Contacts of the helix formed by residues 384 - 398 (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 THR 384 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A SER* 3.4 19.5 - - - +
380A LYS* 5.6 5.8 - - - +
383A PRO* 1.3 77.0 - - - +
385A ARG* 1.3 66.8 + - - +
386A ALA* 3.1 8.6 + - - +
387A GLU* 2.7 51.4 + - - +
388A THR* 3.4 11.1 + - - -
372C GLN* 3.0 23.7 + - - +
375C GLU* 4.6 17.3 - - + +
387C GLU* 5.0 7.0 + - - +
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Residues in contact with ARG 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A PRO 4.0 12.1 + - - -
384A THR* 1.3 72.4 - - - +
386A ALA* 1.3 61.3 + - - +
388A THR* 3.7 10.5 + - - +
389A SER* 3.2 22.5 + - - -
221C ASP* 3.1 24.6 + - - -
337C ARG* 2.9 54.4 + - + +
338C GLY* 2.7 27.5 + - - +
341C GLY* 3.5 15.2 - - - -
342C ILE* 3.6 13.5 - - - +
346C ALA* 6.2 2.9 - - - -
349C VAL* 4.9 8.7 - - + -
371C THR 3.9 16.2 - - - +
372C GLN* 2.7 47.4 + - + +
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Residues in contact with ALA 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A THR* 3.1 7.4 + - - +
385A ARG* 1.3 76.7 - - - +
387A GLU* 1.3 55.3 + - - +
389A SER* 3.4 2.8 + - - -
390A ASP* 2.7 35.2 + - - +
372C GLN 3.6 21.0 + - - +
386C ALA* 3.9 11.5 - - + +
387C GLU* 4.0 15.5 - - + -
390C ASP* 3.6 31.8 + - + -
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLN 4.7 0.9 - - - +
373A MET 3.1 20.3 - - - +
374A LEU* 3.7 12.4 - - + -
375A GLU* 3.0 16.2 + - - +
376A SER* 2.5 49.4 + - - -
383A PRO* 3.5 5.6 - - + +
384A THR* 2.7 35.0 + - - +
386A ALA* 1.3 74.5 - - + +
388A THR* 1.3 65.7 + - - +
390A ASP* 3.0 11.8 + - - +
391A VAL* 3.0 18.2 + - - +
384C THR* 4.9 7.1 + - - +
386C ALA* 3.9 15.0 - - + -
387C GLU* 5.7 1.8 - - + +
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Residues in contact with THR 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 4.4 1.2 - - - +
383A PRO* 4.1 18.6 - - - +
384A THR 3.4 7.4 + - - -
385A ARG* 3.8 12.3 - - - +
387A GLU* 1.3 79.5 - - - +
389A SER* 1.3 67.9 + - - +
391A VAL* 3.2 3.5 + - - +
392A ALA* 3.1 17.8 + - - +
420A MET* 4.1 4.2 - - - +
424A ILE* 3.8 24.1 - - + +
346C ALA* 3.3 31.3 + - - +
347C GLU* 4.9 2.2 - - - -
349C VAL* 4.9 4.9 - - + -
350C PHE* 4.6 22.0 - - + +
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Residues in contact with SER 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ARG 3.2 10.9 + - - -
386A ALA 3.5 1.6 + - - -
387A GLU 3.3 0.2 - - - -
388A THR* 1.3 83.3 - - - +
390A ASP* 1.3 65.8 + - - +
392A ALA* 4.4 6.3 - - - +
393A ASN* 2.8 43.5 + - - +
337C ARG* 4.1 5.6 - - - -
350C PHE* 4.5 12.6 - - - -
353C GLN* 5.2 7.4 + - - -
354C LYS* 6.3 0.4 - - - -
390C ASP* 2.6 31.5 + - - -
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Residues in contact with ASP 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ARG* 2.6 45.8 + - - -
353A GLN* 5.1 2.1 + - - -
373A MET* 3.7 20.0 - - - +
386A ALA 2.7 20.2 + - - +
387A GLU 3.0 9.8 + - - +
389A SER* 1.3 74.4 + - - +
391A VAL* 1.3 62.1 + - - +
393A ASN* 3.4 2.2 + - - +
394A ALA* 3.0 22.5 + - - +
386C ALA* 3.6 17.6 - - + +
389C SER* 2.6 24.5 + - - +
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Residues in contact with VAL 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A MET* 3.8 23.3 - - + +
374A LEU* 3.6 23.6 - - + -
