Contacts of the helix formed by residues 370 - 384 (chain A) in PDB entry 2DW1
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 SER 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A TYR* 4.2 2.3 - - - -
344A ASP* 2.5 39.5 + - - -
348A CYS* 4.2 0.7 - - - -
349A SER 3.3 27.1 - - - -
350A CYS* 3.9 2.8 - - - +
355A CYS* 4.2 7.1 - - - +
357A MET 5.8 0.2 - - - +
368A PHE 4.2 0.4 + - - -
369A PHE* 1.3 78.2 - - - +
371A ASN* 1.3 65.5 + - - +
372A CYS* 3.3 5.2 + - - +
373A SER* 3.0 27.9 + - - -
374A TYR* 3.2 12.3 + - - +
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Residues in contact with ASN 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TYR* 4.0 15.4 + - - +
349A SER* 3.0 25.4 + - - +
370A SER* 1.3 71.2 - - - +
372A CYS* 1.3 73.4 + - - +
374A TYR* 3.1 12.8 + - - +
375A PHE* 3.2 28.2 + - + -
1C NAG 1.5 66.0 + - - +
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Residues in contact with CYS 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ASP* 4.0 3.4 - - - +
347A TYR 4.2 0.9 - - - -
348A CYS* 2.0 55.6 - - - -
370A SER* 3.1 5.3 - - - +
371A ASN* 1.3 87.6 + - - +
373A SER* 1.3 62.5 + - - +
375A PHE* 3.6 5.7 + - - +
376A GLU* 3.1 30.7 + - - +
1C NAG 3.9 20.9 - - - -
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Residues in contact with SER 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MET* 3.6 3.9 - - - +
341A ILE* 3.6 21.5 - - - +
342A ASN 5.6 0.2 - - - -
344A ASP* 3.4 5.0 + - - -
357A MET* 3.2 21.5 - - - +
369A PHE* 3.7 24.9 - - - -
370A SER* 3.0 27.7 + - - -
372A CYS* 1.3 76.8 - - - +
374A TYR* 1.3 64.2 + - - +
376A GLU* 3.9 0.6 - - - -
377A CYS* 3.0 25.3 + - - +
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Residues in contact with TYR 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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238A TYR* 3.4 59.9 - + + +
239A MET* 3.9 18.5 - - - +
240A TYR* 3.6 21.5 - + - -
370A SER 3.2 2.7 + - - +
371A ASN* 3.1 9.5 + - - +
373A SER* 1.3 78.3 - - - +
375A PHE* 1.3 92.2 + + - +
377A CYS* 3.0 13.2 + - - +
378A TRP* 3.2 45.4 + + + -
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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
----------------------------------------------------------
371A ASN* 3.2 30.2 + - + +
372A CYS* 4.2 3.8 - - - +
374A TYR* 1.3 104.3 - + - +
376A GLU* 1.3 58.7 + - - +
378A TRP* 3.5 3.5 + - - +
379A ASP* 2.9 30.4 + - - +
1C NAG 3.4 27.4 - - + -
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Residues in contact with GLU 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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340A GLY 3.6 13.0 - - - +
341A ILE* 3.9 4.3 - - - +
342A ASN* 2.9 58.3 + - - +
372A CYS* 3.1 21.2 + - - +
373A SER* 4.0 3.8 - - - +
375A PHE* 1.3 77.5 - - - +
377A CYS* 1.3 63.0 + - - +
379A ASP* 3.2 11.5 - - + +
380A PHE* 3.1 22.2 + - - +
511B TYR* 5.6 0.3 + - - -
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Residues in contact with CYS 377 (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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239A MET* 3.7 18.4 - - + -
241A ILE* 3.9 28.5 - - - -
339A LEU* 3.8 28.4 - - - +
341A ILE* 3.8 7.2 - - + +
373A SER 3.0 14.5 + - - +
374A TYR 3.0 10.0 + - - +
376A GLU* 1.3 74.0 - - - +
378A TRP* 1.3 64.5 + - + +
379A ASP 3.0 4.0 - - - -
380A PHE* 3.0 8.0 + - - +
381A ILE* 3.0 34.3 + - - +
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Residues in contact with TRP 378 (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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196A PRO 3.6 21.1 - - - -
198A ARG* 4.0 22.2 - - + -
239A MET* 2.8 31.6 + - - +
240A TYR* 3.3 23.6 - + + -
241A ILE* 4.5 0.2 - - + -
374A TYR* 3.2 50.4 + + + +
375A PHE* 4.3 4.0 - - - +
377A CYS* 1.3 80.8 - - + +
379A ASP* 1.3 65.0 + - - +
381A ILE* 3.6 40.4 - - + +
382A MET* 3.0 39.5 + - + +
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Residues in contact with ASP 379 (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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375A PHE 2.9 19.6 + - - +
376A GLU* 3.2 15.2 - - - +
377A CYS 3.0 0.2 - - - -
378A TRP* 1.3 78.3 - - - +
380A PHE* 1.3 64.9 + - - +
382A MET* 3.1 4.0 + - - +
383A ASN* 3.0 48.3 + - - +
384A HIS* 6.0 0.5 - - - -
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Residues in contact with PHE 380 (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 GLY* 3.1 43.1 - - - -
306A SER* 3.9 1.8 - - - -
307A MET* 4.1 22.4 - - + -
338A ASN 4.2 4.5 - - - -
339A LEU* 3.6 25.4 - - + +
340A GLY* 4.1 6.7 - - - +
376A GLU 3.1 7.6 + - - +
377A CYS 3.0 8.0 + - - +
379A ASP* 1.3 83.0 + - - +
381A ILE* 1.3 53.7 + - + +
384A HIS* 2.6 80.1 + + + +
385A ASN 6.2 0.2 - - - -
386A PRO* 3.6 23.8 - - + -
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Residues in contact with ILE 381 (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 ARG* 3.8 32.8 + - + +
241A ILE* 4.1 22.2 - - + -
339A LEU* 5.2 3.6 - - + -
377A CYS* 3.0 21.0 + - - +
378A TRP* 3.6 57.0 - - + +
379A ASP 3.3 0.2 - - - -
380A PHE* 1.3 79.0 - - + +
382A MET* 1.3 61.2 + - - +
384A HIS 3.1 11.2 - - - +
385A ASN* 4.6 4.7 + - - -
386A PRO* 3.6 23.6 - - + +
389A ILE* 4.4 5.2 - - + -
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Residues in contact with MET 382 (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 ARG* 5.7 3.8 - - - -
378A TRP* 3.0 29.4 + - + +
379A ASP* 3.7 4.3 - - - +
380A PHE 3.1 0.2 - - - -
381A ILE* 1.3 86.5 - - + +
383A ASN* 1.3 73.9 + - - +
384A HIS 3.3 5.3 - - - +
385A ASN* 5.2 1.6 - - - +
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Residues in contact with ASN 383 (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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379A ASP* 3.0 34.3 + - - +
382A MET* 1.3 80.1 - - - +
384A HIS* 1.3 76.8 + - + +
385A ASN 4.2 0.3 + - - -
383B ASN* 5.8 2.2 + - - -
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Residues in contact with HIS 384 (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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379A ASP* 6.0 0.9 - - - -
380A PHE* 2.6 66.5 + + + +
381A ILE 3.1 8.8 - - - +
382A MET 3.6 1.9 - - - +
383A ASN* 1.3 90.7 + - + +
385A ASN* 1.3 60.6 + - - +
386A PRO* 3.0 8.2 - - - +
578A GLU* 6.1 0.4 - - - -
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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