Contacts of the helix formed by residues 367 - 376 (chain A) in PDB entry 6PAU
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 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A ASN* 5.5 1.7 + - - +
350A ARG* 3.5 18.6 - - - +
365A VAL 4.1 0.4 + - - -
366A MET* 1.3 75.1 - - - +
368A GLU* 1.3 65.9 + - - +
369A GLU* 3.2 11.2 + - - +
370A GLU* 2.8 39.6 + - - +
371A VAL* 3.0 19.8 + - - +
509A GOL 3.5 27.7 + - - -
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Residues in contact with GLU 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* 3.6 22.8 - - + +
347A LYS* 3.6 45.8 + - + +
350A ARG* 3.7 33.5 + - + +
367A ASP* 1.3 75.6 - - - +
369A GLU* 1.3 64.1 + - - +
371A VAL* 3.3 2.7 + - - +
372A ALA* 3.0 21.1 + - - +
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Residues in contact with GLU 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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204A PRO* 3.7 24.2 - - + +
367A ASP* 3.2 10.7 + - - +
368A GLU* 1.3 78.7 - - - +
370A GLU* 1.3 58.8 + - - +
372A ALA* 3.3 6.9 + - - +
373A HIS* 2.9 28.6 + - - +
509A GOL 4.3 10.0 + - - -
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Residues in contact with GLU 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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203A PRO* 5.8 0.4 - - + -
204A PRO* 4.0 26.8 - - + +
230A PRO 4.7 1.7 - - - +
231A ALA* 4.7 3.3 - - - +
232A ASN* 4.4 8.9 + - - -
365A VAL 3.6 5.7 - - - +
366A MET* 3.2 19.1 - - + -
367A ASP* 2.8 48.9 + - - +
369A GLU* 1.3 72.8 - - - +
371A VAL* 1.3 67.1 + - - +
373A HIS* 3.3 0.3 + - - +
374A TRP* 2.9 45.2 + - + +
509A GOL 2.9 32.8 + - - -
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Residues in contact with VAL 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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341A MET* 4.2 7.8 - - + +
346A ILE* 3.8 16.4 - - + +
349A VAL* 3.5 30.7 - - + -
350A ARG* 3.6 31.4 - - + -
353A ILE* 4.6 4.3 - - + -
366A MET* 3.9 19.0 - - + -
367A ASP 3.0 18.3 + - - +
368A GLU 3.7 6.3 - - - +
370A GLU* 1.3 76.1 - - - +
372A ALA* 1.3 63.6 + - - +
375A PHE* 3.0 34.9 + - + +
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Residues in contact with ALA 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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341A MET* 5.0 0.4 - - - -
346A ILE* 3.6 32.3 - - + +
368A GLU 3.0 15.7 + - - +
369A GLU* 3.7 6.7 - - - +
371A VAL* 1.3 76.2 - - - +
373A HIS* 1.3 63.7 + - - +
376A LEU* 3.1 45.0 + - + +
378A ARG* 5.5 0.5 + - - -
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Residues in contact with HIS 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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198A LEU 4.7 0.7 - - - -
199A TRP* 2.6 55.7 + + - -
202A ARG 3.0 25.5 + - - -
203A PRO* 3.4 26.8 - - + +
204A PRO* 3.7 12.2 - - + +
369A GLU 2.9 17.3 + - - +
370A GLU 3.6 4.5 - - - +
371A VAL 3.2 0.2 - - - -
372A ALA* 1.3 80.4 - - - +
374A TRP* 1.3 78.2 + + + +
375A PHE 3.4 0.3 + - - -
376A LEU 4.4 2.9 + - - +
378A ARG* 3.4 32.3 + - - +
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Residues in contact with TRP 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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199A TRP* 3.4 57.2 - + - +
200A ALA* 3.8 22.0 - - - -
203A PRO* 3.5 28.1 - - + +
229A ILE* 4.1 5.6 - - + -
230A PRO 6.1 0.2 - - - -
366A MET* 3.8 18.7 - - + +
370A GLU* 2.9 41.2 + - + +
373A HIS* 1.3 83.4 - + - +
375A PHE* 1.3 74.4 + - + +
382A ILE* 3.5 6.3 - - - +
422A PHE* 3.4 15.9 - - + -
496A GLN* 3.7 20.0 - - - -
506A GOL 2.9 41.8 + - - -
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Residues in contact with PHE 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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341A MET* 3.6 18.6 - - + +
349A VAL* 4.4 9.0 - - + -
353A ILE* 3.5 26.5 - - + -
366A MET* 3.7 26.9 - - + -
371A VAL* 3.0 31.6 + - + +
374A TRP* 1.3 87.2 - - + +
376A LEU* 1.3 68.9 + - - +
377A PRO* 3.2 1.2 - - - +
382A ILE* 4.2 2.6 - - - +
384A THR* 2.6 41.7 + - + +
397A PHE* 3.9 13.0 - + - -
399A SER* 3.7 22.2 - - - -
422A PHE* 3.8 12.8 - + - -
423A TYR* 3.7 22.2 - + + -
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Residues in contact with LEU 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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341A MET* 3.8 24.0 - - + -
342A GLU* 3.8 24.9 - - - +
343A PRO* 3.8 17.0 - - + -
346A ILE* 4.4 8.7 - - + -
372A ALA* 3.1 41.2 + - + +
373A HIS 4.7 1.2 - - - +
375A PHE* 1.3 76.4 - - - +
377A PRO* 1.3 78.8 - - + +
378A ARG* 3.3 11.1 + - + +
382A ILE* 3.5 10.4 - - - +
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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