Contacts of the helix formed by residues 362 - 376 (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 GLU 362 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C TYR* 4.2 2.2 - - - -
360C LYS* 3.8 11.6 - - - +
361C LEU* 1.3 76.4 - - - +
363C LYS* 1.3 66.8 + - - +
364C GLU* 3.3 11.4 - - - +
365C GLU* 2.7 21.6 + - + +
366C PHE* 3.0 16.5 + - - +
402C TYR* 2.8 29.9 + - - +
406C GLN* 4.1 9.1 + - - +
407C HIS* 3.0 37.3 + - - -
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Residues in contact with LYS 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU* 4.2 20.6 - - + -
245C GLU* 4.0 30.6 - - - +
315C TYR* 3.4 39.1 + - + +
362C GLU* 1.3 72.7 - - - +
364C GLU* 1.3 66.1 + - - +
366C PHE* 2.8 23.7 + - + +
367C VAL* 3.0 22.6 + - + +
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Residues in contact with GLU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C TYR* 2.6 38.8 + - + +
238C VAL* 3.7 15.1 - - + +
242C LEU* 4.1 20.5 - - + +
362C GLU* 3.8 5.4 - - - +
363C LYS* 1.3 83.9 + - - +
365C GLU* 1.3 53.1 + - + +
367C VAL* 3.1 14.3 - - - +
368C THR* 2.5 30.5 + - - -
402C TYR* 3.5 36.6 + - + -
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Residues in contact with GLU 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C LEU* 3.4 11.4 - - + -
362C GLU* 2.7 46.5 + - + +
363C LYS 3.0 0.4 - - - -
364C GLU* 1.3 76.9 - - - +
366C PHE* 1.3 65.3 + - - +
368C THR* 3.9 3.8 - - - -
369C LEU* 2.9 28.4 + - - +
399C LEU* 4.9 8.0 - - + +
402C TYR* 3.7 16.8 - - + -
403C GLU* 2.8 32.2 - - - +
407C HIS* 3.8 0.5 + - - -
413C ARG* 2.8 30.0 + - - -
417C MET* 3.3 15.5 - - + +
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Residues in contact with PHE 366 (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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245C GLU* 4.4 12.1 - - - -
311C LEU* 3.6 32.8 - - + -
312C GLY* 3.9 15.9 - - - -
315C TYR* 3.7 50.7 - + + -
316C ARG* 5.9 1.3 - - + -
361C LEU* 3.9 11.5 - - + +
362C GLU 3.0 7.8 + - - +
363C LYS* 2.8 13.3 + - + +
365C GLU* 1.3 75.4 - - - +
367C VAL* 1.3 62.6 + - + +
369C LEU* 2.9 9.5 + - - +
370C LYS* 2.8 73.3 + - + +
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Residues in contact with VAL 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C VAL* 4.8 3.1 - - + +
241C LEU* 4.2 32.6 - - + +
242C LEU* 4.4 13.0 - - + +
245C GLU* 3.5 28.7 - - + +
282C TRP* 4.3 7.1 - - - +
363C LYS* 3.0 21.5 + - + +
364C GLU* 3.1 29.4 - - - +
366C PHE* 1.3 86.5 - - + +
368C THR* 1.3 58.9 + - - +
370C LYS* 3.5 12.4 + - - +
371C ALA* 3.1 25.3 + - - +
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Residues in contact with THR 368 (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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238C VAL* 4.4 10.9 - - + +
241C LEU* 4.1 21.1 - - + +
364C GLU 2.5 25.2 + - - -
365C GLU* 4.1 4.5 - - - -
366C PHE 3.2 0.6 - - - -
367C VAL* 1.3 78.4 - - - +
369C LEU* 1.3 61.1 + - - +
371C ALA* 3.3 1.7 + - - +
372C ILE* 2.8 37.7 + - + +
395C LEU* 3.8 25.8 - - + +
398C ALA* 4.4 7.2 - - + -
399C LEU* 4.3 24.0 - - + +
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Residues in contact with LEU 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C LEU* 4.0 14.4 - - + -
356C TYR* 3.4 39.9 - - + +
361C LEU* 5.0 4.7 - - + -
365C GLU 2.9 18.9 + - - +
366C PHE* 2.9 6.7 + - - +
368C THR* 1.3 75.3 - - - +
370C LYS* 1.3 59.0 + - - +
372C ILE* 3.1 16.3 + - + +
373C ALA* 2.8 32.4 + - - +
399C LEU* 5.1 4.9 - - + +
417C MET* 4.3 30.3 - - + +
418C LEU* 4.7 4.3 - - + -
420C THR* 4.0 4.5 - - - +
421C LEU* 3.9 27.1 - - + -
