Contacts of the helix formed by residues 330 - 347 (chain A) in PDB entry 4WNG
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 ASN 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A TYR* 3.1 32.7 + - + +
326A THR* 4.9 0.4 - - - -
328A LEU* 3.4 7.0 - - + -
329A GLY* 1.3 73.4 - - - +
331A HIS* 1.3 58.6 + - - +
332A ASP* 3.2 5.5 + - - +
333A GLN* 2.5 57.9 + - - +
334A ALA* 3.4 13.5 + - - +
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Residues in contact with HIS 331 (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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326A THR* 5.3 4.0 - - - +
329A GLY 3.1 11.8 + - - +
330A ASN* 1.3 71.6 - - - +
332A ASP* 1.3 57.6 + - - +
334A ALA* 4.4 5.6 - - + +
335A MET* 3.2 25.4 + - + +
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Residues in contact with ASP 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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330A ASN* 3.2 4.2 - - - +
331A HIS* 1.3 77.8 - - - +
333A GLN* 1.3 57.5 + - - +
334A ALA 3.2 1.3 - - - -
335A MET* 3.5 4.2 - - - +
336A HIS* 2.7 33.7 + - - +
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Residues in contact with GLN 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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325A TYR* 3.4 35.5 - - + -
330A ASN* 2.5 36.7 + - - +
332A ASP* 1.3 71.8 - - - +
334A ALA* 1.3 58.7 + - - +
336A HIS* 3.3 29.9 + - - +
337A PHE* 2.9 28.1 + - - +
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Residues in contact with ALA 334 (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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322A GLY* 3.2 30.8 - - - +
325A TYR* 3.6 5.9 - - - +
326A THR* 3.3 26.9 - - - +
330A ASN 3.4 11.9 + - - +
331A HIS* 4.4 5.4 - - + +
333A GLN* 1.3 73.6 - - - +
335A MET* 1.3 56.0 + - - +
336A HIS 3.0 3.4 - - - -
337A PHE* 2.7 28.9 + - - +
338A ALA* 3.5 6.6 + - - +
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Residues in contact with MET 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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331A HIS* 3.2 21.6 + - + +
332A ASP* 3.5 5.3 + - - +
334A ALA* 1.3 77.3 - - - +
336A HIS* 1.3 61.3 + - - +
338A ALA* 4.4 10.1 + - - +
339A GLU* 4.6 3.3 + - - +
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Residues in contact with HIS 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 ASP 2.7 21.4 + - - +
333A GLN* 3.3 31.3 + - - +
334A ALA 2.9 0.2 + - - -
335A MET* 1.3 72.5 - - - +
337A PHE* 1.3 60.8 + - - +
339A GLU* 2.7 47.0 + - + +
340A LYS* 4.1 10.3 + - + +
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Residues in contact with PHE 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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318A CYS* 4.0 14.5 - - - +
321A LEU* 4.4 8.5 - - + -
322A GLY* 3.5 27.6 - - - +
325A TYR* 5.0 2.2 - - + -
333A GLN 2.9 14.3 + - - +
334A ALA 2.7 15.5 + - - +
336A HIS* 1.3 77.2 - - - +
338A ALA* 1.3 62.0 + - - +
339A GLU 3.1 1.0 + - - -
340A LYS* 3.3 13.8 + - - +
341A HIS* 3.4 10.4 + - - +
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Residues in contact with ALA 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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318A CYS 5.2 1.5 + - - -
319A TRP* 6.3 2.2 - - + +
322A GLY* 5.2 1.4 - - - -
334A ALA 3.5 7.5 + - - +
335A MET* 4.6 8.3 - - - +
336A HIS 3.0 0.8 + - - -
337A PHE* 1.3 77.7 - - - +
339A GLU* 1.3 55.7 + - - +
341A HIS* 3.2 14.5 + - + +
342A LEU* 2.9 31.1 + - - +
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Residues in contact with GLU 339 (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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335A MET 4.6 4.6 + - - +
336A HIS* 2.7 31.5 + - + +
338A ALA* 1.3 74.2 - - - +
340A LYS* 1.3 59.5 + - - +
342A LEU* 3.5 6.7 + - - +
343A GLU* 3.3 19.8 + - - +
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Residues in contact with LYS 340 (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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318A CYS* 4.5 13.5 - - - -
336A HIS* 4.1 11.5 + - + +
337A PHE* 3.3 9.6 + - - +
339A GLU* 1.3 75.6 - - - +
341A HIS* 1.3 63.1 + - - +
343A GLU* 3.4 10.0 - - - +
344A ILE* 3.3 20.1 + - - +
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Residues in contact with HIS 341 (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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315A GLY* 3.5 26.1 + - - -
318A CYS* 3.5 24.3 - - + -
319A TRP* 4.0 28.7 + + + +
337A PHE 3.4 2.6 + - - +
338A ALA* 3.2 19.3 + - + +
339A GLU 3.2 0.2 - - - -
340A LYS* 1.3 75.0 - - - +
342A LEU* 1.3 62.4 + - + +
343A GLU 3.1 1.6 - - - -
344A ILE* 3.1 7.2 + - - +
345A SER* 2.7 43.9 + - - -
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Residues in contact with LEU 342 (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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338A ALA 2.9 19.5 + - - +
339A GLU* 3.8 7.2 - - - +
341A HIS* 1.3 78.9 - - + +
343A GLU* 1.3 56.7 + - - +
345A SER* 3.3 9.3 - - - -
346A ARG* 2.9 30.5 + - - +
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Residues in contact with GLU 343 (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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339A GLU 3.3 11.2 + - - +
340A LYS* 3.4 14.8 - - - +
341A HIS 3.1 0.2 - - - -
342A LEU* 1.3 79.9 - - - +
344A ILE* 1.3 57.7 + - - +
346A ARG* 3.4 5.5 + - - +
347A GLU* 3.0 28.1 + - - +
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Residues in contact with ILE 344 (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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311A ARG* 4.8 11.3 - - + +
314A GLU* 5.2 5.4 - - + -
315A GLY* 4.6 22.2 - - - +
340A LYS 3.3 8.1 + - - +
341A HIS 3.1 7.2 + - - +
343A GLU* 1.3 74.2 - - - +
345A SER* 1.3 68.4 + - - +
347A GLU* 3.1 24.3 + - - -
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Residues in contact with SER 345 (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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315A GLY* 6.1 0.2 - - - -
341A HIS* 2.7 29.7 + - - -
342A LEU* 3.3 16.6 - - - -
344A ILE* 1.3 74.2 - - - +
346A ARG* 1.3 63.7 + - - +
347A GLU 3.8 4.0 - - - -
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Residues in contact with ARG 346 (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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342A LEU 2.9 19.3 + - - +
343A GLU* 3.8 5.8 - - - +
345A SER* 1.3 73.6 - - - +
347A GLU* 1.3 59.4 + - - +
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Residues in contact with GLU 347 (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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311A ARG* 6.3 2.9 - - - -
343A GLU 3.0 17.7 + - - +
344A ILE* 3.1 21.5 + - - +
345A SER 3.8 3.6 - - - -
346A ARG* 1.3 81.0 - - - +
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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