Contacts of the helix formed by residues 326 - 339 (chain A) in PDB entry 3W0A
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 HIS 326 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ASN 4.1 4.3 - - - -
325A LEU* 1.3 78.0 - - - +
327A GLU* 1.3 65.9 + - - +
328A GLU* 3.5 14.6 + - - +
329A GLU* 2.9 21.0 + - - +
330A HIS* 3.0 19.6 + - - +
366A TYR* 2.7 26.4 + - + +
370A ARG 3.6 23.6 - - - -
371A HIS* 3.5 35.0 + + - -
372A PRO* 4.0 9.8 - - + +
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Residues in contact with GLU 327 (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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136A LEU* 3.8 15.2 - - + +
139A HIS* 3.3 30.8 + - + +
140A HIS* 3.0 34.3 + - - -
277A GLU* 4.8 5.2 - - - +
325A LEU 3.8 1.2 + - - -
326A HIS* 1.3 71.8 - - - +
328A GLU* 1.4 67.6 + - - +
330A HIS* 3.3 9.3 + - + +
331A VAL* 3.0 27.1 + - + +
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Residues in contact with GLU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 3.6 28.5 - - + -
136A LEU* 3.9 24.5 - - + +
326A HIS* 3.5 4.6 - - + +
327A GLU* 1.4 84.5 + - - +
329A GLU* 1.3 55.5 + - - +
331A VAL* 3.4 5.2 - - - +
332A LEU* 3.2 36.1 + - + +
366A TYR* 3.5 44.6 + - + -
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Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU* 3.5 9.1 - - + +
326A HIS* 2.9 28.2 + - + +
328A GLU* 1.3 72.7 - - - +
330A HIS* 1.3 60.4 + - - +
332A LEU* 3.4 0.7 + - - +
333A LEU* 2.9 31.7 + - - +
363A LEU* 3.8 23.1 - - + -
366A TYR* 3.5 26.5 - - + -
367A ILE* 3.6 12.0 - - + +
371A HIS* 2.6 37.0 + - - -
379A LEU* 3.8 10.9 - - - +
383A MET* 3.5 18.6 - - + +
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Residues in contact with HIS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A HIS* 4.2 17.6 + + - -
273A LEU* 3.4 31.9 - - + +
274A ARG* 4.2 7.5 + - - -
276A ASN* 5.0 8.3 + - + +
277A GLU* 4.1 18.4 + - + -
320A LEU* 5.6 4.0 - - + +
325A LEU* 4.1 24.4 - - + +
326A HIS 3.0 12.6 + - - +
327A GLU* 3.6 12.6 - - + +
329A GLU* 1.3 76.9 - - - +
331A VAL* 1.3 59.0 + - + +
333A LEU* 3.4 4.5 + - - +
334A MET* 3.1 55.3 + - + +
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 4.9 2.5 - - + +
135A LEU* 3.6 36.5 - - + +
136A LEU* 4.1 8.5 - - + +
139A HIS* 3.5 40.8 - - + +
244A PHE* 3.6 9.9 - - + -
327A GLU* 3.0 25.2 + - + +
328A GLU* 3.4 16.8 - - - +
330A HIS* 1.3 75.3 - - + +
332A LEU* 1.3 68.9 + - + +
334A MET* 3.5 10.2 + - + -
335A ALA* 3.0 23.9 + - - +
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Residues in contact with LEU 332 (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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131A ILE* 4.4 1.6 - - + -
132A ILE* 4.2 14.4 - - + -
135A LEU* 3.6 24.7 - - + -
328A GLU* 3.2 26.7 + - + +
329A GLU* 3.4 3.3 + - - +
331A VAL* 1.3 77.6 - - + +
333A LEU* 1.3 58.0 + - - +
335A ALA* 3.1 3.3 + - - +
336A ILE* 2.8 35.2 + - + +
359A LEU* 3.7 30.7 - - + +
362A THR* 3.8 24.5 - - + +
363A LEU* 3.9 35.7 - - + -
366A TYR* 4.8 4.7 - - + -
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Residues in contact with LEU 333 (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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273A LEU* 3.9 30.3 - - + -
320A LEU* 4.3 8.1 - - + -
325A LEU* 4.2 14.6 - - + -
329A GLU 2.9 18.7 + - - +
