Contacts of the helix formed by residues 358 - 373 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346B GLU* 3.4 24.9 - - + -
347B GLY* 3.4 18.6 - - - -
348B LYS* 4.0 4.9 - - + +
349B LEU* 4.4 0.2 - - - -
356B GLY 3.7 1.8 + - - -
357B LEU* 1.3 73.3 - - - +
359B PHE* 1.3 76.2 + + - +
360B ARG* 3.3 47.7 - - + +
361B GLU* 2.8 46.6 + - + +
362B ALA 2.9 8.8 + - - -
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Residues in contact with PHE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B TRP* 3.5 64.0 - + + +
343B VAL* 4.8 5.4 - - + -
347B GLY* 2.7 29.1 + - - +
349B LEU* 3.8 17.7 - - + +
357B LEU 3.8 0.4 + - - -
358B TYR* 1.3 97.4 - + - +
360B ARG* 1.3 80.6 + - + +
362B ALA* 4.1 0.4 - - - -
363B ASN* 2.9 27.5 + - - +
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Residues in contact with ARG 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ASP* 5.8 2.6 + - - -
232B TRP* 6.1 0.4 - - - -
358B TYR* 2.9 29.0 + - + +
359B PHE* 1.3 102.5 - - + +
361B GLU* 1.3 62.1 + - + +
363B ASN* 3.4 18.6 - - - +
364B ARG* 3.7 6.8 + - - +
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Residues in contact with GLU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B GLY 4.6 1.2 - - - +
357B LEU* 3.7 18.5 - - + +
358B TYR* 2.8 47.1 + - + +
360B ARG* 1.3 70.3 - - + +
362B ALA* 1.3 66.1 + - - +
363B ASN 3.1 1.8 - - - -
364B ARG* 3.2 8.0 + - - +
365B ALA* 3.1 20.4 + - - +
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Residues in contact with ALA 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B TRP* 4.7 2.2 - - + -
349B LEU* 3.8 32.1 - - + -
354B PHE* 4.5 4.9 - - + -
357B LEU* 3.9 20.1 - - + +
358B TYR 2.9 7.2 + - - +
359B PHE 3.7 8.3 - - - +
361B GLU* 1.3 76.6 - - - +
363B ASN* 1.3 57.9 + - - +
365B ALA* 4.2 1.8 - - - -
366B ILE* 2.7 48.8 + - + +
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Residues in contact with ASN 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ASP* 3.7 28.9 - - - +
231B PRO* 3.2 25.4 - - - +
232B TRP* 2.9 50.1 - - + +
359B PHE 2.9 16.0 + - - +
360B ARG* 3.4 15.4 - - - +
361B GLU 3.1 0.4 - - - -
362B ALA* 1.3 79.3 - - - +
364B ARG* 1.3 60.1 + - - +
366B ILE* 3.6 3.3 + - - +
367B LEU* 3.3 20.1 + - - +
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Residues in contact with ARG 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B ARG 3.7 6.8 + - - +
361B GLU* 3.2 9.2 + - - +
363B ASN* 1.3 76.5 - - - +
365B ALA* 1.3 65.7 + - - +
367B LEU* 3.4 9.5 + - + +
368B ARG* 3.3 22.1 + - + +
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Residues in contact with ALA 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B PHE* 4.0 18.3 - - + -
357B LEU* 4.1 14.8 - - + -
361B GLU 3.1 15.3 + - - +
362B ALA 3.6 4.0 - - - +
364B ARG* 1.3 76.3 - - - +
366B ILE* 1.3 58.5 + - - +
368B ARG* 3.3 6.3 + - - +
369B ASP* 2.9 30.4 + - - +
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Residues in contact with ILE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B PRO* 3.5 36.8 - - + +
