Contacts of the strand formed by residues 437 - 443 (chain A) in PDB entry 1WKB
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 ALA 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ILE* 3.7 23.8 - - + -
211A ILE 3.2 11.7 - - - +
212A ILE* 4.1 5.8 - - - -
213A LYS* 4.8 1.3 - - - -
431A MET* 3.1 29.3 + - + +
432A LEU* 3.3 27.5 - - + +
435A GLY* 4.1 4.1 - - - -
436A ILE* 1.3 78.8 - - - +
438A GLU* 1.3 69.1 + - - +
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Residues in contact with GLU 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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210A ILE* 3.4 5.4 - - - +
211A ILE* 2.5 54.8 + - + +
213A LYS* 2.8 37.0 + - - +
256A ARG* 6.0 2.4 - - - -
263A TRP* 3.3 12.4 - - - -
278A ARG* 3.1 31.0 + - - +
432A LEU* 3.9 5.8 - - - -
435A GLY* 5.2 2.6 - - - +
437A ALA* 1.3 79.8 - - - +
439A ILE* 1.3 61.5 + - - +
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Residues in contact with ILE 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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208A ASP* 4.0 21.3 - - + +
209A TYR 3.2 10.8 - - - +
210A ILE* 4.1 15.7 - - + -
211A ILE* 4.5 0.7 - - - -
276A GLN* 4.5 1.7 + - - -
278A ARG* 3.0 24.5 + - - +
432A LEU* 4.2 22.9 - - + +
438A GLU* 1.3 79.2 - - - +
440A MET* 1.3 68.5 + - - +
441A TYR* 3.9 36.6 - - + +
460A ILE* 6.2 0.3 - - - +
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Residues in contact with MET 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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209A TYR* 2.9 36.3 + - + +
211A ILE* 3.6 23.1 - - + -
269A ALA* 4.3 2.5 - - - +
272A LYS* 3.7 36.1 - - + -
273A LEU* 4.0 26.2 - - + -
276A GLN* 3.7 11.2 - - - +
278A ARG* 5.0 0.2 - - - +
318A ALA* 3.6 43.7 - - - +
319A THR* 3.9 12.3 - - - -
438A GLU 4.1 0.6 + - - -
439A ILE* 1.3 77.4 - - - +
441A TYR* 1.3 74.5 + - - +
442A GLU* 5.0 1.1 - - + +
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Residues in contact with TYR 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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182A ARG* 3.5 58.5 + - + +
206A ILE* 3.8 4.7 - - + -
207A LEU 3.3 2.7 - - - -
208A ASP* 3.6 28.8 + - - -
272A LYS* 5.8 0.9 - - - +
276A GLN* 2.9 45.7 - - - +
439A ILE* 3.9 18.9 - - + +
440A MET* 1.3 81.7 - - - +
442A GLU* 1.3 62.3 + - - +
458A ILE* 3.7 23.4 - - + +
460A ILE* 3.8 22.4 - - + +
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Residues in contact with GLU 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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207A LEU* 2.7 40.9 + - - +
209A TYR* 3.7 24.5 - - + -
272A LYS* 2.8 38.5 + - - +
316A ASP 3.8 1.4 - - - +
317A ASN* 3.6 15.9 - - - +
318A ALA* 2.9 29.9 + - - +
440A MET* 4.7 1.3 - - + +
441A TYR* 1.3 76.5 - - - +
443A PHE* 1.3 95.9 + - - +
446A LYS* 6.6 0.2 - - - -
455A ARG* 5.4 3.1 + - - -
458A ILE* 3.7 8.0 - - - +
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Residues in contact with PHE 443 (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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184A ARG* 3.6 38.8 - - + -
204A VAL* 3.9 8.3 - - + -
205A PRO 3.6 4.0 - - - -
206A ILE* 3.9 17.7 - - + -
207A LEU* 4.7 1.9 - - - +
209A TYR* 5.5 0.3 + - - -
317A ASN* 4.5 6.1 + - - -
442A GLU* 1.3 102.6 + - - +
444A ALA* 1.3 64.1 + - - +
445A GLU 3.2 21.9 + - - +
448A VAL* 3.7 26.7 - - + -
455A ARG* 5.4 7.6 - - - +
456A ALA* 3.6 29.6 - - + -
457A VAL* 4.1 7.6 - - - -
458A ILE* 3.5 29.2 - - + -
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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