Contacts of the helix formed by residues 348 - 364 (chain A) in PDB entry 2VGB
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 LYS 348 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A ILE* 4.0 12.8 - - + -
345A PRO* 3.0 35.0 + - + +
347A GLU* 1.3 79.5 - - + +
349A VAL* 1.3 68.3 + - - +
350A PHE 3.3 2.2 - - - -
351A LEU* 3.0 28.3 + - + +
352A ALA 3.2 3.6 + - - -
78C ILE* 3.0 37.0 + - + +
80C SER 3.6 12.9 + - - -
81C GLU* 3.1 31.3 + - - -
427C GLU* 2.8 43.7 + - - +
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ARG* 3.8 33.2 - - + +
340A LEU* 4.1 20.6 - - + +
341A GLY* 3.5 33.4 - - - +
344A ILE* 3.8 9.1 - - + +
345A PRO 3.7 5.1 + - - +
346A ALA* 3.7 14.6 + - - +
347A GLU 3.7 0.6 - - - -
348A LYS* 1.3 76.1 - - - +
350A PHE* 1.3 56.5 + - - +
352A ALA* 2.6 26.2 + - - +
353A GLN* 2.8 16.0 + - + +
385C ARG* 5.2 7.0 - - + -
388C THR* 4.9 5.2 - - + -
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Residues in contact with PHE 350 (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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347A GLU 3.1 28.5 - - - -
348A LYS 3.3 0.2 - - - -
349A VAL* 1.3 76.6 - - - +
351A LEU* 1.3 86.5 + - + +
353A GLN* 3.7 10.6 - - - +
354A LYS* 2.9 56.6 + - + +
76C LEU* 5.6 0.2 - - + -
388C THR* 4.7 7.8 - - + +
389C SER* 4.6 17.7 - - - -
392C ALA* 3.4 31.0 - - + -
393C ASN* 6.0 0.2 - - - +
396C LEU* 4.0 15.0 - - + -
424C ILE* 4.5 5.6 - - + -
427C GLU* 3.5 12.3 - - + -
428C ALA* 3.4 28.7 - - + -
431C ALA* 4.2 3.8 - - + -
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Residues in contact with LEU 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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348A LYS* 3.0 28.1 + - + +
349A VAL 2.9 0.2 + - - -
350A PHE* 1.3 101.9 - - + +
352A ALA* 1.3 64.9 + - - +
355A MET* 3.1 27.0 + - - +
60C GLN* 3.8 23.8 - - - +
76C LEU* 4.2 24.1 - - + +
77C ASP 4.4 3.1 - - - +
78C ILE* 4.1 10.8 - - + +
427C GLU* 3.3 31.4 - - + +
431C ALA* 3.8 19.1 - - + -
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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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320A VAL* 4.2 11.9 - - + -
340A LEU* 3.8 25.6 - - + -
344A ILE* 4.7 1.6 - - + -
348A LYS 3.2 2.6 + - - +
349A VAL* 2.6 15.3 + - - +
351A LEU* 1.3 74.6 - - - +
353A GLN* 1.3 62.4 + - - +
355A MET* 3.8 7.5 - - - +
356A MET* 2.9 38.9 + - + +
78C ILE* 3.8 19.9 - - + +
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Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A VAL* 3.8 24.9 - - + +
337A ARG* 3.0 34.9 + - - +
349A VAL* 2.8 13.7 + - + +
350A PHE* 3.7 13.1 - - - +
352A ALA* 1.3 77.5 - - - +
354A LYS* 1.3 66.2 + - + +
356A MET* 3.9 0.9 - - - +
357A ILE* 3.0 42.4 + - + +
369A CYS* 3.7 18.8 - - - -
390A ASP* 5.1 2.4 + - - -
393A ASN* 4.9 0.6 - - - +
394A ALA* 4.1 11.9 - - - +
397A ASP* 2.8 26.0 + - - +
389C SER* 5.2 4.8 - - - -
393C ASN* 6.0 0.8 - - - +
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Residues in contact with LYS 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 PHE* 2.9 43.7 + - + +
353A GLN* 1.3 75.7 - - + +
355A MET* 1.3 56.6 + - - +
357A ILE* 4.1 4.7 - - - +
358A GLY* 3.0 26.3 + - - -
393A ASN* 5.2 0.6 + - - +
397A ASP* 2.6 44.9 + - - +
69C PHE* 6.4 0.4 - - - -
73C LEU* 3.9 32.1 - - + +
76C LEU* 4.2 13.5 - - + -
393C ASN* 2.9 32.0 + - - +
396C LEU* 4.0 20.0 - - + +
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Residues in contact with MET 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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320A VAL* 4.0 33.7 - - + +
323A PHE* 4.6 4.0 - - + -
351A LEU 3.1 19.3 + - - +
352A ALA* 4.5 4.7 - - - +
354A LYS* 1.3 74.7 - - - +
356A MET* 1.3 79.3 - - + +
358A GLY* 3.4 1.0 + - - -
359A ARG* 3.0 58.4 + - - +
73C LEU 3.2 15.7 + - - +
74C CYS* 3.7 17.7 - - - +
76C LEU* 3.4 24.2 - - + +
77C ASP* 6.3 0.2 - - - -
78C ILE* 6.2 1.1 - - + +
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Residues in contact with MET 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* 3.6 33.9 - - + -
320A VAL* 4.5 3.6 - - + -
323A PHE* 3.5 41.3 - - + -
333A ILE* 4.4 6.7 - - + -
335A VAL* 3.9 29.6 - - + -
340A LEU* 4.1 6.1 - - + -
