Contacts of the helix formed by residues 394 - 416 (chain C) in PDB entry 2VIG
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 THR 394 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C SER* 4.2 1.7 + - - +
389C GLU 3.5 4.0 - - - +
390C ILE* 3.2 26.4 + - + +
393C GLY* 1.3 78.9 - - - +
395C SER* 1.3 64.4 + - - +
396C GLU* 3.4 6.4 + - - -
397C ILE* 3.1 20.8 + - - +
398C GLN* 2.9 18.5 + - - +
501C FAD 2.4 66.2 + - - +
365D GLN* 4.0 6.3 - - - +
368D GLY* 5.3 2.2 - - - -
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Residues in contact with SER 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C LYS* 4.8 1.3 + - - +
350C LEU* 3.8 23.5 - - - +
353C SER* 4.2 2.8 + - - -
354C GLU* 3.7 10.0 + - - -
389C GLU* 3.1 33.5 + - - +
394C THR* 1.3 73.5 - - - +
396C GLU* 1.3 60.8 + - - +
398C GLN* 3.2 7.0 + - - +
399C ARG* 3.0 46.4 + - - +
365D GLN* 3.7 10.2 + - - +
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Residues in contact with GLU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 3.7 18.1 - - + -
394C THR* 3.4 1.4 + - - -
395C SER* 1.3 78.1 - - - +
397C ILE* 1.3 66.1 + - - +
399C ARG* 3.3 9.0 + - - +
400C LEU* 3.1 26.2 + - - +
501C FAD 3.1 43.0 + - - +
309D VAL* 4.0 14.6 - - + -
310D ILE* 5.7 0.2 - - + -
313D LYS* 2.7 40.7 + - - +
362D GLN* 5.4 0.2 + - - -
365D GLN* 2.9 31.5 + - - +
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Residues in contact with ILE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C SER* 3.8 18.6 - - - +
272C ARG* 3.9 19.5 - - - +
393C GLY* 3.9 10.1 - - - -
394C THR* 3.1 24.0 + - - +
396C GLU* 1.3 79.0 - - - +
398C GLN* 1.3 58.6 + - - +
400C LEU* 2.9 12.7 + - + +
401C VAL* 2.9 33.4 + - + +
501C FAD 3.8 41.1 - - + +
502C COS 3.6 32.1 - - + +
300D PHE* 5.3 2.9 - - + -
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Residues in contact with GLN 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ARG* 3.3 21.5 + - - +
346C ALA* 3.2 40.1 - - - +
349C LYS* 3.7 21.9 - - + +
350C LEU* 4.1 13.0 - - + -
392C GLU 3.1 18.6 + - - -
393C GLY* 2.9 24.7 + - - +
394C THR 2.9 17.7 + - - +
395C SER* 3.4 10.8 - - - +
397C ILE* 1.3 75.7 - - - +
399C ARG* 1.3 61.7 - - - +
401C VAL* 3.2 5.5 + - - +
402C ILE* 3.0 28.6 + - - +
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Residues in contact with ARG 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 3.6 41.6 - - + +
315A ALA* 3.4 16.5 - - + +
316A ASP* 3.0 34.6 + - - +
319A LEU* 5.9 0.8 - - - +
350C LEU* 3.7 20.4 - - + +
354C GLU* 3.1 40.1 + - - -
395C SER* 3.0 31.3 + - - +
396C GLU* 3.7 12.1 + - - +
397C ILE 3.3 0.2 - - - -
398C GLN* 1.3 74.8 - - - +
400C LEU* 1.3 58.0 + - - +
402C ILE* 3.5 3.3 + - - -
403C ALA* 2.9 31.4 + - - +
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Residues in contact with LEU 400 (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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308A GLN* 4.1 14.6 - - + +
311A GLN* 3.6 28.1 - - + +
312A PHE* 3.7 22.7 - - + -
396C GLU 3.1 16.3 + - - +
397C ILE* 2.9 16.2 + - + +
399C ARG* 1.3 75.6 - - - +
401C VAL* 1.3 59.2 + - + +
403C ALA* 3.9 2.8 - - - +
404C GLY* 3.0 25.5 + - - -
501C FAD 3.7 37.0 - - + +
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Residues in contact with VAL 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ARG* 4.2 19.1 - - - +
