Contacts of the helix formed by residues 358 - 373 (chain A) in PDB entry 1WK8
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 TYR 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A GLU 3.9 18.6 - - - -
347A GLY* 3.6 10.8 - - - -
348A LYS* 4.0 14.4 - - + +
356A GLY 3.7 2.8 + - - -
357A LEU* 1.3 71.3 - - - +
359A PHE* 1.3 98.2 + + - +
360A ARG* 3.7 36.4 - - + -
361A GLU* 3.0 19.1 + - + +
362A ALA 2.9 18.5 + - - -
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Residues in contact with PHE 359 (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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232A TRP* 3.3 65.7 - + + +
343A VAL* 5.2 1.6 - - + -
347A GLY* 2.8 32.1 + - - +
349A LEU* 3.8 15.9 - - + -
357A LEU 3.4 0.6 + - - -
358A TYR* 1.3 98.8 - + - +
360A ARG* 1.3 80.7 + - + +
362A ALA* 3.7 3.2 - - - +
363A ASN* 2.8 28.2 + - - +
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Residues in contact with ARG 360 (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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202A ASP* 4.3 20.2 + - - +
358A TYR* 3.2 30.1 - - + -
359A PHE* 1.3 105.1 - - + +
361A GLU* 1.3 61.5 + - - +
363A ASN* 3.4 18.4 + - - +
364A ARG* 3.5 15.9 + - - +
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Residues in contact with GLU 361 (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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357A LEU* 3.9 30.6 - - + +
358A TYR* 3.0 22.6 + - + +
360A ARG* 1.3 75.4 - - - +
362A ALA* 1.3 67.8 + - - +
363A ASN 3.1 0.2 - - - -
364A ARG* 3.2 20.0 + - + +
365A ALA* 3.0 22.3 + - + +
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Residues in contact with ALA 362 (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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232A TRP* 4.8 1.3 - - + -
349A LEU* 4.0 31.0 - - + -
354A PHE* 4.5 8.3 - - + -
357A LEU* 4.3 14.1 - - + +
358A TYR 2.9 11.9 + - - +
359A PHE* 3.7 8.7 - - - +
361A GLU* 1.3 79.3 - - - +
363A ASN* 1.3 55.8 + - - +
365A ALA* 4.1 7.4 - - - -
366A ILE* 2.8 42.1 + - + +
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Residues in contact with ASN 363 (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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202A ASP* 3.7 27.8 + - - +
203A PRO 5.5 0.6 + - - -
231A PRO* 3.4 16.8 - - - +
232A TRP* 3.1 42.5 + - + +
359A PHE 2.8 14.2 + - - +
360A ARG* 3.5 13.5 - - - +
361A GLU 3.1 0.2 - - - -
362A ALA* 1.3 77.7 - - - +
364A ARG* 1.3 64.2 + - + +
366A ILE* 3.4 4.3 + - - +
367A LEU* 3.1 42.7 + - - +
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Residues in contact with ARG 364 (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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202A ASP* 5.7 3.1 - - - +
360A ARG 3.5 14.1 + - - +
361A GLU* 3.2 19.5 + - + +
363A ASN* 1.3 82.3 - - + +
365A ALA* 1.3 62.5 + - - +
367A LEU* 3.4 11.4 + - + +
368A ARG* 3.1 28.0 + - + +
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Residues in contact with ALA 365 (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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354A PHE* 4.1 19.7 - - + -
357A LEU* 4.7 7.4 - - + -
361A GLU* 3.0 18.4 + - + +
362A ALA* 3.2 7.6 + - - +
364A ARG* 1.3 76.8 - - - +
366A ILE* 1.3 59.6 + - - +
368A ARG* 3.3 8.0 + - - +
369A ASP* 2.9 30.0 + - - +
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Residues in contact with ILE 366 (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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231A PRO* 3.7 23.3 - - + +