232B TRP* 3.7 14.6 - - - -
234B LEU* 4.2 1.6 - - + -
235B PRO* 3.9 22.0 - - + -
293B TYR* 3.6 18.6 - - + +
354B PHE* 3.5 23.8 - - + -
362B ALA* 2.7 27.4 + - + +
363B ASN 3.8 4.0 - - - +
365B ALA* 1.3 77.7 - - - +
367B LEU* 1.3 58.1 + - - +
369B ASP* 3.2 1.8 + - - +
370B LEU* 2.8 46.0 + - + +
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Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ASP* 6.3 0.4 - - + -
203B PRO* 4.1 19.5 - - + +
205B VAL* 3.7 25.8 - - + -
231B PRO* 5.6 6.7 - - + -
363B ASN 3.3 12.2 + - - +
364B ARG* 3.8 11.4 - - + +
365B ALA 3.4 0.4 - - - -
366B ILE* 1.3 79.5 - - - +
368B ARG* 1.3 59.0 + - - +
370B LEU* 3.9 5.4 - - + +
371B ARG* 2.9 41.8 + - - +
376B LEU* 3.3 30.1 - - + -
379B GLU* 3.8 17.5 - - - +
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Residues in contact with ARG 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B ARG* 3.3 10.9 + - + +
365B ALA* 3.8 8.7 - - - +
366B ILE 3.3 0.4 - - - -
367B LEU* 1.3 79.4 - - - +
369B ASP* 1.3 62.6 + - - +
371B ARG* 3.4 13.3 + - - +
372B GLY* 3.0 21.0 + - - -
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Residues in contact with ASP 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B TYR* 2.6 30.4 + - + +
353B PRO* 5.7 1.9 - - - +
354B PHE* 4.7 7.2 - - + -
365B ALA 2.9 17.9 + - - +
366B ILE* 3.6 3.6 - - - +
368B ARG* 1.3 74.3 - - - +
370B LEU* 1.3 65.0 + - - +
372B GLY* 3.4 2.1 + - - -
373B ARG* 2.8 61.2 + - - +
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B VAL* 5.1 4.5 - - + -
207B VAL* 4.0 23.3 - - + -
231B PRO* 5.4 1.1 - - + -
234B LEU* 3.8 15.9 - - + -
292B PRO* 3.8 26.2 - - + -
293B TYR* 3.6 16.8 - - + +
366B ILE* 2.8 34.5 + - + +
367B LEU* 3.9 6.3 - - - +
369B ASP* 1.3 78.3 - - - +
371B ARG* 1.3 64.0 + - - +
373B ARG* 3.3 2.9 + - - -
374B GLY 3.2 3.3 + - - -
375B LEU* 3.0 45.6 + - + -
376B LEU* 3.5 19.6 + - + +
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Residues in contact with ARG 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B LEU* 2.9 33.1 + - - +
368B ARG* 3.6 12.9 - - - +
370B LEU* 1.3 78.4 - - - +
372B GLY* 1.3 63.9 + - - +
374B GLY* 3.1 14.4 + - - -
376B LEU* 3.7 26.4 - - + +
379B GLU* 2.2 47.1 + - - -
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Residues in contact with GLY 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B ARG 3.0 15.6 + - - -
369B ASP* 3.9 1.3 - - - -
370B LEU 3.4 0.4 - - - -
371B ARG* 1.3 77.1 - - - +
373B ARG* 1.3 61.6 + - - +
374B GLY 3.2 1.3 + - - -
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Residues in contact with ARG 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B THR* 6.2 1.2 - - - +
291B PRO 4.8 2.6 + - - -
292B PRO* 2.9 32.1 + - - +
293B TYR* 3.5 8.7 + - - -
294B PRO* 5.4 1.8 - - - +
369B ASP* 2.8 58.4 + - - +
370B LEU* 4.1 2.9 - - - +
371B ARG 3.2 0.4 - - - -
372B GLY* 1.3 77.4 - - - +
374B GLY* 1.3 62.0 + - - +
375B LEU* 3.3 37.7 + - + +
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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