342C ILE* 3.8 30.3 - - + +
343C LYS* 5.0 0.2 - - - -
346C ALA* 3.9 18.6 - - + -
397C ILE* 2.9 26.9 + - + +
398C GLN* 3.5 8.1 - - - +
400C LEU* 1.3 74.7 - - + +
402C ILE* 1.3 67.3 + - - +
404C GLY* 3.4 1.4 + - - -
405C HIS* 3.1 34.3 + - + +
408C ARG* 4.9 0.6 + - - +
502C COS 5.5 3.1 - - - +
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Residues in contact with ILE 402 (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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315A ALA* 4.0 23.1 - - + +
318A ALA* 4.6 5.2 - - + -
319A LEU* 5.1 2.5 - - + -
343C LYS* 4.2 14.1 - - + +
346C ALA* 3.9 12.8 - - + -
347C MET* 3.6 55.4 - - + +
350C LEU* 3.6 28.9 - - + -
398C GLN 3.0 24.7 + - - +
399C ARG* 3.9 6.1 - - - +
401C VAL* 1.3 76.8 - - - +
403C ALA* 1.3 56.5 + - - +
405C HIS* 3.2 3.8 + - - +
406C LEU* 2.8 28.3 + - + +
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Residues in contact with ALA 403 (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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311A GLN* 3.4 47.1 - - + +
314A LEU* 5.4 1.6 - - + -
315A ALA* 4.0 5.4 - - + +
399C ARG 2.9 18.6 + - - +
400C LEU 3.9 3.6 - - - +
402C ILE* 1.3 75.5 - - - +
404C GLY* 1.3 58.0 + - - +
406C LEU* 3.3 8.1 + - - +
407C LEU* 2.9 38.8 + - + +
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Residues in contact with GLY 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLN* 5.2 2.4 + - - -
400C LEU 3.0 17.6 + - - -
401C VAL 3.4 1.8 + - - -
402C ILE 3.3 0.2 - - - -
403C ALA* 1.3 76.7 - - - +
405C HIS* 1.3 58.1 + - - +
407C LEU* 3.5 6.0 + - - +
408C ARG* 3.0 51.9 + - - +
411C ARG* 5.4 0.7 + - - -
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Residues in contact with HIS 405 (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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342C ILE* 3.2 52.0 - - + +
343C LYS* 3.9 26.2 - - + +
401C VAL* 3.1 29.5 + - + +
402C ILE 3.8 3.4 - - - +
404C GLY* 1.3 74.1 - - - +
406C LEU* 1.3 65.4 + - - +
408C ARG* 3.4 30.7 + - + +
409C SER* 3.1 24.8 + - - -
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Residues in contact with LEU 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.5 9.6 - - + -
291A VAL* 4.4 14.6 - - + -
314A LEU* 3.6 41.3 - - + +
315A ALA* 4.8 0.7 - - - +
318A ALA* 3.9 22.0 - - + -
322A GLU* 5.0 6.7 - - - +
343C LYS* 5.0 9.1 - - + +
402C ILE* 2.8 17.5 + - + +
403C ALA* 3.5 8.3 - - - +
405C HIS* 1.3 77.0 - - - +
407C LEU* 1.3 63.5 + - + +
409C SER* 3.2 15.0 + - - +
410C TYR* 3.2 42.8 + - + -
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Residues in contact with LEU 407 (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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291A VAL* 3.8 26.2 - - + -
295A GLU* 3.7 23.5 - - - +
305A THR* 3.7 39.5 - - + +
311A GLN* 4.7 11.7 - - + -
314A LEU* 4.2 13.7 - - + -
403C ALA* 2.9 25.0 + - + +
404C GLY* 4.0 5.2 - - - +
406C LEU* 1.3 80.7 - - + +
408C ARG* 1.3 60.2 + - - +
410C TYR* 3.4 4.3 + - - +
411C ARG* 3.1 42.0 + - - +
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Residues in contact with ARG 408 (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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401C VAL* 4.9 0.8 + - - +
404C GLY* 3.0 32.7 + - - +
405C HIS* 3.4 44.9 + - + +
406C LEU 3.3 0.2 - - - -
407C LEU* 1.3 73.6 - - - +
