Contacts of the helix formed by residues 342 - 357 (chain A) in PDB entry 2VGL
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 GLU 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A VAL* 3.5 31.6 - - + +
303A SER* 5.7 1.3 - - - +
304A ASN* 4.9 4.7 - - - +
340A HIS* 3.1 33.0 + - + +
341A ARG* 1.3 84.5 - - - +
343A THR* 1.3 64.1 + - - +
344A ASN* 3.1 16.9 + - + +
345A LEU* 3.8 24.3 - - + +
346A ARG* 3.2 17.0 + - - +
48S ASN* 5.6 0.2 + - - -
60S ARG* 5.0 4.9 + - - -
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Residues in contact with THR 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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341A ARG 3.2 4.4 + - - -
342A GLU* 1.3 71.2 + - - +
344A ASN* 1.3 57.5 + - - +
346A ARG* 3.4 21.9 + - - +
347A TYR* 2.9 27.5 + - - +
382A ASP* 3.7 20.3 - - + +
385A VAL* 3.5 25.6 - - + -
45S LYS* 3.0 21.9 + - - +
46S HIS 4.4 4.9 - - - -
47S THR* 3.5 17.0 - - + -
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Residues in contact with ASN 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASN* 5.4 2.8 + - - +
342A GLU* 3.0 17.5 + - + +
343A THR* 1.3 77.8 - - - +
345A LEU* 1.3 64.3 + - + +
347A TYR* 3.4 1.7 + - - +
348A LEU* 3.0 29.6 + - - +
46S HIS 5.5 0.2 - - - -
47S THR* 3.1 11.3 - - - -
48S ASN* 2.6 52.7 + - - +
49S PHE* 3.1 25.5 - - + -
60S ARG* 4.8 1.4 - - - +
78S LEU* 4.5 9.9 - - + +
81S LEU* 3.7 14.3 - - - +
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Residues in contact with LEU 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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303A SER* 5.5 4.0 - - - -
304A ASN* 5.2 4.7 - - - +
307A ASN* 3.6 33.2 - - + +
311A PHE* 4.5 8.0 - - + -
337A PHE* 4.1 23.3 - - + +
340A HIS* 3.2 44.2 - - + +
342A GLU* 3.2 17.6 + - + +
344A ASN* 1.3 74.9 - - + +
346A ARG* 1.3 66.6 + - - +
348A LEU* 3.9 3.0 - - - +
349A ALA* 2.9 26.8 + - - +
78S LEU* 3.9 27.6 - - + -
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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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337A PHE 3.7 13.6 + - - +
338A LEU* 3.5 29.6 - - + +
340A HIS 2.8 19.1 + - - +
341A ARG* 2.6 28.1 + - - +
342A GLU 3.2 5.9 + - - -
343A THR* 3.5 33.0 + - - +
345A LEU* 1.3 72.1 - - - +
347A TYR* 1.3 66.9 + - - +
349A ALA* 3.1 3.5 + - - +
350A LEU* 2.9 31.3 + - + +
376A ALA* 5.3 4.7 - - + -
380A GLU* 2.7 43.5 + - - +
381A ARG* 5.0 2.0 - - - +
382A ASP* 5.2 0.2 - - - +
385A VAL* 4.0 12.3 - - + -
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Residues in contact with TYR 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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343A THR 2.9 18.0 + - - +
344A ASN* 3.7 4.5 - - - +
346A ARG* 1.3 78.5 - - - +
348A LEU* 1.3 76.4 + - + +
350A LEU* 3.3 4.6 + - - +
351A GLU* 3.0 34.5 + - + +
384A SER* 3.3 40.6 - - - -
385A VAL* 4.1 11.3 - - + +
388A ARG* 3.3 41.7 + - + +
188M GLN* 5.5 2.4 + - - -
47S THR* 3.9 15.9 - - + -
49S PHE* 4.6 11.4 - + + -
51S GLU* 4.7 10.7 + - - +
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Residues in contact with LEU 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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311A PHE* 3.7 30.1 - - + -
344A ASN 3.0 22.5 + - - +
345A LEU* 4.0 1.1 - - - +
346A ARG 3.2 0.2 - - - -
347A TYR* 1.3 79.1 - - + +
349A ALA* 1.3 60.8 + - - +
351A GLU* 3.2 19.8 + - - +
352A SER* 2.8 34.0 + - - -
49S PHE* 4.0 17.0 - - + -
77S ASN* 3.4 30.5 - - + +
78S LEU* 3.8 35.4 - - + -
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Residues in contact with ALA 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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311A PHE* 4.3 0.6 - - - -
334A LEU* 3.6 39.7 - - + +
337A PHE* 3.7 12.6 - - + -
338A LEU* 4.1 10.3 - - + +
