Contacts of the helix formed by residues 360 - 373 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A THR* 5.5 4.5 - - + -
359A ASP* 1.3 100.4 + - + +
361A ASP* 1.3 70.2 + - + +
363A GLU* 2.8 26.8 + - - +
364A LYS* 3.5 8.6 + - - +
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Residues in contact with ASP 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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352A GLN 4.6 5.2 - - - +
355A GLU* 4.9 1.4 - - - +
357A THR* 2.9 33.4 + - + +
358A SER 3.3 5.2 - - - +
359A ASP 2.8 23.2 + - - +
360A TYR* 1.3 77.5 - - - +
362A ARG* 1.3 70.3 + - - +
364A LYS* 3.1 15.4 + - - +
365A LEU* 2.7 42.1 + - - +
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Residues in contact with ARG 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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352A GLN 4.6 0.2 + - - -
353A ILE* 2.9 27.6 + - + -
354A GLU* 4.5 2.0 - - - +
355A GLU* 3.5 40.0 + - - +
358A SER* 2.9 36.9 + - - +
359A ASP* 4.4 5.2 - - - +
360A TYR 2.8 4.2 + - - -
361A ASP* 1.3 92.6 + - - +
363A GLU* 1.3 61.6 + - - +
365A LEU* 3.0 38.3 - - + +
366A GLN* 3.1 12.4 + - + +
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Residues in contact with GLU 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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359A ASP* 5.8 3.8 + - - +
360A TYR* 2.8 14.4 + - - +
362A ARG* 1.3 79.8 - - - +
364A LYS* 1.3 70.3 + - - +
366A GLN* 3.8 3.2 - - - +
367A GLU* 2.8 60.1 + - - +
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Residues in contact with LYS 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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284A ARG* 2.8 63.1 - - + +
360A TYR 3.5 6.7 + - - +
361A ASP* 3.1 16.7 + - - +
363A GLU* 1.3 92.2 + - - +
365A LEU* 1.3 58.5 + - - +
367A GLU* 3.4 11.9 - - + +
368A ARG* 2.8 31.2 + - - +
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Residues in contact with LEU 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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349A ILE* 4.7 6.2 - - + +
352A GLN* 4.1 9.4 - - + +
353A ILE* 3.4 55.0 - - + +
361A ASP* 2.7 18.5 + - - +
362A ARG* 3.0 57.7 - - + +
364A LYS* 1.3 71.0 - - - +
366A GLN* 1.3 83.2 + - + +
368A ARG* 3.4 7.5 + - - +
369A VAL* 2.8 35.4 + - + +
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Residues in contact with GLN 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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172A GLU* 3.8 35.7 + - - +
174A VAL* 4.7 7.9 - - + +
353A ILE* 5.2 4.7 - - - +
362A ARG* 3.1 12.7 + - + +
363A GLU* 4.1 3.4 - - - +
365A LEU* 1.3 90.9 - - + +
367A GLU* 1.3 63.9 + - - +
369A VAL* 4.2 10.3 - - - +
370A ALA* 3.1 30.9 + - - +
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Residues in contact with GLU 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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174A VAL* 5.7 5.3 - - - +
288A MET* 6.2 2.0 - - - -
363A GLU* 2.8 40.7 + - - +
364A LYS* 3.4 14.8 - - + +
366A GLN* 1.3 80.2 - - - +
368A ARG* 1.3 63.8 + - - +
370A ALA* 3.7 3.4 + - - +
371A LYS* 2.7 51.3 + - - +
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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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287A ALA* 3.8 28.7 + - - +
288A MET* 4.7 20.0 - - + +
291A ASP* 2.9 28.3 + - - +
345A ARG* 4.2 4.0 - - - +
348A GLN* 3.9 3.2 - - - +
349A ILE* 3.3 37.3 - - - +
352A GLN* 2.8 33.9 + - - +
364A LYS 2.8 20.4 + - - +
365A LEU* 3.9 6.6 - - - +
367A GLU* 1.3 72.7 - - - +
369A VAL* 1.3 65.7 + - - +
371A LYS* 3.3 11.8 + - + +
372A LEU* 3.1 30.1 + - + +
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Residues in contact with VAL 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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172A GLU* 4.7 10.8 - - + +
346A VAL* 6.3 0.2 - - + -
349A ILE* 3.6 28.7 - - + -
350A ARG* 3.9 26.2 - - - +
353A ILE* 4.7 10.1 - - + -
365A LEU 2.8 29.3 + - - +
366A GLN* 3.9 20.9 - - - +
368A ARG* 1.3 76.4 - - - +
370A ALA* 1.3 63.3 + - - +
372A LEU* 3.2 8.0 + - - +
373A ALA* 3.1 31.0 + - + +
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Residues in contact with ALA 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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172A GLU* 3.8 17.9 - - - +
173A GLY* 5.2 0.4 - - - -
174A VAL* 3.1 42.4 - - + +
366A GLN* 3.1 16.5 + - - +
367A GLU 4.0 3.6 - - - +
368A ARG 3.3 0.2 - - - -
369A VAL* 1.3 77.1 - - - +
371A LYS* 1.3 63.6 + - + +
374A GLY 3.3 30.0 + - - +
375A GLY* 3.8 3.6 + - - +
376A VAL* 5.3 1.8 - - + -
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Residues in contact with LYS 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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192A GLY 4.0 14.8 - - - +
193A MET* 3.5 40.7 - - + +
194A GLN 3.4 26.7 - - - +
195A PHE* 4.4 10.8 - - - +
196A ASP* 5.8 2.5 - - - -
288A MET* 5.3 12.4 - - - -
295A LEU* 5.5 1.6 - - - +
367A GLU* 2.7 54.5 + - - +
368A ARG* 3.3 12.0 + - + +
370A ALA* 1.3 78.9 - - + +
372A LEU* 1.3 62.1 + - + +
373A ALA 3.8 0.2 + - - -
374A GLY 4.1 4.3 - - - +
375A GLY* 5.9 0.4 - - - -
376A VAL* 4.9 15.9 - - + -
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Residues in contact with LEU 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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193A MET* 4.8 14.6 - - + -
291A ASP* 3.3 57.0 - - + +
292A ILE* 6.0 0.4 - - + -
295A LEU* 5.1 13.2 - - + +
342A ILE* 5.2 9.7 - - - +
345A ARG* 5.9 3.8 - - + +
346A VAL* 5.9 6.5 - - + +
349A ILE* 3.6 17.9 - - + -
368A ARG* 3.1 26.5 - - + +
369A VAL* 3.2 6.0 + - - +
370A ALA 3.2 0.6 - - - -
371A LYS* 1.3 81.4 - - + +
373A ALA* 1.3 59.7 + - + +
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Residues in contact with ALA 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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172A GLU* 5.4 8.3 - - + -
346A VAL* 5.2 15.7 - - + -
350A ARG* 5.9 3.6 - - - +
369A VAL* 3.1 19.4 + - + +
372A LEU* 1.3 81.1 - - + +
374A 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