Contacts of the strand formed by residues 376 - 385 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372C LEU* 3.2 6.2 - - - -
373C LYS* 2.8 50.6 + - + +
374C GLY 3.1 3.1 - - - +
375C SER* 1.3 80.0 + - - +
377C ILE* 1.3 61.2 + - - +
378C GLU* 3.0 3.5 + - + -
403C GLY* 3.4 32.5 - - - +
404C GLN 3.5 3.6 - - - -
405C ASP* 3.1 27.8 + - - +
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Residues in contact with ILE 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C LEU* 4.1 20.6 - - + -
371C THR 3.6 4.0 - - - +
372C LEU* 3.9 14.1 - - + -
375C SER 4.0 0.2 + - - -
376C LYS* 1.3 69.3 - - - +
378C GLU* 1.3 62.5 + - - +
379C THR 4.0 20.0 - - - +
380C ALA* 4.4 5.4 - - + -
401C LEU* 3.4 50.7 - - + +
402C ILE* 3.7 4.7 - - - +
403C GLY* 2.8 27.9 + - - -
404C GLN* 2.9 21.2 + - + +
405C ASP 4.1 13.5 - - - +
406C PHE* 4.2 11.9 - - + -
410C THR* 5.0 0.2 - - + -
411C ILE* 4.4 5.6 - - + -
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Residues in contact with GLU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C THR* 2.7 31.0 + - + +
372C LEU 4.5 0.2 - - - -
373C LYS* 3.3 49.8 - - + +
376C LYS* 3.0 2.2 + - + -
377C ILE* 1.3 72.0 - - - +
379C THR* 1.3 66.7 + - - +
402C ILE* 3.2 23.9 - - - +
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Residues in contact with THR 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C ASN 4.5 1.1 - - - -
370C LEU* 3.2 4.9 - - - +
371C THR* 2.8 49.4 + - - +
377C ILE* 4.0 4.5 - - - +
378C GLU* 1.3 82.7 + - + +
380C ALA* 1.3 64.1 + - - +
381C ARG* 5.9 3.1 - - - -
402C ILE* 5.3 1.1 - - - -
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Residues in contact with ALA 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C ASN 3.5 4.0 - - - -
370C LEU* 3.4 19.1 - - + -
377C ILE* 4.4 11.0 - - + -
379C THR* 1.3 76.9 - - - +
381C ARG* 1.3 63.0 + - - +
382C ILE* 4.2 5.6 - - + -
393C ARG* 3.4 8.1 + - - -
398C GLU* 3.2 43.5 - - + +
401C LEU* 4.8 3.4 - - + -
402C ILE* 5.4 4.6 - - + +
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Residues in contact with ARG 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C ILE* 2.5 36.3 + - - +
300C ALA* 3.1 31.4 - - - +
301C MET 4.6 0.9 - - - -
302C GLY* 3.6 20.4 - - - +
317C PRO* 5.3 4.4 - - - +
319C GLU* 3.2 30.1 + - - -
367C CYS 3.7 1.3 - - - +
368C LEU* 3.3 2.6 - - - -
369C ASN* 2.6 48.7 + - + +
379C THR* 5.9 4.0 - - + -
380C ALA* 1.3 72.7 - - - +
382C ILE* 1.3 59.1 + - - +
383C ALA 4.1 1.1 - - - -
393C ARG* 3.7 32.3 - - - +
398C GLU* 3.4 2.9 - - - -
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Residues in contact with ILE 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C CYS 3.4 3.6 - - - +
368C LEU* 4.1 26.5 - - + -
370C LEU* 3.8 20.0 - - + -
380C ALA* 4.2 0.9 - - + -
381C ARG* 1.3 77.0 - - - +
383C ALA* 1.3 61.4 + - - +
384C PHE* 3.8 24.7 - - + -
393C ARG* 3.2 5.4 - - - +
394C ALA* 2.9 36.9 + - + +
397C PHE* 3.8 30.3 - - + -
398C GLU* 2.6 26.7 + - + +
401C LEU* 3.8 21.1 - - + -
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Residues in contact with ALA 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C PRO* 3.6 28.2 - - + +
299C ILE* 3.7 27.4 - - + -
300C ALA* 4.2 4.9 - - - +
365C CYS 3.9 0.3 - - - +
366C GLY* 3.6 0.3 - - - -
367C CYS* 2.8 32.9 + - - +
381C ARG 4.1 0.2 - - - -
382C ILE* 1.3 75.8 - - - +
384C PHE* 1.3 68.4 + - - +
392C LYS* 3.4 11.2 - - - +
393C ARG* 5.3 0.2 - - - -
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Residues in contact with PHE 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C PRO* 4.1 5.6 - - - +
364C VAL* 3.8 15.0 - - + -
365C CYS 3.3 13.0 - - - -
366C GLY* 3.6 18.8 - - - -
368C LEU* 5.6 3.8 - - + -
382C ILE* 3.8 26.2 - - + -
383C ALA* 1.3 77.9 - - - +
385C GLY* 1.3 57.4 + - - +
387C MET* 3.7 21.3 + - + +
390C VAL 4.5 1.2 - - - +
391C PRO* 3.4 8.1 - - - +
392C LYS 2.9 28.9 + - - -
394C ALA* 4.6 0.9 - - + -
418C LEU* 3.9 19.3 - - + -
422C PHE* 3.6 30.0 - + + -
439C ALA* 3.7 40.4 - - + -
442C MET* 4.0 7.0 - - + -
443C ALA* 5.9 0.4 - - + -
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Residues in contact with GLY 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C PRO 3.5 11.7 - - - -
291C ILE* 4.8 3.1 - - - -
292C GLY 5.2 0.2 - - - -
296C PRO* 3.7 17.3 - - - +
362C SER* 6.0 0.4 - - - -
364C VAL* 3.8 0.9 - - - -
365C CYS* 2.8 36.7 + - - +
384C PHE* 1.3 73.9 - - - +
386C GLY* 1.3 58.0 + - - -
387C MET* 3.1 17.3 + - - +
390C VAL 5.7 0.4 - - - -
391C PRO* 4.9 2.2 - - - -
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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