Contacts of the helix formed by residues 360 - 371 (chain A) in PDB entry 1P4J
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 ASP 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A ARG 3.9 0.6 + - - -
359A LEU* 1.3 75.3 - - - +
361A TRP* 1.3 65.5 + - - +
362A ASP* 3.3 14.2 + - - +
363A LYS* 3.0 38.7 + - - +
364A ALA* 3.0 19.3 + - - +
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Residues in contact with TRP 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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350A MET* 3.4 27.5 - - + +
354A VAL* 4.3 27.6 - - + +
359A LEU 3.7 1.4 + - - -
360A ASP* 1.3 72.0 - - - +
362A ASP* 1.3 64.4 + - - +
364A ALA* 3.0 4.5 + - - +
365A TRP* 2.8 39.0 + + + +
398A ARG* 5.4 5.2 - - - -
402A ILE* 3.9 31.6 - - + -
405A GLU* 3.3 40.6 - - + -
406A ILE* 3.9 20.6 - - + +
409A ARG* 3.4 46.0 - - - +
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Residues in contact with ASP 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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360A ASP* 3.3 9.8 + - - +
361A TRP* 1.3 82.2 - - - +
363A LYS* 1.3 62.2 + - - +
365A TRP* 3.5 5.5 + - - +
366A GLU* 3.1 23.8 + - - +
409A ARG* 3.2 27.2 + - - -
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Residues in contact with LYS 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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326A PHE 5.2 0.4 - - - -
327A ASP* 2.5 51.1 + - - +
359A LEU* 4.2 18.6 - - + -
360A ASP* 3.0 33.5 + - - +
362A ASP* 1.3 73.8 - - - +
364A ALA* 1.3 67.3 + - - +
366A GLU* 3.3 30.8 + - - +
367A VAL* 3.1 30.9 + - + +
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Residues in contact with ALA 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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350A MET* 3.6 16.8 - - - -
353A LEU* 3.8 25.3 - - + +
354A VAL* 3.8 18.8 - - + -
359A LEU* 4.5 7.6 - - + +
360A ASP 3.0 11.0 + - - +
361A TRP 3.0 7.4 + - - +
363A LYS* 1.3 79.6 - - - +
365A TRP* 1.3 55.7 + - - +
367A VAL* 3.2 4.5 + - - +
368A THR* 2.9 31.7 + - - -
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Residues in contact with TRP 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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346A ILE* 4.2 12.3 - - + -
350A MET* 3.5 25.0 - - + -
361A TRP* 2.8 26.5 + + + +
362A ASP* 3.7 7.6 - - - +
364A ALA* 1.3 73.8 - - - +
366A GLU* 1.3 67.5 + - - +
368A THR* 3.3 5.4 + - + -
369A VAL* 3.0 43.5 + - + +
406A ILE* 3.7 47.8 - - + -
410A PHE* 6.2 2.5 - + + -
413A ARG* 6.1 2.6 - - - +
444A LEU 5.6 0.2 - - - -
447A ALA* 3.3 22.9 + - + -
448A GLY* 3.6 20.2 - - - -
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Residues in contact with GLU 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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362A ASP 3.1 14.4 + - - +
363A LYS* 3.5 34.2 + - - +
365A TRP* 1.3 78.3 - - - +
367A VAL* 1.3 64.8 + - - +
369A VAL* 3.5 3.9 + - - +
370A LYS* 3.2 55.9 + - + +
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Residues in contact with VAL 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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326A PHE* 3.3 34.1 - - + +
327A ASP* 4.8 1.6 - - - +
329A PHE* 3.7 30.1 - - + -
330A PRO* 3.8 13.3 - - + +
349A LEU* 5.2 0.7 - - + -
353A LEU* 4.0 18.2 - - + -
359A LEU* 5.1 0.9 - - + -
363A LYS* 3.1 29.7 + - + +
364A ALA* 3.5 8.1 - - - +
366A GLU* 1.3 79.4 - - + +
368A THR* 1.3 63.0 + - - +
370A LYS* 3.3 2.0 + - - -
371A THR* 3.0 27.1 + - - +
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Residues in contact with THR 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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346A ILE* 4.1 37.7 - - + +
349A LEU* 3.6 32.7 - - + +
350A MET* 3.5 19.8 - - + +
353A LEU* 4.1 1.6 - - - +
364A ALA 2.9 20.1 + - - -
365A TRP* 3.3 8.7 + - + -
367A VAL* 1.3 76.3 - - - +
369A VAL* 1.3 63.3 + - - +
371A THR* 3.1 3.1 + - - -
372A CYS* 3.0 27.3 + - - +
448A GLY 4.2 5.8 - - - +
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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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365A TRP* 3.0 58.0 + - + +
366A GLU* 4.0 4.7 - - - +
368A THR* 1.3 74.8 - - - +
370A LYS* 1.3 64.7 + - + +
372A CYS 3.3 4.9 - - - +
447A ALA 4.2 4.0 - - - +
448A GLY* 3.5 15.0 - - - +
449A SER 3.8 20.6 - - - +
450A HIS* 3.1 36.1 + - + +
478A LYS* 5.0 4.9 - - - +
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Residues in contact with LYS 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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80A LYS* 5.4 2.9 + - - -
327A ASP 5.0 6.5 + - - -
330A PRO* 3.7 35.5 - - + +
331A ASP* 5.6 5.5 + - - -
333A VAL 5.0 0.7 - - - +
366A GLU* 3.2 47.0 + - + +
367A VAL* 3.8 0.7 - - - +
369A VAL* 1.3 78.6 - - + +
371A THR* 1.3 58.7 + - - +
450A HIS* 3.4 24.3 + - + -
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Residues in contact with THR 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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329A PHE* 3.3 26.9 - - + -
330A PRO* 3.8 9.6 - - - +
333A VAL* 3.8 25.6 - - + +
334A ALA* 3.7 4.7 - - - +
335A ILE* 2.9 59.4 + - + +
349A LEU* 4.6 4.5 - - + -
367A VAL 3.0 16.7 + - - -
368A THR 3.6 4.5 - - - -
370A LYS* 1.3 80.2 - - - +
372A CYS* 1.3 61.6 + - - +
373A ALA* 5.3 0.3 - - - +
450A HIS* 4.6 3.4 - - - -
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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