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Residues in contact with LYS 370 (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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245C GLU* 2.9 33.1 + - - -
246C PRO* 4.5 5.9 - - - +
279C ILE* 6.1 2.2 - - - +
282C TRP* 3.8 30.7 - - + +
308C ILE* 3.8 34.9 - - + +
311C LEU* 3.6 15.9 - - + +
312C GLY* 5.3 0.2 - - - -
366C PHE* 2.8 49.6 + - + +
367C VAL* 3.6 14.1 - - - +
369C LEU* 1.3 76.6 - - - +
371C ALA* 1.3 64.4 + - - +
373C ALA* 3.2 4.7 + - - +
374C LEU* 3.2 22.5 + - - +
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Residues in contact with ALA 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C LEU* 4.1 17.5 - - + -
282C TRP* 3.8 10.9 - - + -
286C ILE* 4.1 10.2 - - + +
367C VAL 3.1 14.5 + - - +
368C THR 3.6 8.3 - - - +
370C LYS* 1.3 78.6 - - - +
372C ILE* 1.3 56.3 + - - +
374C LEU* 3.5 4.4 - - - +
375C ALA* 3.1 21.5 + - - +
395C LEU* 3.6 38.2 - - + +
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Residues in contact with ILE 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C THR* 2.8 25.8 + - + +
369C LEU* 3.6 9.4 - - + +
371C ALA* 1.3 71.4 - - - +
373C ALA* 1.3 56.8 + - - +
375C ALA* 3.1 6.6 + - + +
376C ASN* 2.7 34.5 + - + +
392C GLN* 5.5 0.7 - - - +
395C LEU* 4.0 34.1 - - + +
396C HIS* 4.4 4.9 - - - +
399C LEU* 4.0 29.6 - - + -
418C LEU* 4.1 7.6 - - + -
421C LEU* 4.0 21.3 - - + -
419F MET* 3.6 26.5 - - + -
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Residues in contact with ALA 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C ALA* 3.7 5.3 - - - +
307C GLU* 3.7 29.4 - - + +
308C ILE* 4.9 5.2 - - + +
311C LEU* 5.1 1.1 - - + -
369C LEU 2.8 19.4 + - - +
370C LYS* 3.2 7.8 + - - +
372C ILE* 1.3 73.6 - - - +
374C LEU* 1.3 61.5 - - - +
376C ASN* 3.7 3.5 - - - -
377C SER* 3.3 24.6 + - - -
421C LEU* 4.8 8.3 - - + -
424C LEU* 4.2 17.3 - - + -
425C ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 374 (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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282C TRP* 4.0 6.5 - - + -
283C ALA* 3.9 20.0 - - + -
286C ILE* 3.5 29.4 - - + -
289C PHE* 3.9 17.5 - - + -
300C LEU* 3.5 39.3 - - + +
301C LEU* 3.8 15.7 - - + +
304C ALA* 3.6 12.2 - - + +
308C ILE* 4.0 12.7 - - + +
370C LYS 3.2 9.3 + - - +
371C ALA* 3.5 8.5 - - - +
373C ALA* 1.3 76.4 - - - +
375C ALA* 1.3 64.6 + - - +
377C SER* 3.1 20.3 + - - -
391C LEU* 6.3 0.7 - - + -
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Residues in contact with ALA 375 (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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300C LEU* 4.5 6.3 - - - +
371C ALA 3.1 14.0 + - - +
372C ILE* 3.1 4.9 + - - +
374C LEU* 1.3 81.2 - - + +
376C ASN* 1.3 56.5 + - - +
377C SER 3.3 3.3 + - - -
378C ASP 5.0 0.5 + - - -
388C VAL* 3.6 12.1 - - - +
391C LEU* 3.9 24.7 - - + -
392C GLN* 2.9 32.6 + - + +
395C LEU* 3.8 20.4 - - + -
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Residues in contact with ASN 376 (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 ILE* 2.7 21.9 + - + +
373C ALA* 3.7 5.2 - - - +
375C ALA* 1.3 71.3 - - - +
377C SER* 1.3 54.6 + - - +
378C ASP* 3.2 18.8 - - - +
392C GLN* 3.6 19.8 + - + +
421C LEU* 4.0 17.6 - - - +
425C ARG* 3.1 17.1 + - - +
355F LYS* 4.5 3.1 + - - -
419F MET* 3.2 56.3 + - + +
422F PRO* 4.2 9.3 - - - +
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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
------------------------------------------------------------
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