Contacts of the helix formed by residues 363 - 377 (chain A) in PDB entry 3W6R
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 PRO 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A LEU* 3.6 22.9 - - + -
354A PHE* 3.4 30.3 - - + +
355A VAL* 3.7 9.1 - - + -
362A ILE* 1.4 91.4 - - + +
364A SER* 1.3 65.5 + - - +
365A ILE* 3.9 18.2 - - + -
366A VAL* 3.1 16.9 + - + +
367A VAL* 3.2 10.6 + - - +
425A PHE* 4.0 11.0 - - + -
472A THR* 3.4 21.5 - - + +
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A PHE 4.4 3.8 + - - -
362A ILE 3.5 3.3 + - - -
363A PRO* 1.3 71.2 - - - +
365A ILE* 1.3 56.4 + - - +
367A VAL* 3.3 7.9 + - - +
368A HIS* 2.7 53.7 + - - -
400A PHE* 6.2 0.4 - - - -
406A VAL* 3.9 11.0 - - - -
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Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO* 3.9 6.7 - - + -
364A SER* 1.3 78.5 - - - +
366A VAL* 1.3 59.0 + - - +
368A HIS* 4.0 0.5 - - - +
369A CYS* 3.0 40.2 + - - -
400A PHE* 3.6 58.9 - - + -
406A VAL* 3.7 19.3 - - + +
407A PRO* 5.9 0.9 - - + -
421A LEU* 4.3 28.0 - - + -
422A LEU* 5.3 1.6 - - + -
425A PHE* 3.7 39.7 - - + -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 3.8 18.4 - - + -
363A PRO* 3.1 19.8 + - + +
365A ILE* 1.3 74.9 - - - +
367A VAL* 1.3 63.6 + - - +
369A CYS* 3.4 1.6 + - - +
370A VAL* 3.0 29.3 + - + +
422A LEU* 3.8 28.3 - - + -
425A PHE* 3.8 27.1 - - + -
426A LEU* 4.2 11.2 - - + -
472A THR* 4.4 9.9 - - + +
475A PHE* 3.9 13.5 - - + -
476A LEU* 5.5 6.3 - - + -
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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
----------------------------------------------------------
362A ILE* 3.8 29.8 - - + +
363A PRO 3.2 13.6 + - - +
364A SER* 3.6 10.3 - - - +
366A VAL* 1.3 76.4 - - - +
368A HIS* 1.3 64.2 + - + +
370A VAL* 3.8 1.4 - - - +
371A ASN* 2.9 52.4 + - - +
475A PHE* 3.8 19.7 - - + -
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Residues in contact with HIS 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A SER* 2.7 42.9 + - - +
365A ILE 4.1 0.7 - - - +
367A VAL* 1.3 79.3 - - + +
369A CYS* 1.3 61.1 + - - +
371A ASN* 3.5 11.9 + - + +
372A GLU* 3.0 33.4 + - + +
406A VAL* 4.1 30.1 - - + +
409A LEU* 3.8 7.4 - - + -
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Residues in contact with CYS 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 ILE* 3.0 32.4 + - - +
366A VAL 3.8 3.1 - - - +
368A HIS* 1.3 75.7 - - - +
370A VAL* 1.3 56.5 + - - +
372A GLU* 3.3 3.3 + - - +
373A ILE* 2.9 36.8 + - + +
409A LEU* 3.7 20.9 - - - -
418A ILE* 3.9 21.1 - - + -
421A LEU* 4.0 20.4 - - - -
422A LEU* 4.1 27.8 - - + -
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Residues in contact with VAL 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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366A VAL* 3.0 23.7 + - + +
367A VAL 3.8 0.4 - - - +
369A CYS* 1.3 71.2 - - - +
371A ASN* 1.3 64.0 + - - +
373A ILE* 3.8 1.1 - - - +
374A GLU* 2.8 32.9 + - + +
422A LEU* 4.2 12.3 - - + -
475A PHE* 3.6 35.0 - - + -
476A LEU* 5.1 3.6 - - + -
479A HIS* 3.5 50.5 - - + +
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Residues in contact with ASN 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* 2.9 44.3 + - - +
368A HIS* 3.6 14.6 - - + +
370A VAL* 1.3 80.9 - - - +
372A GLU* 1.3 63.1 + - + +
374A GLU* 3.6 6.8 + - - +
375A GLN* 3.1 25.1 + - - +
475A PHE* 4.7 4.5 - - - -
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Residues in contact with GLU 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 HIS* 3.0 17.4 + - + +
369A CYS 3.6 4.3 - - - +
371A ASN* 1.3 77.3 - - + +
373A ILE* 1.3 58.2 + - - +
375A GLN* 3.2 22.1 + - - +
376A ARG* 3.0 65.0 + - - +
409A LEU* 3.5 24.9 - - + -
410A SER* 3.7 25.0 + - - -
415A ILE* 4.1 6.5 - - + -
418A ILE* 4.3 13.2 - - + -
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Residues in contact with ILE 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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369A CYS 2.9 26.4 + - - +
372A GLU* 1.3 73.2 - - - +
374A GLU* 1.3 61.9 + - - +
377A GLY* 2.7 29.5 + - - +
378A LEU* 3.4 5.5 + - + +
383A LEU* 3.7 29.2 - - + -
384A TYR* 3.2 26.2 - - + +
415A ILE* 4.0 10.5 - - + -
418A ILE* 3.8 24.0 - - + +
419A CYS* 3.8 25.4 - - - -
422A LEU* 4.4 5.4 - - + -
479A HIS* 3.6 23.6 - - + +
483A VAL* 5.0 0.2 - - + -
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Residues in contact with GLU 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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370A VAL* 2.8 21.2 + - + +
371A ASN* 3.7 7.9 - - - +
373A ILE* 1.3 77.6 - - - +
375A GLN* 1.3 64.8 + - - +
376A ARG 3.6 0.2 + - - -
378A LEU* 3.6 38.0 - - - +
479A HIS* 4.4 9.0 + - - +
482A ARG* 2.9 48.2 + - - +
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Residues in contact with GLN 375 (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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371A ASN 3.1 18.9 + - - +
372A GLU* 3.2 22.8 + - - +
374A GLU* 1.3 81.2 - - + +
376A ARG* 1.3 77.7 + - + +
410A SER* 5.7 2.3 - - - -
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Residues in contact with ARG 376 (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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372A GLU* 3.0 30.5 + - - +
375A GLN* 1.3 90.4 + - + +
377A GLY* 1.3 61.2 + - - +
378A LEU 3.7 1.3 - - - +
379A THR* 4.0 13.3 + - - -
380A GLU* 4.1 9.7 - - - +
409A LEU 3.1 22.0 + - - -
410A SER* 4.0 9.5 + - - +
412A VAL* 2.8 34.8 + - - +
413A ASP* 3.4 17.6 + - - +
415A ILE* 4.0 28.2 - - + +
418A ILE* 4.7 1.0 - - - +
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Residues in contact with GLY 377 (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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373A ILE 2.7 22.9 + - - -
376A ARG* 1.3 73.3 - - - +
378A LEU* 1.3 55.9 + - - +
379A THR 3.1 5.6 - - - -
380A GLU* 3.0 25.7 + - - +
383A LEU* 3.5 24.0 - - - +
415A ILE* 3.8 20.6 - - - +
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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