Contacts of the helix formed by residues 344 - 353 (chain A) in PDB entry 2W3C
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 CYS 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A SER 5.1 1.1 - - - -
304A GLN* 3.6 30.5 - - - +
305A LYS* 4.9 18.2 - - - -
341A ILE 2.8 10.2 + - - +
342A ARG 3.2 0.2 - - - -
343A GLY* 1.3 78.0 - - - +
345A GLN* 1.3 67.3 + - - +
346A VAL* 4.3 7.9 - - - -
347A ASN* 3.0 35.5 + - + -
348A GLN* 2.9 25.2 + - - +
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Residues in contact with GLN 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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343A GLY 4.1 2.2 + - - -
344A CYS* 1.3 71.7 - - - +
346A VAL* 1.3 55.9 + - + +
347A ASN 3.1 0.2 + - - -
348A GLN* 3.3 7.9 + - - +
349A ASP* 2.7 67.5 + - - +
395A LYS 4.4 4.2 - - - +
396A ASN* 2.5 46.4 + - - +
397A GLN 4.8 1.0 + - - -
398A LYS* 4.0 16.5 + - + +
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Residues in contact with VAL 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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305A LYS* 6.2 7.0 - - + -
308A PHE* 3.7 41.0 - - + -
309A GLN* 5.5 0.7 - - - +
344A CYS* 3.4 7.1 - - - -
345A GLN* 1.3 77.8 - - + +
347A ASN* 1.3 60.5 + - - +
349A ASP* 3.8 9.1 - - - +
350A TYR* 3.1 25.3 + - - +
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Residues in contact with ASN 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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304A GLN* 2.9 29.1 + - - +
305A LYS* 5.1 0.3 - - - -
308A PHE* 3.1 27.8 - - - +
313A LEU* 3.6 19.3 - - + +
340A VAL* 2.8 34.3 + - - +
341A ILE* 3.7 12.1 - - - +
344A CYS* 3.0 19.3 + - + +
346A VAL* 1.3 77.5 - - - +
348A GLN* 1.3 57.0 + - - +
350A TYR* 3.3 2.8 + - - +
351A PHE* 2.7 34.7 + - - +
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Residues in contact with GLN 348 (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 ILE* 3.2 21.3 - - + +
343A GLY 3.1 10.9 - - - +
344A CYS 2.9 25.4 + - - +
345A GLN* 3.7 8.5 + - - +
347A ASN* 1.3 73.2 - - - +
349A ASP* 1.3 64.3 + - - +
351A PHE* 3.3 1.9 + - - +
352A ALA* 3.1 18.9 + - - +
391A CYS 2.7 26.8 + - - +
392A PHE* 3.0 37.4 + - + +
394A TYR 3.0 21.7 + - - +
395A LYS 5.0 0.5 - - - -
396A ASN* 3.4 30.3 - - - +
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Residues in contact with ASP 349 (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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345A GLN* 2.7 55.4 + - - +
346A VAL* 3.8 9.3 - - - +
348A GLN* 1.3 72.7 - - - +
350A TYR* 1.3 62.5 + - - +
352A ALA* 3.5 4.8 + - - +
353A SER* 3.4 20.7 + - - -
392A PHE* 5.4 0.6 - - - -
396A ASN* 5.1 0.5 + - - -
398A LYS* 3.3 27.7 + - - +
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Residues in contact with TYR 350 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A PHE* 3.9 22.0 - + + -
313A LEU* 3.8 18.2 - - + -
314A GLN* 3.5 49.2 + - + +
317A CYS* 4.1 11.7 - - - +
346A VAL 3.1 19.5 + - - +
347A ASN 3.6 2.9 - - - +
349A ASP* 1.3 75.0 - - - +
351A PHE* 1.3 69.6 + - - +
353A SER* 2.7 30.3 + - - -
354A VAL* 3.4 27.6 - - + +
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Residues in contact with PHE 351 (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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317A CYS* 4.0 13.7 - - - -
320A LEU* 4.3 15.0 - - + -
337A VAL* 3.8 26.7 - - + -
341A ILE* 4.0 25.1 - - + -
347A ASN 2.7 20.0 + - - +
348A GLN 3.3 4.4 + - - +
350A TYR* 1.3 79.6 - - + +
352A ALA* 1.3 63.5 + - - +
353A SER 3.2 0.9 + - - -
354A VAL* 3.2 22.0 + - + +
364A ALA* 3.5 30.0 - - + +
365A ILE* 4.2 10.8 - - + -
368A LEU* 3.7 33.0 - - + -
388A CYS* 3.6 17.9 - - - -
392A PHE* 4.5 7.0 - + + -
1630A PEG 4.9 3.6 - - - -
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Residues in contact with ALA 352 (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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348A GLN 3.1 8.5 + - - +
349A ASP* 4.0 5.6 - - - +
350A TYR 3.3 0.2 - - - -
351A PHE* 1.3 76.2 - - - +
353A SER* 1.3 58.8 + - - +
354A VAL 3.3 6.8 + - - +
355A ASN* 5.1 1.4 - - - +
363A PRO* 4.8 6.8 - - - +
364A ALA* 4.4 5.8 + - - -
365A ILE* 3.7 20.2 - - + +
392A PHE* 3.5 30.5 - - + -
402A GLU* 5.1 5.4 - - - +
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Residues in contact with SER 353 (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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349A ASP 3.4 10.6 + - - -
350A TYR* 2.7 34.9 + - - -
352A ALA* 1.3 77.9 - - - +
354A VAL* 1.3 59.1 + - - +
355A ASN* 3.7 14.7 + - - -
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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