ASP* 3.9 9.1 + - - +
367A THR* 3.9 4.0 - - - +
368A GLY 3.7 4.7 - - - +
369A GLY* 3.2 33.4 - - - +
402A PHE* 4.4 9.6 - - + -
449A CYS 3.2 35.7 - - - +
450A GLY* 3.4 6.7 - - - +
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Residues in contact with ILE 345 (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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268A LEU* 4.4 17.0 - - + -
272A VAL* 4.5 10.8 - - + -
286A ILE* 3.6 16.4 - - + +
288A MET* 5.8 0.2 - - + -
334A LEU 4.3 7.2 - - - +
335A ALA* 4.4 1.6 - - - -
338A ALA* 3.6 31.9 - - + -
344A VAL* 1.3 77.1 - - - +
346A ASP* 1.3 71.3 + - - +
347A ILE* 4.4 6.5 - - + -
363A CYS* 3.4 51.8 - - + +
364A PRO* 3.3 14.2 - - - +
367A THR* 3.2 9.1 + - + -
369A GLY* 3.2 16.5 - - - -
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Residues in contact with ASP 346 (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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285A ARG* 2.8 42.8 + - - -
286A ILE 2.7 10.7 + - - +
287A MET* 3.5 14.8 - - - +
288A MET* 2.9 23.8 + - - +
344A VAL* 3.9 1.6 + - - +
345A ILE* 1.3 75.1 - - - +
347A ILE* 1.3 67.3 + - - +
348A TYR* 2.9 35.6 + - + -
369A GLY* 3.5 4.5 - - - -
370A TYR* 3.0 26.2 + - - +
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Residues in contact with ILE 347 (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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268A LEU* 5.7 2.7 - - + -
288A MET* 3.6 9.9 - - + -
290A ILE* 4.6 13.7 - - + -
345A ILE* 4.4 7.2 - - + -
346A ASP* 1.3 81.0 - - - +
348A TYR* 1.3 62.7 + - - +
349A ALA* 4.4 10.5 - - + -
357A LEU* 4.1 23.3 - - + -
360A MET* 3.7 38.4 - - + +
361A LYS* 5.6 0.2 - - - -
363A CYS* 4.6 4.7 - - + -
364A PRO* 3.8 30.3 - - + -
370A TYR 3.1 10.2 + - - +
371A MET* 3.6 6.3 - - + +
372A VAL 3.1 24.3 + - - +
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Residues in contact with TYR 348 (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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287A MET* 3.9 12.6 - - + +
288A MET 2.7 21.7 + - - +
289A PHE* 3.3 27.3 - + + -
290A ILE 2.7 31.4 + - - +
346A ASP* 2.9 43.6 + - + -
347A ILE* 1.3 75.6 - - - +
349A ALA* 1.3 53.6 + - - +
350A CYS* 5.4 0.2 - - - -
370A TYR* 3.8 7.1 - + + -
372A VAL* 3.4 37.7 - - + -
377A PHE* 3.8 5.1 - - + -
382A PHE* 4.0 23.3 - + + -
386A PHE* 3.6 24.1 - + + -
389A VAL* 3.6 26.6 - - + +
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Residues in contact with ALA 349 (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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290A ILE* 3.6 7.4 - - + -
347A ILE* 3.9 3.8 - - + -
348A TYR* 1.3 72.8 - - - +
350A CYS* 1.3 62.6 + - - +
351A ALA 4.3 0.4 - - - -
355A THR* 3.6 38.1 - - + +
357A LEU* 4.3 17.0 - - + -
372A VAL 3.0 14.4 + - - +
373A MET* 3.3 7.8 - - + +
374A GLY 3.2 21.7 + - - +
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Residues in contact with CYS 350 (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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139A MET* 6.0 0.3 - - - +
143A ASP* 5.2 3.3 - - - +
290A ILE 3.0 18.6 + - - +
291A GLY* 3.7 7.3 - - - +
349A ALA* 1.3 80.9 - - - +
351A ALA* 1.3 64.8 + - - +
355A THR* 4.6 0.6 + - - -
372A VAL* 5.6 1.8 - - - -
373A MET* 4.6 1.6 - - - -
374A GLY* 3.1 24.0 - - - +
375A ASP 3.7 2.4 - - - +
376A SER* 3.7 11.8 - - - -
377A PHE* 3.7 49.2 - - + +
382A PHE* 4.0 20.0 - - - -
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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