409C SER* 1.3 59.8 + - - +
411C ARG* 3.2 20.7 + - - +
412C SER* 3.0 33.6 + - - +
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Residues in contact with SER 409 (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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405C HIS 3.1 18.6 + - - -
406C LEU* 3.2 8.5 + - - +
408C ARG* 1.3 78.1 - - - +
410C TYR* 1.3 67.0 + - - +
412C SER* 3.6 7.2 + - - -
413C ALA* 3.2 22.0 + - - +
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Residues in contact with TYR 410 (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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284A GLN* 3.6 12.1 + - - -
287A LEU* 3.8 13.3 - - - +
288A ASP* 2.8 41.2 + - + -
291A VAL* 3.7 36.3 - - + -
292A ASN* 5.5 1.8 - - + -
295A GLU* 5.4 2.7 - - + +
406C LEU* 3.2 47.5 + - + +
407C LEU 3.4 6.3 + - - +
408C ARG 3.3 0.2 - - - -
409C SER* 1.3 85.0 + - - +
411C ARG* 1.3 57.6 + - - +
413C ALA* 3.3 8.0 + - + +
414C GLU* 2.9 34.6 + - + +
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Residues in contact with ARG 411 (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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295A GLU* 2.9 39.0 + - - +
305A THR* 4.4 3.8 + - - -
306A LYS* 4.7 15.4 - - - +
404C GLY 5.4 0.6 + - - -
407C LEU* 3.1 38.0 + - - +
408C ARG* 3.2 21.4 + - - +
410C TYR* 1.3 73.0 - - - +
412C SER* 1.3 61.5 + - - +
414C GLU* 3.5 7.7 + - + +
415C ASN* 3.0 41.4 + - - +
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Residues in contact with SER 412 (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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408C ARG* 3.0 17.9 + - - +
409C SER* 3.6 9.0 - - - -
411C ARG* 1.3 77.5 - - - +
413C ALA* 1.3 61.4 + - - +
415C ASN* 3.3 19.4 + - - +
416C LEU* 3.3 17.5 + - - +
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Residues in contact with ALA 413 (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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409C SER 3.2 12.0 + - - +
410C TYR* 3.3 12.5 + - + +
412C SER* 1.3 79.0 - - - +
414C GLU* 1.3 61.9 + - + +
416C LEU* 3.6 17.7 + - - +
417C TYR* 3.5 20.2 - - + -
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Residues in contact with GLU 414 (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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292A ASN* 4.0 16.6 - - - +
296A ASN* 5.2 3.6 + - - -
410C TYR* 2.9 24.1 + - + +
411C ARG* 3.6 9.4 - - - +
413C ALA* 1.3 77.6 - - - +
415C ASN* 1.3 65.1 + - - +
417C TYR* 3.4 32.9 + - - +
418C PHE* 3.7 11.8 - - + -
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Residues in contact with ASN 415 (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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411C ARG* 3.0 27.5 + - - +
412C SER* 3.3 9.8 + - - +
414C GLU* 1.3 74.4 - - - +
416C LEU* 1.3 57.8 + - - +
417C TYR 3.0 2.7 - - - -
418C PHE* 2.7 41.0 + - + +
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Residues in contact with LEU 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C SER 3.3 14.6 + - - +
413C ALA* 3.8 13.9 - - - +
414C GLU 3.3 0.8 - - - -
415C ASN* 1.3 78.8 - - - +
417C TYR* 1.3 62.1 + - + +
418C PHE 3.4 6.2 + - - +
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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