Contacts of the helix formed by residues 475 - 487 (chain B) in PDB entry 2VM8
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 PRO 475 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ASN* 4.0 16.6 - - - +
192B GLY 3.9 5.4 - - - +
194B ILE* 4.0 9.4 - - + -
390B LYS 4.0 12.3 - - - +
391B VAL 3.2 28.3 - - - +
393B ASN* 3.9 19.1 - - + +
473B PRO* 3.4 5.6 - - + -
474B PHE* 1.3 86.0 - - - +
476B ASP* 1.3 56.9 + - - +
477B PHE 3.2 0.7 - - - -
478B VAL* 2.8 12.1 + - + -
479B TYR* 2.7 46.0 + - + -
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Residues in contact with ASP 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLN* 6.0 3.3 - - + +
30A SER* 4.5 11.8 + - - +
376A ASP* 3.6 3.8 - - - +
378A ASN* 5.3 2.0 - - - +
393B ASN* 4.7 3.6 + - - +
474B PHE 3.1 11.9 + - - +
475B PRO* 1.3 70.0 - - - +
477B PHE* 1.3 63.3 - - - +
478B VAL 3.0 1.0 + - - -
479B TYR* 5.2 0.2 - - - -
480B LYS* 2.7 70.4 + - + +
483B LYS* 5.6 4.4 + - - +
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Residues in contact with PHE 477 (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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28A ASP 5.9 1.1 - - - -
376A ASP* 4.0 13.4 - - - +
378A ASN* 6.5 1.3 - - + -
379A GLN* 5.4 10.3 - - + -
275B TYR* 4.0 24.5 - + - -
327B GLN* 6.2 2.5 - - + -
387B ASN* 4.7 11.4 - - + -
390B LYS* 3.6 56.5 - - + +
391B VAL* 4.0 20.9 - - + -
475B PRO 3.0 1.0 + - - -
476B ASP* 1.3 78.6 - - - +
478B VAL* 1.3 58.5 + - + +
481B ARG* 3.1 23.0 + - - -
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Residues in contact with VAL 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE* 4.8 7.4 - - + -
249B PRO* 3.2 39.5 - - + -
273B VAL* 4.0 13.7 - - + +
275B TYR* 3.5 22.4 - - + +
391B VAL* 3.7 39.5 - - + +
475B PRO* 2.8 9.1 + - + +
477B PHE* 1.3 81.5 - - + +
479B TYR* 1.3 69.6 + - + +
480B LYS 3.7 1.1 + - - -
481B ARG* 4.0 6.3 + - - +
482B ILE* 3.5 16.8 + - - +
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Residues in contact with TYR 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE 3.4 7.4 + - - -
189B ARG* 3.5 22.1 - - - -
192B GLY* 3.3 21.2 - - - -
193B ALA 2.6 37.8 + - - -
194B ILE* 5.2 0.4 - - + -
249B PRO* 3.4 19.6 - - + +
474B PHE* 3.7 32.3 - + - -
475B PRO* 2.7 26.1 + - + +
478B VAL* 1.3 78.5 - - + +
480B LYS* 1.3 59.2 + - - +
481B ARG 3.1 2.6 + - - -
482B ILE* 3.8 26.2 - - + -
483B LYS* 2.7 52.5 + - + +
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Residues in contact with LYS 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 5.2 1.8 - - - +
30A SER* 3.3 9.2 + - - +
376A ASP* 3.6 21.8 - - + +
377A GLU* 3.1 34.9 + - + -
378A ASN* 2.8 29.4 + - - +
476B ASP* 2.7 53.1 + - + +
479B TYR* 1.3 74.4 - - - +
481B ARG* 1.3 57.6 + - - +
483B LYS* 3.7 13.2 - - + +
484B ALA* 3.1 25.6 + - - +
487B ARG* 4.8 1.6 + - - -
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Residues in contact with ARG 481 (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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322A SER 5.8 1.8 + - - -
373A GLY* 3.3 19.9 - - - +
374A LYS 3.7 18.2 + - - -
