Contacts of the strand formed by residues 436 - 442 (chain A) in PDB entry 2WK6
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 PRO 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A GLU* 3.8 25.1 - - + +
381A LEU 3.0 10.8 - - - +
382A LEU* 3.2 20.8 - - + -
424A LEU* 3.4 27.7 - - + +
425A VAL* 3.9 7.2 - - - +
434A GLY 3.6 3.4 - - - +
435A THR* 1.3 89.1 + - - +
437A TRP* 1.3 59.5 + - - +
438A LEU 3.6 0.4 - - - -
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Residues in contact with TRP 437 (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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381A LEU* 2.8 55.2 + - + +
382A LEU 3.5 22.5 + - - -
383A ALA* 3.5 7.8 - - - +
384A PRO* 5.2 1.2 - - - +
392A VAL* 3.8 29.2 - - + -
423A LEU* 3.7 6.0 - - + +
424A LEU* 2.9 23.5 + - - -
425A VAL* 3.7 26.8 + - + +
431A LEU* 4.1 11.4 - - + -
436A PRO* 1.3 74.1 - - - +
438A LEU* 1.3 83.6 + - + +
455A LEU* 3.3 25.6 - - + -
456A GLN* 4.0 7.5 - - - +
458A ALA* 4.8 2.0 - - + -
459A LEU* 3.4 41.7 - - + +
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Residues in contact with LEU 438 (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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379A GLU 3.8 0.3 - - - +
380A GLU* 3.1 4.5 - - - +
381A LEU* 2.5 59.3 + - + -
397A LEU* 4.3 10.3 - - + -
421A ALA* 3.8 15.7 - - + -
422A GLU 3.0 32.8 - - - +
423A LEU* 3.7 18.6 - - + -
424A LEU* 3.8 4.6 - - - +
436A PRO 3.6 0.6 - - - -
437A TRP* 1.3 108.5 - - + +
439A ARG* 1.3 65.1 + - - +
440A VAL* 4.1 7.6 - - + -
455A LEU* 4.2 17.9 - - + -
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Residues in contact with ARG 439 (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 ARG* 4.5 11.9 - - - +
378A GLN* 4.1 24.6 - - + +
379A GLU 3.6 3.6 - - - +
380A GLU* 2.7 38.0 + - + +
421A ALA* 3.2 5.7 - - - -
422A GLU* 2.9 61.9 + - - +
424A LEU* 3.6 29.1 - - + +
438A LEU* 1.3 75.2 - - - +
440A VAL* 1.3 61.4 + - - +
441A HIS* 3.7 17.4 - - + +
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Residues in contact with VAL 440 (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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377A GLU 3.3 5.9 - - - +
378A GLN* 3.4 1.0 - - - -
379A GLU* 2.7 48.0 + - + +
381A LEU* 4.6 3.4 - - + -
397A LEU* 6.0 0.2 - - + -
401A LEU* 5.1 4.3 - - + -
404A LEU* 3.9 27.4 - - + -
420A GLY 3.8 8.7 - - - +
421A ALA* 4.6 3.8 - - + +
438A LEU* 4.2 14.4 - - + -
439A ARG* 1.3 74.1 - - - +
441A HIS* 1.3 66.4 - - - +
442A ARG* 3.6 5.9 + - + +
447A LEU* 3.9 18.6 - - + -
455A LEU* 3.8 27.6 - - + -
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Residues in contact with HIS 441 (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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285A LEU* 3.9 28.9 - - + +
369A ARG* 3.9 25.4 - - - -
374A ARG* 5.8 2.0 - - + +
375A ALA* 3.4 9.8 + - + +
377A GLU 3.5 5.2 - - - -
378A GLN* 3.3 22.6 + - + +
418A GLY 3.5 20.5 + - - +
419A VAL* 3.2 10.6 - - - +
420A GLY 2.8 32.9 + - - +
422A GLU* 3.1 25.3 + - + +
439A ARG* 3.7 23.8 - - + -
440A VAL* 1.3 74.9 - - - +
442A ARG* 1.3 58.9 + - - +
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Residues in contact with ARG 442 (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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375A ALA* 3.3 6.8 - - - +
376A ARG* 3.0 5.1 + - - +
377A GLU* 2.6 80.9 + - - +
379A GLU* 2.6 38.8 + - - +
404A LEU* 4.6 15.3 - - + -
419A VAL* 3.8 6.1 - - + -
440A VAL* 4.4 10.3 - - + +
441A HIS* 1.3 75.5 - - - +
443A ASP* 1.3 56.9 + - - +
444A GLY* 2.8 32.3 + - - +
445A PRO 3.0 20.6 + - - -
446A ALA* 3.3 20.1 - - - +
447A LEU* 4.4 13.5 - - - +
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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