387A GLU 3.0 12.8 + - - +
388A THR 3.7 5.4 - - - +
390A ASP* 1.3 72.0 - - - +
392A ALA* 1.3 70.9 + - - +
394A ALA* 3.0 13.2 + - - +
395A VAL* 3.2 11.6 + - + +
402A ILE* 3.7 27.6 - - + -
421A GLN* 4.4 11.0 - - + +
424A ILE* 3.7 28.5 - - + -
425A ALA* 4.5 6.5 - - - +
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A THR 3.1 9.4 + - - +
389A SER 3.8 5.4 - - - +
391A VAL* 1.3 77.0 - - - +
393A ASN* 1.3 60.6 + - - +
395A VAL* 3.0 4.9 + - - +
396A LEU* 2.8 30.2 + - + +
424A ILE* 3.5 13.7 - - + +
428A ALA* 3.8 7.6 - - + +
350C PHE* 3.5 50.7 - - + -
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Residues in contact with ASN 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLN* 4.9 0.4 - - - +
354A LYS* 5.5 0.2 + - - -
389A SER* 2.8 40.6 + - - +
390A ASP* 4.1 3.6 - - - +
392A ALA* 1.3 70.2 - - - +
394A ALA* 1.3 55.1 + - - +
396A LEU* 3.9 7.7 - - - +
397A ASP* 2.7 43.7 + - - +
353C GLN* 6.1 0.4 - - - +
354C LYS* 2.8 36.4 + - - +
389C SER* 5.3 0.2 - - - +
393C ASN* 3.1 51.5 - - - +
397C ASP* 5.1 1.2 + - - -
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLN* 4.1 5.4 - - - +
369A CYS* 4.0 17.0 - - + -
373A MET* 3.5 27.8 - - + -
390A ASP 3.0 6.1 + - - +
391A VAL 3.0 10.6 + - - +
393A ASN* 1.3 76.2 - - - +
395A VAL* 1.3 60.2 + - - +
397A ASP* 3.3 11.6 + - - +
398A GLY 3.1 6.1 + - - -
399A ALA* 3.0 27.5 + - + +
402A ILE* 4.0 11.2 - - + -
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Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR* 3.4 30.3 - - + +
391A VAL 3.2 8.7 + - - +
392A ALA 3.0 8.4 + - - +
394A ALA* 1.3 78.0 - - - +
396A LEU* 1.3 66.8 + - - +
398A GLY* 2.9 6.9 + - - -
399A ALA* 4.3 0.9 - - - +
402A ILE* 4.8 6.7 - - + -
425A ALA* 4.2 19.1 - - + -
428A ALA* 3.6 22.9 - - + +
429A GLU* 3.7 24.5 - - + +
432A VAL* 4.6 2.8 - - + +
510A ARG* 2.9 36.7 + - - +
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Residues in contact with LEU 396 (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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392A ALA 2.8 24.3 + - - +
393A ASN* 3.9 9.4 - - - +
395A VAL* 1.3 76.5 - - - +
397A ASP* 1.3 64.1 + - - +
398A GLY* 3.4 0.7 + - - -
428A ALA* 3.4 26.9 - - + +
431A ALA* 4.0 10.8 - - + +
432A VAL* 3.9 25.6 - - + +
350C PHE* 4.3 15.5 - - + -
354C LYS* 4.0 29.6 - - + +
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Residues in contact with ASP 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLN* 2.8 24.8 + - - -
354A LYS* 2.6 48.7 + - + +
357A ILE* 3.5 27.3 - - + +
358A GLY* 5.6 0.3 - - - -
361A ASN* 3.9 5.7 - - - +
393A ASN* 2.7 29.3 + - - +
394A ALA 3.3 7.4 - - - +
395A VAL 3.1 0.2 - - - -
396A LEU* 1.3 80.4 - - - +
398A GLY* 1.3 56.5 + - - +
70C LEU* 6.1 0.5 - - - +
73C LEU* 4.6 19.9 - - + +
393C ASN* 5.2 0.7 + - - -
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Residues in contact with GLY 398 (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* 3.4 6.3 - - - +
361A ASN* 3.0 33.1 + - - -
367A VAL* 3.9 0.9 - - - +
394A ALA 3.1 0.2 + - - -
395A VAL 2.9 12.2 + - - -
396A LEU 4.2 0.7 - - - -
397A ASP* 1.3 79.0 - - - +
399A ALA* 1.3 66.2 + - - +
400A ASP 3.6 0.5 + - - -
437A LEU* 6.4 2.0 - - - -
488A ARG* 3.6 8.1 + - - -
510A ARG* 3.3 12.3 - - - -
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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