Contacts of the helix formed by residues 360 - 373 (chain B) in PDB entry 4PKO
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 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284B ARG* 5.5 0.8 + - - -
357B THR* 5.5 2.0 - - + -
358B SER 4.0 0.2 + - - -
359B ASP* 1.3 95.2 - - + +
361B ASP* 1.3 59.0 + - - +
362B ARG 3.6 0.4 - - - +
363B GLU* 3.8 23.6 - - - +
364B LYS* 3.4 26.7 - - - -
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Residues in contact with ASP 361 (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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284B ARG* 3.5 29.2 + - - +
352B GLN 4.4 0.3 - - - +
355B GLU* 4.1 14.7 - - - +
357B THR* 3.1 42.8 + - + +
358B SER 4.1 2.7 - - - +
359B ASP 3.2 4.4 + - - -
360B TYR* 1.3 76.7 - - - +
362B ARG* 1.3 63.6 + - - +
363B GLU 3.2 1.8 - - - -
364B LYS* 3.9 1.8 + - - +
365B LEU* 3.0 47.7 + - - +
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Residues in contact with ARG 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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353B ILE 3.7 19.0 + - - +
354B GLU* 4.3 3.1 - - - +
355B GLU* 2.6 41.2 + - + +
358B SER* 3.1 40.9 + - - +
359B ASP* 5.2 3.4 - - - +
361B ASP* 1.3 82.0 - - - +
363B GLU* 1.3 71.3 + - - +
365B LEU* 4.0 3.1 - - + -
366B GLN* 2.7 44.7 + - - +
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Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 4.3 19.8 - - + +
176B THR* 5.2 9.9 - - - +
359B ASP* 5.4 0.6 - - - +
360B TYR* 3.8 24.1 - - - +
361B ASP 3.2 0.2 - - - -
362B ARG* 1.3 81.5 - - - +
364B LYS* 1.3 100.8 + - - +
367B GLU* 3.4 26.7 + - - +
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Residues in contact with LYS 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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284B ARG* 4.3 37.3 - - + +
288B MET* 5.3 2.8 - - - +
360B TYR 3.4 19.4 + - - +
361B ASP 3.9 2.3 + - - +
363B GLU* 1.3 108.3 + - - +
365B LEU* 1.3 58.7 + - - +
367B GLU* 3.2 22.7 - - - +
368B ARG* 3.1 25.2 + - - +
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Residues in contact with LEU 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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349B ILE* 4.2 6.5 - - + -
352B GLN* 2.9 38.1 - - + +
353B ILE* 3.7 21.5 - - + +
361B ASP* 3.0 36.8 + - - +
362B ARG* 3.3 5.4 + - - -
364B LYS* 1.3 72.7 - - - +
366B GLN* 1.3 80.8 + - - +
367B GLU 3.1 1.3 - - - -
368B ARG* 3.2 29.9 + - - +
369B VAL* 3.0 29.4 + - + +
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Residues in contact with GLN 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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172B GLU 3.9 6.7 - - - +
174B VAL* 3.8 15.1 - - + +
353B ILE* 3.1 34.5 - - + +
362B ARG* 2.7 62.1 + - - +
363B GLU 4.4 0.2 - - - +
365B LEU* 1.3 90.3 - - - +
367B GLU* 1.3 60.3 + - - +
369B VAL* 3.7 8.8 - - + +
370B ALA* 2.9 32.1 + - - +
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Residues in contact with GLU 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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174B VAL* 3.7 13.4 - - + +
196B ASP* 5.5 3.3 - - - +
288B MET* 5.3 7.1 - - - +
363B GLU* 3.4 22.2 + - - +
364B LYS* 3.2 34.2 - - - +
366B GLN* 1.3 78.4 - - - +
368B ARG* 1.3 60.0 + - - +
370B ALA* 3.7 2.6 - - - +
371B LYS* 3.0 60.5 + - - +
376B VAL* 4.3 8.8 - - + +
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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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284B ARG* 4.6 20.0 + - - +
287B ALA* 4.0 23.8 + - - +
288B MET* 3.6 27.9 - - + +
291B ASP* 3.0 31.4 - - + +
345B ARG* 5.7 2.8 - - - +
348B GLN* 6.0 0.2 - - - +
349B ILE* 3.1 29.5 - - + +
352B GLN* 2.9 27.9 + - - -
364B LYS 3.1 8.8 + - - +
365B LEU* 3.2 27.6 + - - +
367B GLU* 1.3 78.4 - - - +
369B VAL* 1.3 63.4 + - - +
371B LYS* 3.3 17.2 + - - +
372B LEU* 3.1 23.3 + - + +
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Residues in contact with VAL 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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172B GLU* 4.8 15.9 - - + +
346B VAL* 4.6 9.2 - - + +
349B ILE* 3.6 31.9 - - + -
350B ARG* 3.8 22.4 - - - +
353B ILE* 4.2 10.5 - - + -
365B LEU* 3.0 31.7 + - + +
366B GLN* 3.8 9.0 - - + +
367B GLU 3.4 0.2 - - - -
368B ARG* 1.3 75.2 - - - +
370B ALA* 1.3 65.2 + - - +
372B LEU* 3.2 19.6 + - - +
373B ALA* 3.5 12.7 + - + +
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Residues in contact with ALA 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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172B GLU* 3.2 39.2 + - - +
173B GLY* 4.1 1.8 - - - -
174B VAL 4.7 1.8 - - - +
366B GLN 2.9 14.8 + - - +
367B GLU* 3.7 4.7 - - - +
369B VAL* 1.3 76.1 - - - +
371B LYS* 1.3 59.1 + - - +
374B GLY 2.8 36.9 + - - +
375B GLY* 4.0 15.7 - - - +
376B VAL* 4.3 8.1 - - + -
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Residues in contact with LYS 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B GLY* 3.5 24.1 - - - +
193B MET* 3.3 40.4 + - + +
194B GLN* 2.5 40.1 + - - +
195B PHE* 4.6 6.1 - - + +
288B MET* 5.0 9.6 - - - -
295B LEU* 4.6 0.3 - - - +
367B GLU* 3.0 55.8 + - - +
368B ARG* 3.6 9.9 - - - +
369B VAL 3.3 0.2 - - - -
370B ALA* 1.3 76.3 - - - +
372B LEU* 1.3 61.6 + - + +
373B ALA 4.9 0.2 - - - -
374B GLY 4.2 1.1 - - - +
376B VAL* 3.9 22.6 - - + +
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Residues in contact with LEU 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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193B MET* 4.9 8.7 - - + -
291B ASP* 3.5 52.7 - - + +
295B LEU* 4.3 19.4 - - + +
342B ILE* 3.8 35.1 - - + +
345B ARG* 5.2 12.3 - - + +
346B VAL* 4.6 15.0 - - + -
349B ILE* 5.0 6.3 - - + -
368B ARG* 3.1 20.9 - - + +
369B VAL* 3.2 13.4 + - - +
370B ALA 3.1 1.0 - - - -
371B LYS* 1.3 81.1 - - + +
373B ALA* 1.3 58.7 + - - +
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Residues in contact with ALA 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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172B GLU* 6.0 5.4 - - + -
192B GLY* 5.5 2.1 - - - -
342B ILE* 5.0 1.8 - - + -
343B GLN* 4.7 19.1 - - - +
346B VAL* 4.9 9.6 - - + -
369B VAL* 3.5 7.9 + - + +
370B ALA 3.4 0.8 + - - -
372B LEU* 1.3 81.1 - - + +
374B GLY* 1.3 66.6 + - - +
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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