Contacts of the strand formed by residues 376 - 385 (chain A) in PDB entry 2W3S
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 LYS 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A LEU* 3.5 3.8 - - - -
373A LYS* 3.1 31.5 + - + +
375A SER* 1.3 82.8 - - - +
377A ILE* 1.3 65.3 + - - +
378A GLU* 3.1 7.7 + - + +
403A GLY* 3.4 24.4 + - - +
404A GLN* 3.3 5.8 - - - +
405A ASP* 3.1 33.6 + - - +
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Residues in contact with ILE 377 (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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370A LEU* 3.8 22.2 - - + -
371A THR 4.0 4.9 - - - +
372A LEU* 4.1 3.1 - - + -
375A SER 3.7 0.2 + - - -
376A LYS* 1.3 68.0 - - - +
378A GLU* 1.3 63.3 + - - +
379A THR 4.0 13.0 - - - +
380A ALA* 5.2 0.9 - - + -
401A LEU* 3.3 47.1 - - + +
402A ILE* 3.7 2.5 - - - +
403A GLY* 2.7 30.8 + - - -
404A GLN* 2.6 20.9 + - + +
405A ASP 3.3 19.5 - - - +
406A PHE* 3.8 28.9 - - + -
410A THR* 4.4 0.2 - - + -
411A ILE* 4.1 11.2 - - + -
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Residues in contact with GLU 378 (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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371A THR* 2.8 23.4 + - - +
373A LYS* 3.2 52.9 + - + +
376A LYS* 3.1 6.0 + - + +
377A ILE* 1.3 72.8 - - - +
379A THR* 1.3 64.8 + - - +
380A ALA 4.3 0.3 + - - -
402A ILE* 3.5 24.8 - - - +
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Residues in contact with THR 379 (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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369A ASN* 4.6 5.6 - - - +
370A LEU* 3.3 26.3 - - - +
371A THR* 2.7 27.2 + - - +
377A ILE* 4.0 4.4 - - - +
378A GLU* 1.3 82.5 + - - +
380A ALA* 1.3 70.0 + - - +
381A ARG* 4.0 15.3 - - + +
402A ILE* 6.0 0.2 - - - -
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Residues in contact with ALA 380 (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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370A LEU* 3.4 15.5 - - + -
377A ILE* 5.2 2.2 - - + -
378A GLU 4.3 0.4 + - - -
379A THR* 1.3 78.0 - - - +
381A ARG* 1.3 58.2 + - - +
382A ILE* 4.6 1.6 - - + -
393A ARG* 3.4 8.8 + - - -
398A GLU* 2.7 61.3 - - + +
401A LEU* 4.9 4.9 - - + -
402A ILE* 4.4 12.4 - - + +
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Residues in contact with ARG 381 (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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299A ILE* 2.5 33.7 + - - +
300A ALA* 3.3 29.5 - - - +
301A MET 4.5 0.9 - - - -
302A GLY* 3.4 23.6 - - - +
317A PRO* 5.3 5.1 - - - +
319A GLU* 2.8 31.5 + - - -
367A CYS 4.1 0.7 - - - +
368A LEU* 3.5 1.0 - - - -
369A ASN* 2.7 51.3 + - + +
379A THR* 4.4 13.0 - - + -
380A ALA* 1.3 71.3 - - - +
382A ILE* 1.3 59.0 + - - +
383A ALA 4.1 0.7 - - - -
393A ARG* 3.2 26.9 - - - +
398A GLU* 3.3 4.0 - - - -
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Residues in contact with ILE 382 (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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367A CYS 3.5 2.9 - - - -
368A LEU* 3.8 29.4 - - + -
370A LEU* 3.8 23.3 - - + -
380A ALA 3.8 0.2 - - - -
381A ARG* 1.3 76.7 - - - +
383A ALA* 1.3 59.1 + - - +
384A PHE* 3.6 27.1 - - + -
393A ARG* 3.1 5.7 - - - +
394A ALA* 2.8 42.2 + - + -
397A PHE* 3.6 33.7 - - + -
398A GLU* 3.1 24.0 + - + -
401A LEU* 3.9 10.1 - - + -
418A LEU* 6.3 0.2 - - + -
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Residues in contact with ALA 383 (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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296A PRO* 3.5 26.9 - - + +
299A ILE* 3.9 17.5 - - + -
300A ALA* 3.8 14.6 - - - +
365A CYS 3.6 0.3 - - - +
367A CYS* 2.7 43.3 + - - +
381A ARG 4.1 0.4 - - - -
382A ILE* 1.3 74.1 - - - +
384A PHE* 1.3 68.8 + - - +
392A LYS 3.8 8.3 - - - +
393A ARG* 4.5 2.0 - - + -
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Residues in contact with PHE 384 (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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296A PRO* 4.3 6.8 - - - +
364A VAL* 3.8 11.0 - - + -
365A CYS 3.0 15.5 - - - -
366A GLY* 3.9 13.5 - - - -
367A CYS 5.5 0.2 - - - -
368A LEU* 5.7 4.3 - - + -
382A ILE* 3.6 27.1 - - + -
383A ALA* 1.3 80.7 - - - +
385A GLY* 1.3 57.2 + - - +
387A MET* 3.7 26.7 - - + -
390A VAL 4.6 0.5 - - - +
391A PRO* 3.4 9.9 - - - +
392A LYS 3.1 28.5 + - - +
394A ALA* 4.6 1.6 - - + -
418A LEU* 4.3 15.3 - - + -
422A PHE* 3.9 28.9 - + + -
439A ALA* 3.4 47.8 - - + -
442A MET* 4.1 3.6 - - + -
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Residues in contact with GLY 385 (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 PRO 3.3 11.2 - - - -
291A ILE* 5.0 3.1 - - - -
296A PRO* 3.9 15.9 - - - +
362A SER* 5.9 0.9 - - - -
364A VAL* 3.6 3.2 - - - -
365A CYS* 3.0 36.5 + - - +
384A PHE* 1.3 72.9 - - - +
386A GLY* 1.3 59.3 + - - -
387A MET* 3.2 14.7 + - - +
390A VAL 5.7 0.4 - - - -
391A PRO* 4.9 2.7 - - - -
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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