Contacts of the helix formed by residues 368 - 383 (chain B) in PDB entry 1P5Q
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 368 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B HIS* 2.8 36.6 + - + +
364B LEU 4.4 0.4 + - - -
366B VAL* 4.2 13.0 - - + +
367B ASN* 1.3 72.7 - - - +
369B PHE* 1.3 65.4 + - - +
370B GLU* 3.1 8.3 - - - +
371B LEU* 2.8 50.9 + - - +
372B ALA* 3.0 9.6 + - - -
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Residues in contact with PHE 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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364B LEU* 4.4 21.0 - - + +
367B ASN* 3.2 45.1 - - + -
368B ASP* 1.3 73.8 - - - +
370B GLU* 1.3 65.9 + - + +
372B ALA* 3.4 6.1 + - - +
373B ARG* 2.9 27.0 + - - +
396B CYS* 3.9 9.3 - - + +
399B ARG* 3.1 57.0 - - + -
400B ILE* 3.2 24.2 - - + +
403B GLN* 3.2 35.2 - - + -
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Residues in contact with GLU 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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368B ASP* 2.8 8.3 + - - +
369B PHE* 1.3 77.2 - - + +
371B LEU* 1.3 68.1 + - + +
373B ARG* 3.3 30.1 + - - +
374B ALA* 3.2 18.2 + - - +
400B ILE* 4.0 18.4 - - - +
403B GLN* 3.9 17.1 - - - +
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Residues in contact with LEU 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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363B HIS* 3.8 33.3 - - + +
368B ASP* 2.8 39.7 + - - +
370B GLU* 1.3 81.9 - - + +
372B ALA* 1.3 60.6 + - - +
374B ALA* 3.3 11.7 - - + +
375B ASP* 3.3 22.7 + - - +
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Residues in contact with ALA 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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360B GLY* 3.5 13.0 - - - +
363B HIS* 3.8 6.6 - - + +
364B LEU* 3.5 40.8 - - + +
368B ASP 3.0 6.8 + - - +
369B PHE* 3.8 6.7 - - - +
371B LEU* 1.3 73.3 - - - +
373B ARG* 1.3 57.4 + - - +
375B ASP* 3.1 2.4 + - - +
376B PHE* 2.8 42.7 + - + -
396B CYS* 3.9 8.1 - - - -
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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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369B PHE 2.9 16.8 + - - +
370B GLU* 3.3 30.7 + - - +
372B ALA* 1.3 74.8 - - - +
374B ALA* 1.3 53.5 + - - +
376B PHE* 3.1 2.6 + - - +
377B GLN* 2.6 61.5 + - - +
393B LEU* 4.0 21.9 - - + +
396B CYS* 4.0 13.6 - - + -
397B GLN* 3.7 29.0 + - - +
400B ILE* 3.7 25.6 - - + +
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Residues in contact with ALA 374 (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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370B GLU 3.2 8.6 + - - +
371B LEU* 3.3 15.9 - - + +
372B ALA 3.1 0.2 - - - -
373B ARG* 1.3 80.8 - - - +
375B ASP* 1.3 62.0 + - - +
377B GLN* 3.1 13.0 + - - +
378B LYS* 3.0 28.5 + - - +
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Residues in contact with ASP 375 (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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356B LEU* 3.5 23.3 - - + +
359B ARG* 2.7 53.5 + - - +
360B GLY* 4.0 7.0 - - - -
363B HIS* 3.4 16.0 - - - -
371B LEU 3.3 9.8 + - - +
372B ALA 3.1 7.6 + - - +
374B ALA* 1.3 78.5 - - - +
376B PHE* 1.3 59.4 + - + +
378B LYS* 3.2 6.5 + - - +
379B VAL* 2.8 34.5 + - - +
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Residues in contact with PHE 376 (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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357B SER* 3.9 24.5 - - - -