232A TRP* 3.5 26.9 - - + +
234A LEU* 4.4 0.4 - - + -
235A PRO* 3.7 24.2 - - + -
293A TYR* 3.6 18.8 - - + +
349A LEU* 4.9 0.2 - - + -
354A PHE* 3.4 26.0 - - + -
362A ALA* 2.8 26.2 + - + +
363A ASN* 3.7 3.6 - - - +
365A ALA* 1.3 73.8 - - - +
367A LEU* 1.3 60.0 + - - +
369A ASP* 3.6 1.5 - - - +
370A LEU* 2.8 53.5 + - + +
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Residues in contact with LEU 367 (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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203A PRO* 3.8 27.6 - - + -
205A VAL* 3.3 34.5 - - + -
231A PRO* 4.0 16.8 - - + -
363A ASN* 3.1 35.5 + - - +
364A ARG* 3.7 10.8 - - + +
365A ALA 3.3 0.2 - - - -
366A ILE* 1.3 75.5 - - - +
368A ARG* 1.3 59.2 + - + +
370A LEU* 3.6 5.9 + - + +
371A ARG* 3.0 41.7 + - - +
376A LEU* 4.1 13.0 - - + +
379A GLU* 4.9 3.4 - - + +
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Residues in contact with ARG 368 (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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364A ARG* 3.1 15.9 + - + +
365A ALA* 3.7 9.4 - - - +
367A LEU* 1.3 79.1 - - + +
369A ASP* 1.3 56.4 + - - +
371A ARG* 3.4 11.6 + - - +
372A GLY* 3.0 26.2 + - - -
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Residues in contact with ASP 369 (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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293A TYR* 2.7 30.7 + - + +
353A PRO* 5.7 1.9 - - - +
354A PHE* 5.0 4.9 - - + -
365A ALA 2.9 17.3 + - - +
366A ILE* 3.6 4.7 - - - +
368A ARG* 1.3 72.0 - - - +
370A LEU* 1.3 68.0 + - - +
372A GLY* 3.3 2.1 + - - -
373A ARG* 2.8 65.0 + - - +
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Residues in contact with LEU 370 (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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205A VAL* 5.1 5.6 - - + -
207A VAL* 4.1 20.6 - - + -
231A PRO* 5.1 1.6 - - + -
234A LEU* 3.8 16.6 - - + -
292A PRO* 3.8 25.4 - - + -
293A TYR* 3.5 18.4 - - + +
366A ILE* 2.8 39.4 + - + +
367A LEU* 3.9 7.4 - - + +
369A ASP* 1.3 76.0 + - - +
371A ARG* 1.3 62.7 + - - +
373A ARG* 3.3 1.3 + - - -
374A GLY 3.2 3.6 + - - -
375A LEU* 2.9 48.4 + - + +
376A LEU* 4.0 17.3 - - + +
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Residues in contact with ARG 371 (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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367A LEU* 3.0 28.7 + - - +
368A ARG* 3.6 12.3 - - - +
369A ASP 3.2 0.2 - - - -
370A LEU* 1.3 78.5 - - - +
372A GLY* 1.3 62.9 - - - +
374A GLY* 3.1 14.2 + - - -
376A LEU* 3.5 26.4 + - + +
379A GLU* 2.7 42.0 + - - -
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Residues in contact with GLY 372 (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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368A ARG 3.0 16.1 + - - -
369A ASP 3.3 1.1 + - - -
371A ARG* 1.3 77.5 - - - +
373A ARG* 1.3 60.2 + - - +
374A GLY 3.2 1.1 + - - -
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Residues in contact with ARG 373 (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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290A THR* 6.2 1.0 - - - +
291A PRO 5.0 2.2 + - - -
292A PRO* 2.9 33.3 + - - +
293A TYR* 3.5 8.9 - - - -
294A PRO* 5.4 2.4 - - - +
369A ASP* 2.8 58.6 + - - +
370A LEU 3.3 3.1 + - - +
372A GLY* 1.3 77.4 - - - +
374A GLY* 1.3 61.6 + - - +
375A LEU* 3.3 35.6 + - + +
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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