330A HIS* 3.6 5.8 - - - +
332A LEU* 1.3 74.8 - - - +
334A MET* 1.4 58.5 + - - +
336A ILE* 3.3 8.1 + - + +
337A CYS* 2.9 30.1 + - - +
363A LEU* 5.0 4.9 - - + -
383A MET* 3.8 42.1 - - + +
384A ILE* 5.6 0.4 - - + -
386A LYS* 4.9 4.3 - - + -
387A LEU* 3.8 34.8 - - + -
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Residues in contact with MET 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A HIS* 3.6 30.1 - - + -
244A PHE* 3.9 26.9 - - + -
270A VAL* 4.1 13.1 - - + +
273A LEU* 3.9 26.7 - - + -
274A ARG* 3.8 40.4 - - - +
330A HIS* 3.1 35.7 + - + +
331A VAL* 3.8 8.7 - - - +
332A LEU 3.4 0.2 - - - -
333A LEU* 1.4 74.4 - - - +
335A ALA* 1.4 57.1 + - - +
337A CYS* 3.3 3.3 + - - +
338A ILE* 3.1 32.6 + - - +
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Residues in contact with ALA 335 (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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135A LEU* 4.1 17.7 - - + -
244A PHE* 4.0 2.2 - - + -
248A ILE* 3.8 28.0 - - + -
331A VAL 3.0 17.5 + - - +
332A LEU 3.1 4.2 + - - +
334A MET* 1.4 76.5 - - - +
336A ILE* 1.3 55.8 + - - +
338A ILE* 3.3 1.7 + - - +
339A VAL* 3.0 34.5 + - - +
359A LEU* 3.9 18.4 - - + -
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Residues in contact with ILE 336 (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 LEU 2.8 27.0 + - - +
333A LEU* 3.8 7.0 - - + +
335A ALA* 1.3 68.7 - - - +
337A CYS* 1.3 65.5 + - - +
339A VAL 3.4 5.8 - - - +
340A SER* 3.2 2.8 + - - -
356A GLN* 3.0 47.2 + - + +
359A LEU* 3.7 26.5 - - + +
360A SER* 4.0 26.2 - - - +
363A LEU* 3.7 29.8 - - + -
380A TYR* 5.5 1.3 - - + -
384A ILE* 5.2 4.5 - - + -
387A LEU* 3.6 26.2 - - + +
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Residues in contact with CYS 337 (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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266A SER* 4.4 1.1 - - - -
269A GLU* 3.3 42.2 - - - -
270A VAL* 3.8 14.4 - - + -
273A LEU* 4.0 14.1 - - + -
333A LEU 2.9 13.9 + - - +
334A MET 3.3 9.8 + - - +
336A ILE* 1.3 74.9 - - - +
338A ILE* 1.3 58.7 + - - +
340A SER* 2.8 20.8 + - - -
343A ARG* 3.1 18.9 + - - +
387A LEU* 3.8 21.2 - - + +
390A LEU* 4.4 1.1 - - - -
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Residues in contact with ILE 338 (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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241A VAL* 4.0 20.9 - - + -
244A PHE* 3.8 28.5 - - + -
245A ALA* 4.2 10.1 - - + -
248A ILE* 3.9 15.0 - - + -
251A PHE* 3.8 27.6 - - + -
262A LEU* 3.6 25.7 - - + +
263A LEU* 4.7 4.7 - - + -
266A SER* 3.8 16.2 - - - +
270A VAL* 3.4 21.5 - - + -
334A MET 3.1 21.9 + - - +
335A ALA 3.7 3.6 - - - +
337A CYS* 1.3 76.6 - - - +
339A VAL* 1.3 59.0 + - + +
340A SER* 3.0 7.1 + - - -
343A ARG* 5.0 0.5 + - - -
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 4.1 23.6 - - + -
251A PHE* 4.0 23.6 - - + -
254A LEU* 4.8 2.5 - - + -
262A LEU* 4.5 6.5 - - + -
335A ALA 3.0 17.6 + - - +
336A ILE 3.5 3.1 - - - -
337A CYS 3.4 0.2 - - - -
338A ILE* 1.3 75.6 - - - +
340A SER* 1.3 56.6 + - - +
341A PRO* 3.9 0.3 - - - +
352A ILE* 3.6 32.5 - - + +
355A ILE* 3.6 24.9 - - + -
356A GLN* 3.1 30.7 + - + +
359A LEU* 4.3 6.5 - - + -
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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