Contacts of the helix formed by residues 384 - 398 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A GLN* 2.9 22.6 + - - +
375A GLU* 4.6 19.7 - - + +
387A GLU* 4.9 6.2 + - - +
376C SER* 3.3 26.5 - - - +
380C LYS* 5.9 4.7 - - + +
382C ARG 5.4 0.2 - - - +
383C PRO* 1.3 78.5 - - - +
385C ARG* 1.3 64.2 + - - +
386C ALA* 3.5 8.2 + - - +
387C GLU* 2.6 45.2 + - - +
388C THR* 3.4 10.2 + - - -
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Residues in contact with ARG 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ASP* 3.9 16.0 + - - -
337A ARG* 3.1 53.5 + - + +
338A GLY* 2.8 29.4 + - - +
341A GLY* 3.9 13.2 - - - -
342A ILE* 3.8 15.6 - - - +
346A ALA* 6.5 0.4 - - - -
349A VAL* 5.2 6.1 - - + -
371A THR 3.7 18.2 - - - +
372A GLN* 2.5 51.1 + - + +
383C PRO 3.9 11.9 + - - -
384C THR* 1.3 72.6 - - - +
386C ALA* 1.3 60.4 + - - +
388C THR* 3.8 9.0 + - - +
389C SER* 3.4 21.3 + - - -
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Residues in contact with ALA 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A GLN 3.6 20.4 + - - +
373A MET 4.2 0.2 - - - +
386A ALA* 3.9 5.6 - - + +
387A GLU* 3.9 24.7 - - + -
390A ASP* 3.6 32.3 + - + -
384C THR* 3.2 5.4 + - - +
385C ARG* 1.3 76.0 - - - +
387C GLU* 1.3 56.3 + - - +
389C SER* 3.5 2.6 + - - -
390C ASP* 2.7 34.1 + - - +
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Residues in contact with GLU 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A THR* 5.0 7.2 + - - +
386A ALA* 4.0 14.6 - - + -
387A GLU* 5.7 1.9 - - + +
372C GLN 4.8 0.3 - - - +
373C MET 3.2 21.3 - - - +
374C LEU* 3.9 12.9 - - + -
375C GLU* 3.2 14.9 + - - +
376C SER* 2.6 39.6 + - - -
383C PRO* 3.4 6.0 - - + +
384C THR* 2.6 45.3 + - - +
386C ALA* 1.3 76.1 - - + +
388C THR* 1.3 67.8 + - - +
390C ASP* 2.9 12.3 + - - +
391C VAL* 2.9 18.9 + - - +
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Residues in contact with THR 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ALA* 3.3 31.0 + - - +
347A GLU* 5.1 1.8 - - - -
349A VAL* 4.9 4.7 - - + -
350A PHE* 4.7 18.8 - - + +
374C LEU* 4.6 0.8 - - - +
383C PRO* 4.0 18.9 - - - +
384C THR 3.4 6.4 + - - -
385C ARG* 3.9 13.7 - - - +
387C GLU* 1.3 78.5 - - - +
389C SER* 1.3 67.3 + - - +
391C VAL* 3.3 4.2 + - - +
392C ALA* 3.1 18.4 + - - +
420C MET* 4.2 3.5 - - - +
424C ILE* 3.7 25.2 - - + +
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Residues in contact with SER 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ARG* 3.9 5.8 - - - -
350A PHE* 4.6 11.9 - - - -
353A GLN* 5.2 6.3 - - - -
354A LYS* 6.5 0.2 - - - -
389A SER 5.5 0.2 - - - -
390A ASP* 2.6 34.1 + - - +
385C ARG 3.4 12.0 + - - -
386C ALA 3.6 0.2 + - - -
387C GLU 3.3 0.2 - - - -
388C THR* 1.3 80.4 - - - +
390C ASP* 1.3 68.1 + - - +
392C ALA* 4.5 5.8 - - - -
393C ASN* 2.9 42.6 + - - +
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Residues in contact with ASP 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ALA* 3.6 17.5 - - + +
389A SER* 2.6 24.4 + - - +
337C ARG* 2.6 45.7 + - - -
353C GLN* 5.2 1.6 + - - -
373C MET* 3.6 22.0 - - - +
386C ALA 2.7 19.9 + - - +
387C GLU 2.9 9.8 + - - +
389C SER* 1.3 75.7 + - - +
391C VAL* 1.3 63.4 + - - +
393C ASN* 3.7 2.3 - - - +
394C ALA* 2.9 22.2 + - - +
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Residues in contact with VAL 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C MET* 3.9 16.6 - - + +
