Contacts of the helix formed by residues 392 - 398 (chain C) in PDB entry 2VPG
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 CYS 392 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345C ILE* 6.3 0.4 - - + -
359C CYS* 3.3 10.7 - - - -
363C CYS* 4.0 1.3 - - - -
367C PHE* 3.5 33.2 - - + -
390C TRP* 3.6 20.9 - - + -
391C GLY* 1.3 74.7 - - - +
393C ASP* 1.3 61.2 + - - +
394C THR* 3.8 11.7 - - - -
395C CYS* 3.3 16.9 + - - +
396C MET* 2.9 27.3 + - - +
1400C ZN 2.5 32.8 - - - -
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Residues in contact with ASP 393 (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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372C THR 5.3 5.0 - - - +
390C TRP* 5.0 0.6 - - - -
392C CYS* 1.3 75.2 - - - +
394C THR* 1.3 58.3 + - - +
396C MET* 3.8 5.5 - - - +
397C ALA* 2.9 31.2 + - - +
181D SER* 5.2 3.6 - - - -
182D THR* 4.2 23.5 + - - -
183D GLU 5.5 0.3 + - - -
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Residues in contact with THR 394 (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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392C CYS* 3.8 10.3 - - - -
393C ASP* 1.3 77.9 - - - +
395C CYS* 1.3 65.3 + - - +
397C ALA* 3.3 6.7 + - - +
398C ASP* 3.1 41.5 + - - +
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Residues in contact with CYS 395 (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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359C CYS* 4.0 4.5 - - - -
361C ALA* 4.9 4.7 - - + -
362C SER* 3.5 34.3 - - - +
363C CYS* 3.6 12.1 - - - -
392C CYS* 3.3 8.9 + - - +
394C THR* 1.3 81.3 - - - +
396C MET* 1.3 64.1 + - - +
398C ASP* 3.3 29.3 + - - +
1400C ZN 2.4 35.2 - - - -
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Residues in contact with MET 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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361C ALA* 4.4 5.4 - - - -
391C GLY* 3.3 26.0 - - - +
392C CYS 2.9 20.1 + - - +
393C ASP* 3.8 5.4 - - - +
395C CYS* 1.3 73.8 - - - +
397C ALA* 1.3 65.9 + - - +
398C ASP 3.3 7.8 - - - +
179D VAL* 3.7 37.7 - - + +
180D PHE 4.5 0.2 - - - +
181D SER* 3.8 31.9 - - - +
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Residues in contact with ALA 397 (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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393C ASP 2.9 18.1 + - - +
394C THR* 3.3 7.8 + - - +
396C MET* 1.3 77.9 - - - +
398C ASP* 1.3 64.1 + - - +
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Residues in contact with ASP 398 (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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394C THR* 3.1 30.5 + - - +
395C CYS* 3.4 19.8 - - - +
396C MET 3.3 9.8 - - - +
397C ALA* 1.3 84.2 - - - +
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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