Contacts of the helix formed by residues 384 - 398 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B SER* 3.3 19.7 - - - +
380B LYS* 5.6 6.3 - - - +
382B ARG 5.4 0.2 - - - +
383B PRO* 1.3 79.4 - - - +
385B ARG* 1.3 65.0 + - - +
386B ALA* 3.3 11.5 + - - +
387B GLU* 2.6 47.8 + - - +
388B THR* 3.4 11.4 + - - -
372D GLN* 3.1 23.7 + - - +
375D GLU* 4.9 14.1 - - + +
387D GLU* 5.1 6.2 + - - +
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Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B PRO 4.0 12.5 + - - -
384B THR* 1.3 73.2 - - - +
386B ALA* 1.3 60.9 + - - +
388B THR* 3.9 8.7 + - - +
389B SER* 3.4 16.6 + - - -
221D ASP* 3.1 24.8 + - - -
337D ARG* 2.9 58.4 + - + +
338D GLY* 2.7 27.4 + - - +
341D GLY* 3.5 16.0 + - - -
342D ILE* 3.6 12.1 - - - +
346D ALA* 6.2 3.8 - - - -
349D VAL* 4.9 8.5 - - + -
371D THR* 3.9 17.0 - - + +
372D GLN* 2.8 47.5 + - + +
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Residues in contact with ALA 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B THR* 3.1 7.6 + - - +
385B ARG* 1.3 77.5 - - - +
387B GLU* 1.3 61.1 + - + +
389B SER* 3.5 2.6 + - - -
390B ASP* 2.8 28.8 + - - +
372D GLN 3.6 21.1 + - - +
373D MET 4.5 0.2 - - - +
386D ALA* 3.9 11.5 - - - +
387D GLU* 4.1 15.3 - - + -
390D ASP* 3.7 31.2 - - + +
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B GLN 4.6 0.7 - - - +
373B MET 3.3 22.7 - - - +
374B LEU* 3.9 16.4 - - + -
375B GLU* 3.1 11.8 + - - +
376B SER* 2.5 50.7 + - - -
383B PRO* 3.4 5.4 - - + +
384B THR* 2.6 35.8 + - - +
386B ALA* 1.3 78.8 - - + +
388B THR* 1.3 66.0 + - - +
390B ASP* 3.0 13.0 + - - +
391B VAL* 3.0 13.7 + - - +
384D THR* 5.1 6.8 + - - +
386D ALA* 4.1 14.1 - - + -
387D GLU* 5.8 1.9 - - + +
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Residues in contact with THR 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 4.5 1.4 - - - +
383B PRO* 4.1 18.0 - - - +
384B THR 3.4 7.1 + - - -
385B ARG* 3.9 13.0 - - - +
387B GLU* 1.3 78.6 - - - +
389B SER* 1.3 67.6 + - - +
391B VAL* 3.2 3.8 + - - +
392B ALA* 3.1 18.0 + - - +
420B MET* 4.2 1.0 - - - +
424B ILE* 3.8 23.4 - - + +
346D ALA* 3.3 33.8 + - - +
347D GLU* 5.0 2.0 - - - -
349D VAL* 4.9 5.2 - - + -
350D PHE* 4.6 20.9 - - + +
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Residues in contact with SER 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ARG 3.4 11.3 + - - -
386B ALA 3.6 1.9 + - - -
387B GLU 3.3 0.4 - - - -
388B THR* 1.3 79.0 - - - +
390B ASP* 1.3 62.6 + - - +
392B ALA* 3.3 0.4 + - - -
393B ASN* 2.8 49.4 + - - +
337D ARG* 4.1 5.2 - - - -
350D PHE* 4.4 19.5 - - - -
353D GLN* 5.1 7.6 + - - -
390D ASP* 2.7 30.8 + - - -
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Residues in contact with ASP 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ARG* 2.5 45.9 + - - -
353B GLN* 5.1 3.1 + - - -
373B MET* 3.7 20.9 - - - +
386B ALA 2.8 20.3 + - - +
387B GLU* 3.2 9.6 - - - +
389B SER* 1.3 73.2 + - - +
391B VAL* 1.3 63.6 + - - +
393B ASN* 3.4 3.1 + - - +
394B ALA* 2.9 22.2 + - - +
386D ALA* 3.7 16.7 - - + +
389D SER* 2.6 25.5 + - - +
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Residues in contact with VAL 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B MET* 3.8 21.3 - - + +
374B LEU* 3.6 23.8 - - + -
387B GLU 3.0 13.6 + - - +