374C LEU* 3.6 23.6 - - + -
387C GLU 2.9 17.6 + - - +
388C THR 3.6 5.8 - - - +
390C ASP* 1.3 73.9 - - - +
392C ALA* 1.3 66.6 + - - +
394C ALA* 2.8 15.6 + - - +
395C VAL* 3.1 13.2 + - + +
402C ILE* 3.7 27.1 - - + -
421C GLN* 4.3 16.4 - - + +
424C ILE* 3.7 29.4 - - + -
425C ALA 4.4 4.9 - - - +
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Residues in contact with ALA 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A PHE* 3.4 50.5 - - + -
388C THR 3.1 9.4 + - - +
389C SER 3.9 2.9 - - - +
391C VAL* 1.3 76.5 - - - +
393C ASN* 1.3 57.8 + - - +
395C VAL* 2.9 7.8 + - - +
396C LEU* 2.9 30.0 + - + +
424C ILE* 3.6 10.4 - - + +
428C ALA* 3.8 11.2 - - + +
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Residues in contact with ASN 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A PHE* 6.0 0.2 - - - +
353A GLN* 6.0 0.6 - - - +
354A LYS* 2.9 35.9 + - - +
389A SER* 5.3 0.4 - - - +
393A ASN* 3.1 49.1 - - - +
397A ASP* 5.2 0.8 + - - -
353C GLN* 4.9 0.9 - - - +
354C LYS* 5.5 0.2 + - - -
389C SER* 2.9 43.0 + - - +
390C ASP* 4.0 2.5 - - - +
392C ALA* 1.3 71.1 - - - +
394C ALA* 1.3 55.6 + - - +
396C LEU* 3.7 8.0 - - - +
397C ASP* 2.7 44.4 + - - +
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Residues in contact with ALA 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C GLN* 4.0 5.8 - - - +
369C CYS* 4.0 22.2 - - + -
373C MET* 3.6 27.4 - - + -
390C ASP 2.9 7.5 + - - +
391C VAL 2.8 13.6 + - - +
393C ASN* 1.3 71.4 - - - +
395C VAL* 1.3 61.1 + - - +
397C ASP* 3.4 10.3 + - - +
398C GLY 3.1 6.2 + - - -
399C ALA* 3.0 27.4 + - + +
402C ILE* 4.1 8.7 - - + -
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Residues in contact with VAL 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C THR* 3.5 26.5 - - + +
391C VAL* 3.1 11.4 + - + +
392C ALA 2.9 8.0 + - - +
394C ALA* 1.3 78.3 - - - +
396C LEU* 1.3 60.1 + - - +
398C GLY* 2.9 10.6 + - - -
399C ALA 4.4 0.7 - - - +
402C ILE* 4.8 5.6 - - + -
425C ALA* 4.1 20.9 - - + -
428C ALA* 3.5 23.1 - - + +
429C GLU* 3.6 25.6 - - + +
432C VAL* 4.6 2.7 - - + +
510C ARG* 2.7 37.1 + - - +
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Residues in contact with LEU 396 (chain C).
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* 4.0 23.8 - - + -
354A LYS* 4.0 25.8 - - + +
392C ALA 2.9 21.8 + - - +
393C ASN* 3.9 9.4 - - - +
395C VAL* 1.3 73.9 - - - +
397C ASP* 1.3 66.3 + - - +
398C GLY* 3.4 0.9 + - - -
428C ALA* 3.5 26.2 - - + +
431C ALA* 3.9 10.1 - - + +
432C VAL* 3.8 27.7 - - + +
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Residues in contact with ASP 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 4.8 16.6 - - - +
393A ASN* 5.1 0.7 + - - -
353C GLN* 2.9 26.5 + - - -
354C LYS* 2.8 47.2 + - + +
357C ILE* 3.4 28.2 - - + +
358C GLY* 5.3 0.9 + - - -
361C ASN* 3.8 5.4 - - - +
393C ASN* 2.7 27.7 + - - +
394C ALA 3.4 5.6 - - - +
396C LEU* 1.3 79.5 - - - +
398C GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ILE* 3.4 6.0 - - - +
361C ASN* 2.8 34.9 + - - -
367C VAL* 3.9 0.5 - - - +
394C ALA 3.1 0.8 + - - -
395C VAL 2.9 13.8 + - - -
396C LEU 4.2 1.1 - - - -
397C ASP* 1.3 79.1 - - - +
399C ALA* 1.3 63.3 + - - +
400C ASP 3.7 0.7 + - - -
437C LEU* 6.4 2.0 - - - -
488C ARG* 3.5 6.3 + - - -
510C ARG* 3.3 12.6 - - - -
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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