Contacts of the helix formed by residues 362 - 374 (chain A) in PDB entry 1P9W
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 THR 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A THR* 4.2 2.2 + - - -
360A THR* 3.4 16.4 + - - -
361A ASN* 1.3 86.2 - - + +
363A ALA* 1.3 65.3 + - - +
364A VAL* 3.9 12.3 - - + +
365A GLY* 2.9 28.6 + - - -
366A ALA 3.5 0.3 + - - -
389A ALA* 4.2 7.4 - - - -
391A ARG* 5.9 1.3 - - - +
446A GLU* 5.8 2.2 - - - -
464A GLU* 3.9 7.3 + - - +
468A GLU* 5.0 10.5 - - - +
478A ILE* 5.0 8.5 - - + -
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Residues in contact with ALA 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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263A THR* 4.5 0.2 - - - -
362A THR* 1.3 72.7 - - - +
364A VAL* 1.3 63.6 + - - +
366A ALA* 3.2 20.3 + - - +
367A VAL* 4.3 1.0 + - - +
387A VAL* 3.5 27.4 - - + +
389A ALA* 3.5 22.8 - - + +
446A GLU* 3.7 27.2 + - + +
448A LEU* 4.1 23.8 - - + +
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Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A THR* 3.9 6.9 - - + +
363A ALA* 1.3 77.2 - - + +
365A GLY* 1.3 65.4 + - - +
366A ALA 3.1 1.2 + - - -
367A VAL* 3.2 16.5 + - - +
368A THR* 3.5 10.9 + - - -
446A GLU* 5.1 2.9 + - - +
448A LEU* 4.0 13.2 - - + -
464A GLU* 3.7 37.6 - - + +
467A MSE 3.8 39.9 - - + +
468A GLU* 3.9 32.1 - - + +
471A ILE* 4.4 5.2 - - + -
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Residues in contact with GLY 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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360A THR* 3.9 10.8 - - - +
361A ASN 5.7 0.2 - - - -
362A THR* 2.9 25.6 + - - -
364A VAL* 1.3 77.7 - - - +
366A ALA* 1.3 55.2 + - - +
368A THR* 3.5 3.1 - - - -
369A ARG* 2.9 30.0 + - - +
464A GLU* 3.8 17.7 - - - -
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Residues in contact with ALA 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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261A LEU* 4.4 4.0 - - + -
263A THR* 4.1 8.1 - - + -
358A LEU* 3.9 23.2 - - + +
360A THR* 3.8 5.1 + - - +
362A THR 3.5 3.4 + - - -
363A ALA 3.2 14.4 + - - +
364A VAL 3.1 1.0 + - - -
365A GLY* 1.3 73.1 - - - +
367A VAL* 1.3 65.4 + - - +
369A ARG* 3.2 3.6 + - - +
370A LEU* 2.9 29.8 + - + +
387A VAL* 3.8 27.6 - - + -
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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
----------------------------------------------------------
363A ALA 5.4 2.2 - - - +
364A VAL 3.2 8.6 + - - +
366A ALA* 1.3 78.4 - - + +
368A THR* 1.3 65.6 - - - +
370A LEU* 3.2 10.6 + - - +
371A ARG* 3.0 24.6 + - + +
380A ILE* 4.2 9.4 - - + +
384A LEU* 3.8 28.2 - - + +
387A VAL* 5.6 0.9 - - + -
448A LEU* 5.8 2.5 - - + -
458A ILE* 4.1 28.0 - - + +
467A MSE 3.5 37.0 - - + -
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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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364A VAL 3.5 3.9 + - - -
365A GLY* 3.3 6.7 + - - -
367A VAL* 1.3 81.1 - - - +
369A ARG* 1.3 63.2 + - - +
371A ARG* 3.3 20.2 + - - +
372A ASP* 3.0 43.9 + - - +
464A GLU* 2.9 42.5 + - + +
467A MSE 6.0 0.5 - - - -
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Residues in contact with ARG 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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335A ILE 5.0 2.2 + - - -
336A ARG* 3.5 25.9 + - - +
358A LEU* 4.4 18.8 - - + +
359A HIS* 5.4 14.5 + - - -
360A THR* 3.7 22.2 - - + -
365A GLY 2.9 20.3 + - - +
366A ALA 3.6 4.0 - - - +
368A THR* 1.3 73.1 - - - +
370A LEU* 1.3 63.9 + - - +
372A ASP* 3.4 12.3 + - - +
373A MSE 3.0 53.0 + - - +
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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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259A ILE* 6.3 3.1 - - + -
261A LEU* 4.1 20.2 - - + -
335A ILE* 4.8 7.2 - - + -
341A ALA* 4.6 8.7 - - + -
345A VAL* 5.8 7.4 - - + -
358A LEU* 4.4 17.3 - - + -
366A ALA* 2.9 19.6 + - + +
367A VAL* 3.6 7.4 - - - +
369A ARG* 1.3 75.9 - - - +
371A ARG* 1.3 63.4 + - - +
373A MSE 3.2 35.5 + - + +
374A GLY 3.3 7.3 + - - -
375A ILE* 3.3 15.4 + - + +
380A ILE* 3.7 35.9 - - + -
384A LEU* 4.9 10.5 - - + -
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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 VAL* 3.0 15.2 + - + +
368A THR* 3.6 20.8 - - - +
370A LEU* 1.3 74.5 - - - +
372A ASP* 1.3 84.2 + - - +
374A GLY* 2.8 26.0 + - - -
375A ILE 3.9 6.1 + - - +
377A PRO* 4.1 20.4 - - + -
380A ILE* 3.6 12.8 - - + +
461A GLU* 3.3 41.8 + - + +
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Residues in contact with ASP 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 THR* 3.0 33.3 + - - +
369A ARG* 3.7 13.9 + - - +
371A ARG* 1.3 106.5 + - - +
373A MSE 1.3 60.4 + - - +
374A GLY* 3.4 1.0 + - - -
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Residues in contact with MSE 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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335A ILE* 4.1 13.2 - - + +
336A ARG 4.3 4.0 - - - +
337A ASP* 4.0 21.5 - - - +
338A LEU* 3.2 34.6 - - + +
341A ALA* 3.5 22.2 - - + -
358A LEU* 5.2 0.7 - - + -
369A ARG* 3.0 49.6 + - + +
370A LEU* 3.4 42.8 - - + +
371A ARG 3.1 0.4 - - - -
372A ASP* 1.3 76.3 - - - +
374A GLY* 1.3 57.8 + - - +
375A ILE* 4.5 1.1 - - + -
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Residues in contact with GLY 374 (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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338A LEU* 3.5 19.1 - - - +
342A GLN* 4.9 3.1 + - - +
370A LEU 3.3 0.6 + - - -
371A ARG 2.8 14.5 + - - -
372A ASP 3.2 1.4 - - - -
373A MSE 1.3 79.1 - - - +
375A ILE* 1.3 61.5 + - - +
376A GLU 3.7 1.7 + - - -
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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