Contacts of the helix formed by residues 235 - 244 (chain C) in PDB entry 2GPV
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 ASN 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234C TYR* 1.3 77.6 - - - +
236C LYS* 1.3 64.9 + - - +
237C ILE* 2.7 36.6 + - - +
238C VAL* 3.1 25.8 + - + +
239C SER* 3.0 25.2 + - - -
397C GLU* 4.9 2.4 - - - +
398C ALA* 3.5 26.6 - - - +
401C ASP* 3.6 29.9 + - + +
402C TYR* 4.9 6.9 - - + +
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Residues in contact with LYS 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C TYR 3.6 7.6 + - - +
235C ASN* 1.3 75.9 + - - +
237C ILE* 1.3 60.1 + - + +
239C SER* 3.3 8.2 + - - -
240C HIS* 2.9 28.5 + - - +
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Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ASN* 2.7 14.8 + - - +
236C LYS* 1.3 73.1 - - + +
238C VAL* 1.3 64.8 + - - +
240C HIS* 3.6 6.3 - - - +
241C LEU* 2.9 41.6 + - + +
287C PRO* 4.1 27.6 - - + -
394C VAL* 3.2 42.4 - - + +
395C LEU* 4.2 11.9 - - + -
398C ALA* 4.2 11.0 - - + -
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Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C TYR* 4.2 10.3 - - + -
235C ASN* 3.1 32.0 + - + +
237C ILE* 1.3 77.1 - - - +
239C SER* 1.3 65.1 + - - +
241C LEU* 3.0 11.1 + - - +
242C LEU* 2.9 21.8 + - + +
364C GLU* 3.7 45.8 - - + +
367C VAL* 4.8 1.0 - - + +
368C THR* 4.4 9.2 - - - +
398C ALA* 4.1 19.5 - - + +
399C LEU* 5.7 0.2 - - - -
402C TYR* 4.1 12.3 - - + -
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Residues in contact with SER 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C TYR* 4.0 20.1 + - - +
235C ASN 3.0 13.3 + - - -
236C LYS* 3.5 11.1 - - - -
238C VAL* 1.3 78.6 - - - +
240C HIS* 1.3 64.0 + - - +
242C LEU* 2.9 24.8 + - - +
243C VAL* 3.2 18.6 + - - +
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Residues in contact with HIS 240 (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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236C LYS 2.9 19.6 + - - +
237C ILE* 3.3 9.8 + - + +
239C SER* 1.3 72.3 - - - +
241C LEU* 1.3 60.5 + - + +
243C VAL* 3.3 16.7 - - + +
244C ALA* 3.0 24.7 + - + +
285C HIS* 2.8 50.9 + - + +
286C ILE* 5.2 0.2 - - - -
287C PRO* 4.6 12.8 - - + +
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Residues in contact with LEU 241 (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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237C ILE* 2.9 35.9 + - + +
238C VAL* 3.4 6.5 - - - +
240C HIS* 1.3 80.7 - - + +
242C LEU* 1.3 61.9 + - - +
244C ALA* 3.3 7.2 + - + +
245C GLU* 3.2 21.3 + - - +
282C TRP* 4.6 14.7 + - - +
286C ILE* 4.0 33.2 - - + +
287C PRO* 4.9 3.8 - - + -
367C VAL* 4.2 20.5 - - + +
368C THR* 4.1 34.5 - - + +
371C ALA* 4.1 15.0 - - + -
395C LEU* 4.3 1.6 - - + -
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Residues in contact with LEU 242 (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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234C TYR* 4.9 6.5 - - + -
238C VAL* 2.9 14.8 + - + +
239C SER* 2.9 20.0 + - - +
241C LEU* 1.3 76.5 - - - +
243C VAL* 1.3 59.7 + - + +
245C GLU* 3.2 21.5 - - - +
363C LYS* 4.2 33.2 - - + -
364C GLU* 4.1 40.4 - - + +
367C VAL* 4.4 8.5 - - + +
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Residues in contact with VAL 243 (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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239C SER* 3.2 15.5 + - - +
240C HIS* 3.3 21.8 - - + +
242C LEU* 1.3 73.5 - - + +
244C ALA* 1.3 64.0 + - + +
245C GLU 3.0 15.4 + - - +
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Residues in contact with ALA 244 (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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240C HIS* 3.0 21.2 + - + +
241C LEU* 3.3 10.7 + - + +
243C VAL* 1.3 77.4 - - + +
245C GLU* 1.3 61.2 + - - +
246C PRO* 3.3 10.0 - - - +
282C TRP* 3.3 16.9 - - + +
285C HIS* 3.6 42.5 - - + +
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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