Contacts of the helix formed by residues 363 - 373 (chain A) in PDB entry 6WLY
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 LEU 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A PHE* 4.2 10.3 - - + -
308A LEU* 4.3 7.0 - - + -
332A THR* 5.1 4.0 - - + -
352A MET* 4.0 30.5 - - + -
354A LEU* 3.7 35.2 - - + -
357A GLN* 3.9 38.4 - - + +
359A ARG 4.3 1.1 + - - +
360A ARG* 2.9 20.8 + - - +
362A LEU* 1.3 78.7 - - + +
364A PHE* 1.3 61.5 + - - +
365A ASN 3.1 0.9 + - - -
366A GLU* 3.3 23.1 + - + +
367A VAL* 4.1 3.1 + - - +
391A LEU* 3.9 17.2 - - + +
460A GLY* 6.2 0.7 - - - -
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Residues in contact with PHE 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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304A PHE* 3.6 32.8 - + - -
307A ALA* 4.4 19.3 - - + -
308A LEU* 4.0 15.7 - - + -
311A VAL* 3.8 37.2 - - + -
361A GLU* 3.4 26.5 - - + +
362A LEU 3.1 1.2 - - - -
363A LEU* 1.3 75.0 - - - +
365A ASN* 1.3 61.2 + - - +
366A GLU 3.2 0.2 - - - -
367A VAL* 2.9 11.7 + - + +
368A VAL* 2.9 36.9 + - + +
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Residues in contact with ASN 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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361A GLU 4.6 0.2 + - - -
362A LEU* 2.8 31.0 + - - +
364A PHE* 1.3 77.9 - - - +
366A GLU* 1.3 62.1 + - - +
368A VAL* 4.5 7.6 - - - +
369A ILE* 2.9 31.6 + - - +
459A PHE 3.4 18.2 - - - +
460A GLY 3.0 19.8 + - - +
462A CYS* 2.9 42.8 + - - +
463A ALA* 5.1 1.0 - - - -
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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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332A THR* 4.9 0.9 + - - -
350A LYS* 3.0 35.7 + - - +
352A MET* 3.7 22.5 - - + +
363A LEU* 3.6 17.7 - - + +
364A PHE 3.2 0.6 - - - -
365A ASN* 1.3 76.2 - - - +
367A VAL* 1.3 63.7 + - + +
369A ILE* 5.0 1.3 - - - -
370A MET* 3.1 29.9 + - - +
381A MET* 3.3 29.4 - - + +
391A LEU* 4.5 5.8 - - + -
393A VAL* 4.2 13.5 - - + +
459A PHE* 4.8 6.7 + - - +
460A GLY* 3.4 25.2 + - - -
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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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308A LEU* 5.0 3.8 - - + -
311A VAL* 4.2 35.4 - - + +
312A VAL* 4.7 6.1 - - + -
363A LEU 4.5 8.7 - - - +
364A PHE* 2.9 15.3 + - + +
366A GLU* 1.3 77.3 - - + +
368A VAL* 1.3 68.8 + - + +
370A MET* 3.3 7.2 + - - +
371A ARG* 3.0 57.1 + - + +
384A SER* 4.4 19.3 - - - +
391A LEU* 5.4 2.7 - - + -
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Residues in contact with VAL 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 PHE* 2.9 26.8 + - + +
365A ASN* 4.0 9.9 - - - +
367A VAL* 1.3 78.2 - - + +
369A ILE* 1.3 67.1 + - + +
371A ARG* 3.4 2.0 + - - +
372A ASP* 3.3 34.9 + - - +
373A TYR* 3.8 10.4 - - + -
464A GLN* 4.2 31.0 - - + +
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Residues in contact with ILE 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 ASN 2.9 20.0 + - - +
366A GLU 4.3 2.0 - - - +
368A VAL* 1.3 80.0 - - + +
370A MET* 1.3 63.5 + - - +
373A TYR* 3.1 65.4 + - + +
378A VAL* 5.2 4.3 - - + -
381A MET* 4.2 13.0 - - - -
431A LEU* 4.9 0.7 - - + -
436A VAL* 4.0 15.9 - - + -
459A PHE* 3.9 41.1 - - + -
462A CYS* 3.7 27.4 - - - -
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Residues in contact with MET 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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313A ASP* 5.3 1.3 - - - +
366A GLU 3.1 23.7 + - - +
367A VAL* 3.7 6.5 - - - +
369A ILE* 1.3 76.5 - - - +
371A ARG* 1.3 59.7 + - + +
373A TYR 5.2 0.4 - - - -
374A GLN* 2.8 21.9 + - - +
381A MET* 3.5 39.0 - - + +
382A TYR 4.1 2.5 - - - +
383A ASN* 3.9 30.7 - - - -
384A SER* 4.1 20.2 - - - -
393A VAL* 3.6 31.6 - - + -
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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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310A LEU 5.0 1.2 + - - -
311A VAL* 3.0 37.9 + - - +
367A VAL* 3.0 37.8 + - + +
368A VAL* 3.4 1.5 + - - +
370A MET* 1.3 81.7 - - + +
372A ASP* 1.3 78.3 + - - +
374A GLN* 3.7 7.2 + - - -
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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 VAL* 3.3 20.9 + - - +
371A ARG* 1.3 95.2 - - - +
373A TYR* 1.3 91.2 + - + +
374A GLN* 4.0 8.9 + - - +
434A GLN* 4.7 4.2 + - - +
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Residues in contact with TYR 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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368A VAL* 3.8 20.2 - - + -
369A ILE* 3.1 41.6 + - + +
370A MET* 5.2 0.2 - - - -
372A ASP* 1.3 96.3 - - + +
374A GLN* 1.3 65.2 + - - +
378A VAL* 4.7 9.2 - - + +
430A VAL* 6.2 0.4 - - + -
431A LEU* 4.2 22.0 - - + -
434A GLN* 3.2 56.5 + - + +
436A VAL* 3.7 17.4 - - + +
464A GLN* 2.9 25.7 + - - -
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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