Contacts of the strand formed by residues 377 - 385 (chain A) in PDB entry 2WP9
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 ASP 377 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A LEU* 4.2 17.3 - - + +
370A THR 3.3 6.6 - - - +
371A VAL* 3.8 7.4 - - - +
375A GLY 3.9 1.4 + - - +
376A GLU* 1.3 76.4 - - - +
378A VAL* 1.3 64.8 + - - +
569A ARG* 2.8 49.1 + - - +
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Residues in contact with VAL 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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369A LEU* 3.6 3.7 - - - -
370A THR* 2.6 49.6 + - + +
372A ASN* 3.7 34.8 - - + +
376A GLU 3.8 3.6 - - - +
377A ASP* 1.3 80.6 - - - +
379A VAL* 1.3 76.4 + - - +
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Residues in contact with VAL 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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363A LYS* 3.9 29.2 - - + +
367A GLN* 4.3 23.6 - - + +
368A ALA 3.6 9.4 - - - +
369A LEU* 4.0 6.7 - - + +
370A THR* 4.8 0.9 - - - +
378A VAL* 1.3 86.7 - - - +
380A VAL* 1.3 76.2 - - - +
381A PRO* 3.2 19.1 - - + +
383A LEU 5.6 0.2 - - - +
425A GLU* 4.5 15.5 - - - +
426A GLN* 5.6 4.9 - - + +
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Residues in contact with VAL 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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171A LYS* 5.3 3.4 - - - +
175A GLY 4.6 8.3 - - - +
177A VAL* 4.2 11.7 - - + -
231A VAL* 4.4 19.1 - - + -
368A ALA* 2.9 22.0 + - + +
369A LEU 3.9 7.6 - - - +
370A THR* 3.9 29.8 - - + -
379A VAL* 1.3 77.6 - - - +
381A PRO* 1.3 81.5 - - + +
382A GLY 3.2 2.6 + - - -
383A LEU* 3.3 34.4 + - + +
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Residues in contact with PRO 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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174A ASP 6.0 1.1 - - - +
175A GLY 5.0 3.4 - - - +
176A ALA* 3.6 24.6 - - + +
177A VAL* 3.0 25.2 + - - +
379A VAL* 3.2 18.1 - - + +
380A VAL* 1.3 87.3 - - + +
382A GLY* 1.3 57.9 + - - +
383A LEU 3.3 2.4 + - - -
426A GLN* 3.9 16.4 - - + +
429A LEU* 4.3 13.5 - - + -
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Residues in contact with GLY 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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177A VAL* 3.3 20.6 - - - +
196A ARG 3.7 13.6 - - - -
197A ALA* 3.5 2.3 - - - -
198A THR* 2.8 34.8 + - - -
380A VAL 3.2 1.0 + - - -
381A PRO* 1.3 70.7 - - - +
383A LEU* 1.3 54.4 + - - +
384A PHE* 3.7 5.5 - - - -
426A GLN* 2.9 24.1 + - - -
429A LEU* 4.0 1.8 - - - -
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Residues in contact with LEU 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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169A LEU* 4.0 20.6 - - + -
177A VAL* 3.9 20.2 - - + -
198A THR* 3.5 13.7 - - + +
200A LEU* 3.8 28.0 - - + -
226A ALA* 5.6 0.4 - - + -
231A VAL* 3.8 33.4 - - + -
360A ILE* 5.0 2.9 - - + -
367A GLN* 3.8 2.4 - - - +
368A ALA* 3.1 37.4 + - + +
379A VAL* 5.6 0.2 - - - +
380A VAL* 3.3 17.8 + - + +
381A PRO 3.3 1.0 - - - -
382A GLY* 1.3 76.4 - - - +
384A PHE* 1.3 79.8 + - - +
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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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197A ALA* 3.5 24.5 - - + -
198A THR 2.9 12.7 + - - +
199A VAL* 3.9 19.3 - - + -
200A LEU* 2.8 25.5 + - - +
365A THR 4.3 6.3 - - - -
366A GLY* 3.1 11.0 - - - +
367A GLN* 3.5 38.1 - - + -
368A ALA* 4.0 2.9 - - - +
382A GLY 3.7 19.3 - - - -
383A LEU* 1.3 97.4 - - - +
385A ALA* 1.3 63.3 + - - +
415A ALA* 5.4 3.8 - - + -
419A LEU* 3.8 20.4 - - + -
422A SER* 3.6 26.2 - - - -
423A ILE* 5.1 1.6 - - + -
426A GLN* 4.2 14.8 - - - -
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Residues in contact with ALA 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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199A VAL* 4.6 0.9 - - - -
200A LEU* 3.2 17.0 - - + +
360A ILE* 4.3 17.9 - - + -
362A THR* 3.6 25.6 + - + +
366A GLY* 2.8 18.6 + - - +
384A PHE* 1.3 76.1 - - - +
386A VAL* 1.3 70.5 + - - +
389A ILE* 4.0 12.3 - - + -
390A ALA* 3.9 7.7 - - + +
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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