360B GLY* 3.4 35.9 - - - -
361B GLU* 3.5 16.4 - - - -
364B LEU* 4.2 7.4 - - + -
372B ALA* 2.8 35.1 + - + +
373B ARG 3.8 2.7 - - - +
375B ASP* 1.3 71.5 - - - +
377B GLN* 1.3 65.5 + - - +
379B VAL* 4.3 4.4 - - + +
380B LEU* 3.4 28.8 + - - +
388B ALA* 5.3 0.9 - - + -
389B ALA* 4.1 18.3 - - + +
392B GLN* 3.4 42.6 - - + -
393B LEU* 3.9 20.0 - - + -
396B CYS* 4.3 4.5 - - - -
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Residues in contact with GLN 377 (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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373B ARG* 2.6 56.4 + - + +
374B ALA* 3.1 9.6 + - - +
376B PHE* 1.3 73.0 - - - +
378B LYS* 1.3 63.2 + - - +
380B LEU* 3.3 8.4 + - - +
381B GLN* 3.1 26.8 + - - +
393B LEU* 4.5 10.1 - - + -
397B GLN* 5.3 4.1 - - - +
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Residues in contact with LYS 378 (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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350B SER 4.6 5.1 + - - -
351B ASN* 3.6 13.7 + - - -
356B LEU* 3.3 22.9 - - + +
374B ALA 3.0 15.9 + - - +
375B ASP* 3.6 2.7 - - - +
377B GLN* 1.3 75.0 - - - +
379B VAL* 1.3 66.9 + - - +
380B LEU 3.0 0.9 + - - -
381B GLN* 3.0 49.5 + - + +
382B LEU* 3.1 36.7 + - + +
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Residues in contact with VAL 379 (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 GLU* 4.0 13.7 - - + +
356B LEU* 3.2 36.8 - - + +
357B SER* 3.6 30.3 - - - +
375B ASP 2.8 22.0 + - - +
376B PHE* 4.3 8.1 - - + +
377B GLN 3.5 0.2 - - - -
378B LYS* 1.3 72.0 - - - +
380B LEU* 1.3 57.9 + - - +
382B LEU* 4.9 0.2 - - - -
383B TYR* 2.9 34.0 + - + +
386B ASN* 4.0 25.6 - - + +
389B ALA* 4.0 8.3 - - + -
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Residues in contact with LEU 380 (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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376B PHE 3.4 19.4 + - - +
377B GLN* 3.3 5.3 + - - +
378B LYS 3.0 1.0 - - - -
379B VAL* 1.3 76.4 - - - +
381B GLN* 1.3 66.9 + - - +
382B LEU 3.1 2.0 - - - -
383B TYR 3.6 4.7 - - - +
384B PRO* 2.9 48.6 - - + +
386B ASN 3.5 24.7 - - - +
389B ALA* 3.5 8.7 - - + -
390B LYS* 3.8 37.0 - - + +
393B LEU* 4.1 19.1 - - + -
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Residues in contact with GLN 381 (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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377B GLN* 3.1 16.8 + - - +
378B LYS* 3.2 51.6 - - + +
380B LEU* 1.3 75.3 - - - +
382B LEU* 1.3 62.8 + - - +
384B PRO* 4.3 8.5 - - - +
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Residues in contact with LEU 382 (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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351B ASN* 3.7 36.8 - - + +
356B LEU* 4.2 11.0 - - + -
378B LYS* 3.1 55.1 + - + +
381B GLN* 1.3 80.8 - - + +
383B TYR* 1.3 93.3 + - + +
384B PRO* 3.9 4.5 - - - +
1006B SO4 5.0 1.0 + - - -
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Residues in contact with TYR 383 (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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351B ASN* 2.7 36.3 + - + +
352B ASN* 4.6 0.7 - - - -
353B GLU* 3.3 52.4 + - + +
356B LEU* 6.0 0.7 - - + -
379B VAL* 2.9 24.1 + - - +
380B LEU* 3.0 8.9 - - - +
382B LEU* 1.3 102.6 - - + +
384B PRO* 1.3 67.6 - - - +
385B ASN 3.0 1.7 + - - -
386B ASN* 3.2 11.2 + - + +
1006B SO4 3.0 28.5 - - - +
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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