345A LEU 2.9 17.5 + - - +
346A ARG 3.6 3.8 - - - +
348A LEU* 1.3 76.6 - - - +
350A LEU* 1.3 58.2 + - - +
352A SER* 3.7 1.2 - - - -
353A MET* 2.9 37.1 + - - +
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 3.2 29.2 - - + -
346A ARG* 2.9 13.1 + - + +
347A TYR 3.7 3.4 - - - +
349A ALA* 1.3 74.8 - - - +
351A GLU* 1.3 64.7 + - - +
353A MET* 3.5 5.0 + - - +
354A CYS* 3.2 26.8 + - - -
373A VAL* 4.6 6.7 - - + -
376A ALA* 6.0 5.4 - - + -
385A VAL* 3.2 47.1 - - + +
388A ARG* 4.0 14.1 - - + -
389A ALA* 3.6 24.2 - - + +
392A LEU* 3.7 22.0 - - + +
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Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A TYR* 3.0 34.1 + - + +
348A LEU* 3.5 28.1 - - - +
350A LEU* 1.3 76.1 - - - +
352A SER* 1.3 69.5 + - - +
354A CYS* 3.1 18.2 + - - +
355A THR* 3.6 8.6 + - - +
388A ARG* 4.3 29.0 + - - +
77S ASN* 5.1 2.3 + - - -
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A PHE* 4.4 13.6 - - - -
314A ILE* 3.8 16.5 - - - +
318A ILE* 4.4 4.9 - - - +
334A LEU* 3.5 18.3 - - - +
348A LEU 2.8 21.3 + - - -
349A ALA 4.0 2.7 - - - -
351A GLU* 1.3 80.8 - - - +
353A MET* 1.3 58.7 + - - +
355A THR* 3.3 18.6 + - - -
356A LEU* 3.3 17.2 + - - +
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Residues in contact with MET 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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331A CYS* 4.6 4.3 - - + +
334A LEU* 3.7 29.8 - - + -
335A GLY* 4.2 6.3 - - - -
338A LEU* 4.2 22.4 - - - -
349A ALA 2.9 18.9 + - - +
350A LEU 3.9 4.5 - - - +
351A GLU 3.1 0.2 - - - -
352A SER* 1.3 73.6 - - - +
354A CYS* 1.3 63.3 + - - +
355A THR 3.1 1.6 - - - -
356A LEU* 3.3 11.2 + - + +
357A ALA* 3.1 24.4 + - - +
366A VAL* 3.7 30.7 - - + +
369A HIS* 4.0 32.1 - - + -
373A VAL* 4.9 1.1 - - + -
392A LEU* 3.8 23.0 - - + +
396A MET* 6.3 0.2 - - - -
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Residues in contact with CYS 354 (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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350A LEU 3.2 18.0 + - - -
351A GLU 3.1 9.9 + - - +
353A MET* 1.3 77.0 - - - +
355A THR* 1.3 63.0 + - - +
356A LEU 3.5 0.2 + - - -
357A ALA* 3.6 12.2 + - - +
358A SER* 4.1 6.4 + - - -
388A ARG* 3.8 29.4 - - - +
391A ASP* 4.1 6.1 - - - -
392A LEU* 3.7 38.4 - - - -
395A ALA* 5.1 7.7 - - + +
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Residues in contact with THR 355 (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 ILE* 4.3 31.5 - - + +
351A GLU* 3.6 13.4 + - - +
352A SER* 3.3 12.0 + - - -
353A MET 3.1 0.8 - - - -
354A CYS* 1.3 79.1 - - - +
356A LEU* 1.3 62.5 + - - +
357A ALA 3.3 0.9 + - - -
358A SER* 3.4 20.2 + - - +
359A SER* 4.4 3.6 + - - -
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Residues in contact with LEU 356 (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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314A ILE* 4.8 2.7 - - + -
318A ILE* 3.8 20.4 - - + -
327A LEU* 3.3 37.0 - - + +
330A ALA* 5.0 3.4 - - + -
331A CYS* 4.2 20.0 - - - +
334A LEU* 3.5 27.4 - - + -
352A SER* 3.3 22.2 + - - +
353A MET* 3.3 10.2 + - + +
355A THR* 1.3 78.8 - - - +
357A ALA* 1.3 61.8 + - - +
358A SER 3.2 0.2 - - - -
359A SER* 3.2 8.2 + - - +
362A SER* 2.8 34.4 + - - +
366A VAL* 3.9 13.5 - - + -
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Residues in contact with ALA 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A MET 3.1 16.1 + - - +
354A CYS* 3.8 8.3 - - - +
355A THR 3.2 0.6 - - - -
356A LEU* 1.3 73.7 - - - +
358A SER* 1.3 57.3 + - - +
359A SER 3.1 6.6 + - - -
363A HIS* 2.7 36.2 + - + +
366A VAL* 3.8 22.4 - - + +
392A LEU* 4.6 2.5 - - + -
395A ALA* 4.3 26.8 - - + +
396A MET* 5.0 0.7 - - + +
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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