Contacts of the helix formed by residues 384 - 398 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B GLN* 3.1 23.7 + - - +
375B GLU* 4.8 14.4 - - + +
387B GLU* 5.1 5.5 + - - +
376D SER* 3.3 25.8 - - - +
380D LYS* 6.0 3.8 - - + +
383D PRO* 1.3 77.8 - - - +
385D ARG* 1.3 65.9 + - - +
386D ALA* 3.5 7.6 + - - +
387D GLU* 2.6 47.5 + - - +
388D THR* 3.3 11.1 + - - -
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Residues in contact with ARG 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ASP* 2.8 29.4 + - - -
337B ARG* 3.0 53.1 + - + +
338B GLY* 2.8 26.8 + - - +
341B GLY* 3.6 16.1 + - - -
342B ILE* 3.7 11.9 - - - +
346B ALA* 6.2 3.4 - - - -
349B VAL* 5.1 7.2 - - + -
371B THR* 3.9 16.8 - - + +
372B GLN* 2.8 44.7 + - - +
383D PRO 3.8 15.8 + - - -
384D THR* 1.3 73.3 - - - +
386D ALA* 1.3 59.8 + - - +
388D THR* 3.8 10.3 + - - +
389D SER* 3.3 22.2 + - - -
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Residues in contact with ALA 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B ARG* 4.5 0.4 - - - +
372B GLN 3.6 21.9 + - - +
373B MET 4.5 0.2 - - - +
386B ALA* 3.9 11.5 - - + +
387B GLU* 4.1 15.5 - - + -
390B ASP* 3.7 31.2 - - + -
384D THR* 3.1 6.2 + - - +
385D ARG* 1.3 77.7 - - - +
387D GLU* 1.3 60.1 + - - +
389D SER* 3.4 2.6 + - - -
390D ASP* 2.8 28.6 + - - +
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Residues in contact with GLU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B THR* 5.1 6.8 + - - +
386B ALA* 4.1 15.0 - - + -
387B GLU* 5.8 1.9 - - + +
372D GLN 4.7 0.6 - - - +
373D MET 3.1 21.5 - - - +
374D LEU* 3.7 18.5 - - + -
375D GLU* 3.5 8.2 + - - +
376D SER* 2.5 50.0 + - - -
383D PRO* 3.4 6.1 - - + +
384D THR* 2.6 34.9 + - - +
386D ALA* 1.3 75.9 - - + +
388D THR* 1.3 67.1 + - - +
390D ASP* 3.0 12.3 + - - +
391D VAL* 3.0 17.2 + - - +
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Residues in contact with THR 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ALA* 3.3 35.0 + - - +
347B GLU* 4.9 4.5 - - - -
349B VAL* 4.9 5.4 - - + -
350B PHE* 4.7 18.2 - - + +
374D LEU* 4.4 1.2 - - - +
383D PRO* 4.0 18.1 - - - +
384D THR 3.3 5.9 + - - -
385D ARG* 3.8 14.4 - - - +
387D GLU* 1.3 79.9 - - - +
389D SER* 1.3 65.9 + - - +
391D VAL* 3.3 3.3 + - - +
392D ALA* 3.2 17.0 + - - +
420D MET* 4.3 0.9 - - - +
424D ILE* 3.8 22.9 - - + +
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Residues in contact with SER 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ARG* 4.0 5.6 - - - -
350B PHE* 4.5 18.2 - - - -
353B GLN* 5.2 6.1 - - - -
390B ASP* 2.6 32.2 + - - -
385D ARG 3.3 10.8 + - - -
386D ALA 3.6 1.9 + - - -
387D GLU 3.2 0.6 - - - -
388D THR* 1.3 82.5 - - - +
390D ASP* 1.3 65.3 + - - +
392D ALA* 3.9 0.8 - - - +
393D ASN* 2.8 43.0 + - - +
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Residues in contact with ASP 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B ALA* 3.7 22.2 - - + +
389B SER* 2.7 24.2 + - - +
337D ARG* 2.5 47.5 + - - -
353D GLN* 5.1 2.4 + - - -
373D MET* 3.7 15.5 - - - +
386D ALA 2.8 18.4 + - - +
387D GLU 3.0 9.2 + - - +
389D SER* 1.3 75.2 + - - +
391D VAL* 1.3 63.3 + - - +
393D ASN* 3.7 2.7 - - - +
394D ALA* 2.9 23.2 + - - +
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Residues in contact with VAL 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D MET* 3.8 19.5 - - + +
374D LEU* 3.7 22.0 - - + -
387D GLU 3.0 14.0 + - - +
388D THR 3.3 0.6 + - - +