375A MET* 3.7 24.0 - - - +
376A ASP* 4.0 8.2 + - + +
271B GLY 5.2 1.0 + - - -
272B THR 4.7 3.4 + - - -
273B VAL* 3.7 34.6 - - + +
275B TYR* 3.0 28.1 + - - -
477B PHE* 3.1 22.2 + - - -
478B VAL* 4.0 4.5 + - - +
479B TYR 3.1 0.4 - - - -
480B LYS* 1.3 73.8 - - - +
482B ILE* 1.3 67.2 + - - +
484B ALA* 3.2 6.0 + - - +
485B ARG* 2.9 42.7 + - - +
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Residues in contact with ILE 482 (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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189B ARG* 4.3 5.8 - - + -
247B ASN* 3.2 59.0 + - - +
248B CYS 4.1 1.3 - - - -
249B PRO* 3.8 28.5 - - + -
273B VAL* 4.1 23.1 - - + -
478B VAL 3.5 16.6 - - - +
479B TYR* 3.7 28.7 - - + +
481B ARG* 1.3 76.4 - - - +
483B LYS* 1.3 63.1 + - - +
485B ARG* 3.0 11.6 + - - +
486B SER* 3.0 15.1 + - - +
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Residues in contact with LYS 483 (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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474B PHE* 3.9 31.2 + - + +
476B ASP* 5.6 3.9 + - - +
479B TYR* 2.7 50.1 + - + +
480B LYS* 3.7 13.5 - - - +
482B ILE* 1.3 71.1 - - + +
484B ALA* 1.3 65.3 + - - +
485B ARG 3.2 0.3 + - - -
486B SER* 3.5 8.1 + - - -
487B ARG* 3.2 45.1 + - - +
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Residues in contact with ALA 484 (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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370A VAL 4.2 10.1 - - - +
371A VAL 4.7 4.5 - - - +
373A GLY* 3.7 22.0 - - - +
375A MET 5.6 0.9 - - - +
480B LYS 3.1 16.7 + - - +
481B ARG* 3.2 10.3 + - - +
483B LYS* 1.3 76.2 - - - +
485B ARG* 1.3 61.7 + - - +
487B ARG* 3.2 37.3 - - - +
488B LEU* 3.7 11.2 + - - +
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Residues in contact with ARG 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A THR 4.6 3.4 - - - +
373A GLY* 3.1 34.7 + - - -
374A LYS* 4.3 8.5 + - - +
244B ASN* 5.2 3.4 + - - -
247B ASN* 3.5 24.7 + - - +
271B GLY* 2.7 33.3 + - - -
272B THR* 4.5 1.6 - - - +
273B VAL* 3.4 29.1 - - - +
481B ARG* 2.9 32.8 + - - +
482B ILE* 3.0 6.2 + - - +
484B ALA* 1.3 75.2 - - - +
486B SER* 1.3 60.1 + - - +
488B LEU* 3.0 34.8 + - + +
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Residues in contact with SER 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ARG* 4.8 7.6 - - - +
247B ASN* 3.1 20.7 + - - +
482B ILE* 3.0 12.7 + - - +
483B LYS* 3.8 8.0 - - - -
485B ARG* 1.3 77.6 - - - +
487B ARG* 1.3 60.3 + - - +
488B LEU 3.3 8.8 + - - +
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Residues in contact with ARG 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG* 6.1 2.5 - - - +
480B LYS 4.8 1.8 + - - -
483B LYS* 3.2 36.0 - - - +
484B ALA* 3.2 39.8 - - - +
485B ARG 3.1 1.0 - - - -
486B SER* 1.3 77.2 - - - +
488B LEU* 1.3 64.4 + - + +
489B ALA* 5.2 1.6 - - - +
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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
------------------------------------------------------------
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