388B THR 3.6 5.8 - - - +
390B ASP* 1.3 73.8 - - - +
392B ALA* 1.3 65.7 + - - +
394B ALA* 2.9 14.6 + - - +
395B VAL* 3.1 12.1 + - + +
402B ILE* 3.8 27.8 - - + -
421B GLN* 4.3 12.6 - - + +
424B ILE* 3.7 27.6 - - + -
425B ALA* 4.6 4.5 - - - +
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Residues in contact with ALA 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B THR 3.1 8.6 + - - +
389B SER 3.9 2.5 - - - +
391B VAL* 1.3 76.4 - - - +
393B ASN* 1.3 59.9 + - - +
395B VAL* 3.1 5.7 + - - +
396B LEU* 2.9 32.1 + - + +
424B ILE* 3.5 8.6 - - + +
428B ALA* 3.8 11.3 - - + +
350D PHE* 3.4 54.3 - - + -
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Residues in contact with ASN 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLN* 4.9 0.7 - - - +
389B SER* 2.8 43.0 + - - +
390B ASP* 4.0 2.7 - - - +
392B ALA* 1.3 69.5 - - - +
394B ALA* 1.3 56.6 + - - +
396B LEU* 3.5 7.9 - - + +
397B ASP* 2.6 44.9 + - - +
353D GLN* 6.0 1.0 - - - +
354D LYS* 2.7 37.8 + - - +
389D SER* 5.3 0.2 - - - +
393D ASN* 3.4 48.1 - - - +
397D ASP* 5.2 0.8 + - - -
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLN* 4.1 4.2 - - - +
369B CYS* 3.8 22.0 - - + -
373B MET* 3.5 27.6 - - + -
390B ASP 2.9 6.5 + - - +
391B VAL 2.9 10.3 + - - +
393B ASN* 1.3 75.8 - - - +
395B VAL* 1.3 63.9 + - - +
397B ASP* 3.1 11.8 + - - +
398B GLY 3.0 16.5 + - - -
399B ALA* 3.1 13.6 + - + +
402B ILE* 4.1 8.3 - - + -
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Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B THR* 3.5 29.2 - - + +
391B VAL* 3.1 11.5 + - + +
392B ALA 3.1 7.7 + - - +
394B ALA* 1.3 78.0 - - - +
396B LEU* 1.3 58.4 + - - +
398B GLY* 2.9 18.0 + - - -
399B ALA* 4.4 1.1 - - - +
402B ILE* 4.9 5.8 - - + -
425B ALA* 4.2 16.6 - - + -
428B ALA* 3.5 26.0 - - + +
429B GLU* 3.6 24.2 - - + +
432B VAL* 4.7 3.0 - - + +
510B ARG* 2.9 31.8 + - - +
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Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU* 6.3 0.9 - - + -
392B ALA 2.9 21.7 + - - +
393B ASN* 3.9 8.3 - - - +
395B VAL* 1.3 73.5 - - - +
397B ASP* 1.3 68.2 + - - +
398B GLY* 4.3 0.5 - - - -
428B ALA* 3.5 25.8 - - + +
431B ALA* 4.1 10.5 - - + +
432B VAL* 4.1 24.5 - - + +
69D PHE* 6.2 0.5 - - - -
350D PHE* 4.1 18.8 - - + -
354D LYS* 4.0 31.4 - - + +
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Residues in contact with ASP 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B GLN* 2.8 27.2 + - - -
354B LYS* 2.8 47.7 + - + +
357B ILE* 3.4 28.6 - - + +
358B GLY* 5.5 0.3 - - - -
361B ASN* 4.0 4.7 - - - +
393B ASN* 2.6 30.0 + - - +
394B ALA 3.3 6.3 - - - +
395B VAL 3.1 0.4 - - - -
396B LEU* 1.3 75.5 - - - +
398B GLY* 1.3 57.1 + - - +
70D LEU* 6.2 0.2 - - - +
73D LEU* 4.6 19.9 - - + +
393D ASN* 5.3 0.9 + - - -
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Residues in contact with GLY 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ILE* 3.4 8.1 - - - +
361B ASN* 3.0 31.0 + - - -
367B VAL* 3.9 0.3 - - - +
394B ALA 3.0 0.6 + - - -
395B VAL 2.9 11.3 + - - -
396B LEU 4.3 0.7 - - - -
397B ASP* 1.3 80.2 - - - +
399B ALA* 1.3 67.3 + - - +
400B ASP 3.6 0.9 + - - -
488B ARG* 3.6 9.0 + - - -
510B ARG* 3.4 9.6 - - - -
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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