Contacts of the strand formed by residues 382 - 388 (chain B) in PDB entry 1NU6
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 382 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353B TRP 4.9 1.0 + - - -
355B GLY* 3.6 35.4 + - - +
356B ARG* 3.4 39.6 - - - +
374B ILE* 3.7 21.9 + - + +
375B ILE* 3.5 6.7 - - - +
376B SER* 4.3 22.5 - - - +
381B TYR* 1.3 69.4 - - - +
383B HIS* 1.3 61.7 + - - +
403B GLU* 3.2 23.2 + - - +
404B VAL 2.9 27.7 + - - +
588B ASP* 3.0 33.4 + - - +
591B MET* 3.5 25.5 - - - +
592B HIS* 4.0 8.3 + - - -
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Residues in contact with HIS 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B ILE* 3.5 4.6 - - - +
375B ILE 3.0 30.9 + - - +
377B ASN* 3.8 8.0 + - - +
381B TYR* 3.4 16.0 + - + +
382B ARG* 1.3 76.9 + - - +
384B ILE* 1.3 64.9 + - - +
385B CYS 3.5 0.9 + - - -
396B PHE* 3.9 15.0 - - + -
398B THR* 2.8 34.5 - - - +
399B LYS* 2.9 29.0 + - - -
400B GLY 2.8 34.8 - - - -
402B TRP* 3.0 37.3 + + - -
404B VAL* 4.1 3.8 - - - -
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Residues in contact with ILE 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B TYR* 4.2 15.7 - - + -
373B LYS 3.7 4.5 - - - +
374B ILE* 4.5 0.9 - - + +
383B HIS* 1.3 70.0 - - - +
385B CYS* 1.3 60.8 + - - +
396B PHE* 3.4 4.8 - - - -
397B ILE* 2.9 38.3 + - + +
398B THR* 3.0 17.5 + - + +
404B VAL* 3.8 21.8 - - + -
407B ILE* 4.0 24.7 - - + -
415B LEU* 3.5 41.3 - - + -
417B TYR* 3.7 28.9 - - + -
434B ILE* 4.4 1.3 - - + -
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Residues in contact with CYS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B TYR* 3.3 5.6 - - - -
373B LYS 2.8 36.6 + - - +
375B ILE* 4.4 4.9 - - + -
383B HIS 3.5 0.4 + - - -
384B ILE* 1.3 75.9 - - - +
386B TYR* 1.3 57.6 + - - +
387B PHE* 3.5 16.7 - - + -
394B CYS* 2.0 48.5 - - - -
395B THR 3.4 14.1 - - - -
396B PHE* 3.8 27.8 - - + -
397B ILE* 4.7 0.2 - - - -
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Residues in contact with TYR 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B THR* 4.9 1.2 - - + +
370B SER* 3.5 31.7 + - - -
371B PHE 3.7 6.1 - - - -
372B TYR* 3.4 36.1 - + + -
385B CYS* 1.3 72.2 - - - +
387B PHE* 1.3 62.8 + - - +
388B GLN* 3.4 38.9 + - + +
393B ASP 4.3 0.2 - - - +
394B CYS* 3.1 5.0 - - - -
395B THR* 2.8 42.4 + - - +
397B ILE* 3.2 23.8 - - + +
439B TYR* 4.1 15.3 - - - -
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Residues in contact with PHE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B HIS* 4.1 28.7 - + + -
347B GLU* 5.5 2.9 - - + -
370B SER* 3.1 6.9 - - - -
371B PHE* 2.9 70.8 + + + +
373B LYS* 4.0 8.1 - - + -
375B ILE* 3.2 36.1 - - + -
385B CYS* 3.5 24.7 - - + -
386B TYR* 1.3 73.7 - - - +
388B GLN* 1.3 65.2 + - - +
392B LYS 4.7 2.9 - - - -
393B ASP 4.3 7.6 - - - -
394B CYS* 3.3 32.8 - - + -
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Residues in contact with GLN 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B HIS* 3.7 3.3 - - - -
369B ASN 3.9 6.3 - - - +
370B SER* 4.1 2.2 - - - -
386B TYR* 3.4 39.2 + - + +
387B PHE* 1.3 78.2 - - - +
389B ILE* 1.3 59.4 + - - +
390B ASP 3.5 1.6 - - - +
391B LYS* 2.9 60.2 + - + +
393B ASP 4.9 3.2 + - - -
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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