352A ALA* 2.9 39.9 + - + +
353A GLN 4.0 2.0 - - - +
355A MET* 1.3 86.5 - - + +
357A ILE* 1.3 66.3 + - - +
359A ARG* 3.2 1.7 + - - +
360A CYS* 2.8 29.9 + - - +
367A VAL* 4.8 0.2 - - - -
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Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A VAL* 4.4 4.5 - - + -
353A GLN* 3.0 41.4 + - + +
354A LYS 4.1 2.2 - - - +
356A MET* 1.3 71.8 - - - +
358A GLY* 1.3 58.2 + - - +
360A CYS* 3.8 0.7 - - - +
361A ASN* 2.8 31.3 + - - +
367A VAL* 4.0 23.3 - - + -
369A CYS* 4.8 6.3 - - + -
394A ALA 4.1 0.7 - - - +
397A ASP* 3.5 36.6 - - + +
398A GLY 3.4 28.7 - - - +
399A ALA* 3.6 25.8 - - + -
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Residues in contact with GLY 358 (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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354A LYS 3.0 17.9 + - - -
355A MET 3.8 1.1 - - - -
356A MET 3.2 0.2 - - - -
357A ILE* 1.3 80.3 - - - +
359A ARG* 1.3 56.7 + - - +
361A ASN* 3.2 5.9 + - - +
362A LEU* 3.0 23.6 + - - +
397A ASP 5.6 0.4 - - - -
70C LEU* 4.0 15.2 - - - +
73C LEU* 4.5 10.5 - - - +
74C CYS* 3.5 17.5 - - - -
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Residues in contact with ARG 359 (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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320A VAL 5.3 1.4 + - - -
321A LYS 5.7 2.6 + - - -
323A PHE* 3.6 27.8 - - + +
324A ASP* 3.1 42.1 + - - +
327A LEU* 4.2 5.5 - - + +
355A MET* 3.0 49.0 + - - +
356A MET 3.7 0.4 - - - +
358A GLY* 1.3 70.7 - - - +
360A CYS* 1.3 59.1 + - - +
362A LEU* 3.1 10.4 + - + +
363A ALA* 2.8 28.2 + - - +
74C CYS* 2.7 50.9 + - + +
75C LEU* 4.6 7.9 - - - +
76C LEU 5.1 0.8 + - - -
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Residues in contact with CYS 360 (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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323A PHE* 4.0 7.0 - - - -
327A LEU* 4.4 14.3 - - - +
333A ILE* 3.7 37.0 - - - -
356A MET 2.8 22.5 + - - +
357A ILE 3.8 1.3 - - - +
359A ARG* 1.3 69.2 - - - +
361A ASN* 1.3 67.3 + - - +
363A ALA* 2.8 4.0 + - - +
364A GLY 2.8 21.5 + - - -
365A LYS* 3.3 23.2 + - - +
366A PRO 4.2 5.2 - - - -
367A VAL* 3.7 22.0 - - + -
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Residues in contact with ASN 361 (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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357A ILE* 2.8 22.8 + - - +
358A GLY* 3.3 9.8 - - - +
360A CYS* 1.3 70.8 - - - +
362A LEU* 1.3 61.6 + - - +
364A GLY* 3.3 10.3 + - - -
365A LYS 5.2 1.1 + - - -
367A VAL* 4.5 4.4 - - - +
397A ASP 3.9 6.2 - - - +
398A GLY* 3.0 39.4 + - - -
400A ASP* 4.6 0.4 + - - -
437A LEU* 4.8 10.7 - - - +
441A LEU* 3.8 16.5 - - + +
486A ARG* 3.8 12.6 + - - +
488A ARG* 3.3 25.5 + - - +
70C LEU* 4.3 15.7 - - + +
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Residues in contact with LEU 362 (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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358A GLY 3.0 10.2 + - - +
359A ARG* 3.2 16.2 - - + +
360A CYS 3.0 0.4 - - - -
361A ASN* 1.3 76.4 - - - +
363A ALA* 1.3 57.7 + - - +
441A LEU* 4.7 4.0 - - + +
444A ALA* 4.0 24.2 - - + +
445A ALA* 5.8 1.6 - - - +
486A ARG* 2.7 26.9 + - - +
70C LEU* 3.7 30.0 - - + +
71C GLU* 5.7 2.7 - - - +
74C CYS* 4.2 13.0 - - + -
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Residues in contact with ALA 363 (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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327A LEU* 3.5 32.1 - - + -
359A ARG 2.8 12.0 + - - +
360A CYS 2.8 3.5 + - - +
362A LEU* 1.3 73.0 - - - +
364A GLY* 1.3 58.9 + - - +
365A LYS* 4.2 18.3 - - + +
486A ARG* 3.7 9.1 + - - -
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Residues in contact with GLY 364 (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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360A CYS 2.8 8.8 + - - -
361A ASN* 3.3 6.2 + - - -
362A LEU 3.1 4.8 + - - -
363A ALA* 1.3 78.5 - - - +
365A LYS* 1.3 58.2 + - - +
482A GLN* 3.2 25.6 + - - +
486A ARG* 3.6 33.3 - - - +
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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