Contacts of the strand formed by residues 376 - 382 (chain B) in PDB entry 1NSC
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 MET 376 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365B SER* 3.8 9.4 - - - -
366B ARG* 3.4 33.0 - - - +
367B THR* 3.8 7.0 - - + +
368B MET* 3.9 3.7 - - - +
375B GLY* 1.3 75.0 - - - +
377B GLU* 1.3 62.4 + - - +
398B VAL* 3.8 0.7 - - - -
399B MET* 2.9 44.6 + - + +
400B VAL* 3.0 30.2 + - + +
406B GLY* 3.7 20.9 - - - +
407B TRP 3.4 25.8 - - - +
409B SER* 3.9 9.6 - - - +
426B ILE* 4.0 21.8 - - + -
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Residues in contact with GLU 377 (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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326B ARG* 5.4 0.3 + - - -
365B SER* 3.1 6.9 - - - -
366B ARG* 2.9 42.4 + - + +
367B THR 4.1 1.0 - - - +
368B MET* 3.3 45.4 - - + +
376B MET* 1.3 74.4 - - - +
378B LEU* 1.3 61.5 + - - +
379B TYR* 3.6 28.2 + - + +
395B HIS* 2.7 28.9 + - - +
397B GLY 3.4 13.5 - - - +
398B VAL* 4.3 7.6 - - - +
399B MET* 3.9 4.7 - - - +
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Residues in contact with LEU 378 (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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91B PHE* 3.6 35.4 - - + +
363B TRP* 3.7 33.2 - - + -
364B TYR 3.5 14.8 - - - +
377B GLU* 1.3 72.4 - - - +
379B TYR* 1.3 66.5 + - - +
395B HIS* 3.6 2.6 - - - -
396B SER* 2.7 35.2 + - - +
397B GLY 3.0 15.2 + - - +
399B MET* 3.9 20.6 - - + +
424B ILE* 3.8 24.2 - - + -
453B LEU* 4.0 13.5 - - + -
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Residues in contact with TYR 379 (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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320B THR* 3.7 15.9 - - + -
322B LEU* 4.9 4.0 - - + -
363B TRP* 3.4 8.3 - - - -
364B TYR* 2.8 38.2 + - + +
366B ARG* 3.1 45.3 + - + -
377B GLU* 3.6 32.3 + - + +
378B LEU* 1.3 75.9 - - - +
380B VAL* 1.3 62.1 + - - +
393B LEU* 3.7 37.0 - - + -
394B ALA 3.1 6.3 - - - +
395B HIS* 3.6 44.8 - + + -
396B SER* 4.0 2.7 - - - -
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Residues in contact with VAL 380 (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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362B ARG 3.3 14.8 - - - +
363B TRP* 3.6 40.4 - - + +
364B TYR* 5.0 0.2 - - - -
379B TYR* 1.3 75.6 - - - +
381B ARG* 1.3 74.1 + - - +
382B TYR* 3.8 30.3 - - + -
393B LEU* 3.8 3.9 - - - -
394B ALA* 2.9 44.2 + - + +
396B SER* 3.4 14.6 - - - +
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Residues in contact with ARG 381 (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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360B ILE 3.9 0.5 - - - +
362B ARG* 2.9 36.1 + - + +
364B TYR* 5.1 2.7 - - + -
380B VAL* 1.3 79.5 - - - +
382B TYR* 1.3 77.8 + - - +
383B ASP 4.0 9.3 + - - +
384B GLY* 5.6 0.2 - - - -
389B ASP* 3.8 24.7 + - - -
391B ASP* 3.3 36.0 + - - +
392B ALA 2.8 29.1 + - - -
393B LEU* 3.7 26.6 - - + +
394B ALA* 4.9 1.8 - - - +
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Residues in contact with TYR 382 (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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89B SER* 4.6 10.4 + - - -
354B GLN* 3.0 20.5 + - - -
356B MET* 3.5 27.8 - - + -
359B LYS* 3.7 33.2 - - + -
360B ILE 3.2 4.7 - - - +
361B GLY* 3.4 21.8 - - - -
363B TRP* 3.7 13.0 - - - -
380B VAL* 3.8 26.0 - - + -
381B ARG* 1.3 82.8 + - - +
383B ASP* 1.3 74.9 + - - +
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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