Contacts of the helix formed by residues 337 - 344 (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 ARG 337 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A ARG* 2.9 42.4 + - + +
389A SER* 3.9 7.5 + - - -
335C VAL* 2.9 21.4 + - + +
336C ALA* 1.3 72.1 - - - +
338C GLY* 1.3 55.2 + - - +
340C LEU* 4.1 6.7 - - - -
341C GLY* 2.6 31.0 + - - -
349C VAL* 3.8 21.7 - - + +
353C GLN* 3.0 24.2 + - - +
369C CYS* 3.7 14.2 - - - -
370C ALA 2.6 27.1 + - - +
371C THR 3.0 19.0 + - - -
372C GLN 4.5 0.4 - - - -
373C MET* 3.5 12.7 - - - +
390C ASP* 2.6 45.4 + - - -
581C PGA 3.4 2.2 + - - -
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Residues in contact with GLY 338 (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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385A ARG* 2.7 31.5 + - - -
221C ASP* 5.1 2.5 - - - -
337C ARG* 1.3 78.3 - - - +
339C ASP* 1.3 59.4 + - - -
341C GLY 3.2 2.4 + - - -
342C ILE* 3.3 9.6 - - - +
371C THR* 3.6 19.5 - - - +
581C PGA 3.0 15.5 + - - -
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Residues in contact with ASP 339 (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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253C ASN* 3.2 24.7 + - - +
287C PHE* 3.2 24.7 - - + -
315C GLU* 2.2 26.7 - - + +
337C ARG 3.6 0.2 - - - -
338C GLY* 1.3 67.5 - - - +
340C LEU* 1.3 68.8 + - - +
341C GLY 3.0 1.8 - - - -
342C ILE* 2.8 17.4 + - - +
343C GLU* 2.9 16.4 + - + +
581C PGA 2.8 8.0 + - - +
591C MN 1.7 42.3 + - - -
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Residues in contact with LEU 340 (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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314C ILE 4.1 6.7 - - - +
315C GLU* 3.3 7.1 + - - +
316C ASN* 3.5 31.4 - - - +
320C VAL* 3.8 17.0 - - + -
335C VAL* 4.4 11.7 - - + -
336C ALA 3.0 20.8 + - - +
337C ARG* 3.7 4.3 - - - +
339C ASP* 1.3 76.1 - - - +
341C GLY* 1.3 57.9 + - - +
342C ILE 3.0 0.3 + - - -
343C GLU* 4.5 0.4 - - - -
344C ILE* 3.0 52.1 + - + +
349C VAL* 4.2 10.5 - - + -
352C ALA* 3.9 26.0 - - + -
356C MET* 4.0 17.3 - - + -
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Residues in contact with GLY 341 (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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382A ARG* 5.2 4.7 + - - -
385A ARG* 3.5 16.2 + - - -
337C ARG 2.6 23.3 + - - -
339C ASP 3.0 0.6 - - - -
340C LEU* 1.3 73.2 - - - +
342C ILE* 1.3 61.4 + - - +
344C ILE 3.5 9.5 - - - +
346C ALA* 4.2 16.8 + - - +
349C VAL* 3.6 17.7 - - - -
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Residues in contact with ILE 342 (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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382A ARG* 6.3 0.4 - - - +
385A ARG* 3.6 8.3 - - - +
218C TYR* 4.2 17.3 - - + -
221C ASP* 3.7 14.6 - - - +
222C GLY* 3.6 34.8 - - - +
253C ASN* 3.5 43.5 - - + +
255C PRO* 3.7 13.1 - - - +
338C GLY 3.3 21.1 - - - +
339C ASP* 2.8 7.0 + - - +
341C GLY* 1.3 80.7 - - - +
343C GLU* 1.3 65.9 + - - +
344C ILE 3.4 5.1 + - - +
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Residues in contact with GLU 343 (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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253C ASN* 2.8 32.3 - - - +
254C LEU 4.1 7.4 + - - +
255C PRO* 4.0 30.8 - - - +
259C VAL* 6.2 0.3 - - - +
287C PHE* 5.3 5.8 - - + -
315C GLU 3.3 19.3 - - - +
316C ASN* 3.8 26.2 + - + +
317C HIS* 4.6 5.1 - - + +
339C ASP* 2.9 20.4 + - + +
340C LEU 4.0 1.8 - - - +
342C ILE* 1.3 79.5 - - - +
344C ILE* 1.3 63.1 + - + +
345C PRO* 4.8 0.2 - - - +
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Residues in contact with ILE 344 (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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78A ILE* 4.2 19.1 - - + -
317C HIS* 4.0 43.1 - - + +
340C LEU* 3.0 40.9 + - + +
341C GLY 3.5 10.7 - - - +
342C ILE 3.7 4.3 - - - +
343C GLU* 1.3 80.8 - - - +
345C PRO* 1.3 81.0 - - + +
346C ALA 3.5 1.6 + - - -
348C LYS* 3.9 15.3 - - + +
349C VAL* 3.9 28.3 - - + +
352C ALA* 4.7 3.1 - - + -
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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