390D ASP* 1.3 73.3 - - - +
392D ALA* 1.3 66.9 + - - +
394D ALA* 3.0 14.2 + - - +
395D VAL* 3.2 14.0 + - + +
402D ILE* 3.7 28.0 - - + -
421D GLN* 4.3 16.2 - - + +
424D ILE* 3.6 34.5 - - + -
425D ALA 4.5 2.2 - - - +
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Residues in contact with ALA 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B PHE* 3.5 52.0 - - + -
388D THR 3.2 6.9 + - - +
389D SER 3.9 5.2 - - - +
391D VAL* 1.3 76.4 - - - +
393D ASN* 1.3 60.5 + - - +
395D VAL* 3.1 7.2 + - - +
396D LEU* 2.8 29.7 + - - +
424D ILE* 3.5 13.4 - - + +
428D ALA* 3.8 7.0 - - + +
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Residues in contact with ASN 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B PHE* 5.9 0.2 - - - +
353B GLN* 6.1 0.8 - - - +
354B LYS* 2.8 36.9 + - - +
389B SER* 5.3 0.2 - - - +
393B ASN* 3.4 49.0 - - - +
397B ASP* 5.3 1.0 + - - -
353D GLN* 4.9 0.9 - - - +
354D LYS* 5.4 0.3 + - - -
389D SER* 2.8 38.9 + - - +
390D ASP* 4.0 3.4 - - - +
392D ALA* 1.3 73.8 - - - +
394D ALA* 1.3 56.1 + - - +
396D LEU* 3.7 7.1 - - - +
397D ASP* 2.7 42.6 + - - +
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Residues in contact with ALA 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D GLN* 4.1 5.3 - - - +
369D CYS* 3.9 22.2 - - + -
373D MET* 3.6 21.1 - - + -
390D ASP 2.9 13.8 + - - +
391D VAL 3.0 8.9 + - - +
393D ASN* 1.3 72.3 - - - +
395D VAL* 1.3 65.7 + - - +
397D ASP* 3.3 11.3 + - - +
398D GLY 3.1 6.4 + - - -
399D ALA* 3.1 23.9 + - + +
402D ILE* 4.1 8.1 - - + -
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Residues in contact with VAL 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D THR* 3.5 25.4 - - + +
391D VAL* 3.2 11.4 + - + +
392D ALA 3.1 8.1 + - - +
394D ALA* 1.3 76.6 - - - +
396D LEU* 1.3 56.1 + - - +
398D GLY* 2.7 22.3 + - - -
399D ALA 4.3 1.1 - - - +
402D ILE* 4.8 5.6 - - + -
425D ALA* 4.2 21.3 - - + -
428D ALA* 3.6 21.1 - - + +
429D GLU* 3.8 24.0 - - + +
432D VAL* 4.7 2.6 - - + +
510D ARG* 2.9 32.1 + - - +
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Residues in contact with LEU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B PHE* 4.0 17.7 - - + -
354B LYS* 3.9 32.3 - - + +
392D ALA* 2.8 22.2 + - + +
393D ASN* 3.9 8.5 - - - +
395D VAL* 1.3 77.6 - - - +
397D ASP* 1.3 63.7 + - - +
398D GLY* 3.3 0.7 + - - -
428D ALA* 3.4 27.1 - - + +
431D ALA* 4.1 19.7 - - + +
432D VAL* 4.2 12.7 - - + +
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Residues in contact with ASP 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 4.7 18.3 - - + +
393B ASN* 5.2 0.3 + - - -
353D GLN* 2.8 27.7 + - - -
354D LYS* 2.7 48.4 + - + +
357D ILE* 3.4 28.7 - - + +
358D GLY* 5.2 0.9 + - - -
361D ASN* 4.0 5.2 - - - +
393D ASN* 2.7 29.3 + - - +
394D ALA 3.3 7.0 - - - +
395D VAL 3.1 0.2 - - - -
396D LEU* 1.3 74.1 - - - +
398D GLY* 1.3 56.8 + - - +
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Residues in contact with GLY 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D ILE* 3.3 6.8 - - - +
361D ASN* 2.9 34.7 + - - -
367D VAL* 3.9 0.7 - - - +
394D ALA 3.1 0.8 + - - -
395D VAL 2.7 13.9 + - - -
396D LEU 4.2 1.1 - - - -
397D ASP* 1.3 78.8 - - - +
399D ALA* 1.3 62.3 + - - +
400D ASP 3.7 0.3 + - - -
437D LEU* 6.5 1.1 - - - -
488D ARG* 3.6 7.0 + - - -
510D ARG* 3.4 11.2 - - - -
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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