Contacts of the strand formed by residues 364 - 373 (chain E) 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 VAL 364 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353E LEU* 3.0 32.8 + - + +
362E SER* 3.7 4.8 - - - -
363E ALA* 1.3 87.3 - - + +
365E CYS* 1.3 64.5 + - - +
384E PHE* 3.8 27.4 - - + -
385E GLY 3.6 7.9 - - - +
387E MET* 4.2 8.3 - - + -
434E TYR* 6.1 0.2 - - + -
435E ARG* 3.5 38.8 - - + +
438E ALA* 3.9 9.9 - - + -
439E ALA* 4.5 4.9 - - - -
442E MET* 3.7 22.6 - - + +
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Residues in contact with CYS 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E LEU* 4.6 12.6 - - - -
291E ILE 6.0 0.9 - - - +
292E GLY 5.8 0.4 - - - +
293E ASP* 3.6 29.4 - - - +
296E PRO* 4.5 10.3 - - + +
351E TYR 3.1 14.8 - - - -
352E LYS* 4.7 0.7 - - - -
362E SER* 4.0 6.5 - - - +
364E VAL* 1.3 80.9 - - - +
366E GLY* 1.3 59.5 + - - +
367E CYS* 3.9 16.8 + - - -
383E ALA 3.8 0.5 - - - +
384E PHE* 3.4 7.1 - - - -
385E GLY* 2.8 43.6 + - - -
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Residues in contact with GLY 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349E ARG 3.7 1.6 - - - +
350E CYS* 3.7 1.0 - - - -
351E TYR* 2.7 43.0 + - - +
365E CYS* 1.3 72.1 - - - +
367E CYS* 1.3 64.2 + - - -
368E LEU* 3.9 7.2 - - - +
383E ALA 3.7 0.2 - - - -
384E PHE* 3.7 14.6 - - - -
442E MET* 3.4 21.0 - - - -
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Residues in contact with CYS 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E LEU* 4.7 1.3 - - - -
296E PRO* 3.5 26.0 - - - +
297E ALA* 3.3 32.5 - - - -
300E ALA* 3.5 13.6 - - + +
349E ARG 3.3 5.2 - - - +
350E CYS* 3.8 21.3 - - - -
365E CYS* 3.9 10.0 + - - -
366E GLY* 1.3 76.1 - - - -
368E LEU* 1.3 61.9 + - - +
382E ILE* 3.6 0.3 - - - -
383E ALA 2.7 40.2 + - - +
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Residues in contact with LEU 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E ALA* 4.5 0.4 - - - -
347E GLY 3.6 1.4 - - - +
348E LEU* 3.4 1.2 - - - +
349E ARG 2.8 34.4 + - - +
351E TYR* 4.3 20.2 - - + -
366E GLY* 3.9 18.6 - - - +
367E CYS* 1.3 79.2 - - - +
369E ASN* 1.3 61.6 + - - +
370E LEU* 5.2 2.2 - - + -
381E ARG 3.5 4.3 - - - +
382E ILE* 4.0 32.3 - - + -
384E PHE* 5.0 5.2 - - + -
397E PHE* 5.3 3.1 - - + -
442E MET* 4.2 13.7 - - + +
443E ALA* 4.2 12.3 - - + -
446E TYR* 3.6 39.1 - - + -
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Residues in contact with ASN 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E ALA 3.1 30.9 + - - +
301E MET* 3.7 14.6 - - - +
345E ALA* 4.0 18.7 - - - +
347E GLY* 3.6 3.8 - - - -
348E LEU* 3.5 22.1 + - + +
368E LEU* 1.3 77.4 - - - +
370E LEU* 1.3 71.2 + - - +
371E THR* 5.0 2.3 + - - -
379E THR* 4.2 1.9 - - - +
380E ALA* 3.7 0.2 - - - -
381E ARG* 2.7 41.9 + - - +
446E TYR* 3.7 4.0 + - - -
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Residues in contact with LEU 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346E PRO 4.8 2.6 - - - +
347E GLY* 4.4 7.6 - - - -
368E LEU* 5.2 2.2 - - + -
369E ASN* 1.3 89.4 + - - +
371E THR* 1.3 65.4 + - - +
372E LEU* 4.3 9.9 - - + +
377E ILE* 3.8 26.7 - - + -
379E THR* 3.1 6.5 - - - +
380E ALA* 3.2 32.3 - - + -
381E ARG 4.0 0.2 - - - +
382E ILE* 4.1 16.4 - - + -
401E LEU* 4.5 9.0 - - + -
406E PHE* 4.2 27.1 - - + -
411E ILE* 5.5 2.0 - - + -
446E TYR* 3.2 28.7 + - + +
450E LEU* 6.1 0.7 - - + -
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Residues in contact with THR 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E ASN* 5.0 2.6 + - - -
370E LEU* 1.3 76.4 + - - +
372E LEU* 1.3 60.3 + - - +
377E ILE 3.7 0.2 - - - -
378E GLU* 2.7 62.2 + - - +
379E THR* 2.8 31.9 + - - +
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Residues in contact with LEU 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E LEU* 4.6 11.0 - - + +
371E THR* 1.3 82.1 - - - +
373E LYS* 1.3 58.2 + - - +
374E GLY* 3.2 13.1 + - - +
375E SER 4.9 4.0 - - - +
376E LYS 3.4 6.5 - - - +
377E ILE* 3.7 37.9 - - + -
378E GLU* 4.4 4.9 - - - +
406E PHE* 3.6 38.4 - - + -
450E LEU* 5.4 5.4 - - + -
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Residues in contact with LYS 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372E LEU* 1.3 67.8 - - - +
374E GLY* 1.3 70.3 + - - +
376E LYS* 3.0 24.7 + - + +
378E GLU* 3.3 36.4 - - + +
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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