Contacts of the helix formed by residues 401 - 413 (chain C) in PDB entry 1VLP
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 ASP 401 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387C HIS* 3.5 46.9 + - + +
388C ALA 4.6 1.4 + - - -
389C ILE* 4.0 4.2 - - - +
400C GLY* 1.3 67.6 - - - +
402C PRO* 1.4 74.7 - - - +
403C ALA* 3.6 11.9 + - - +
404C THR* 2.7 35.1 + - - +
405C VAL* 3.0 22.0 + - - +
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Residues in contact with PRO 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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400C GLY 3.3 10.1 - - - +
401C ASP* 1.4 86.4 - - - +
403C ALA* 1.3 58.6 + - - +
405C VAL* 3.2 8.1 + - + +
406C LYS* 2.9 31.5 + - - +
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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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401C ASP* 3.3 11.9 + - - +
402C PRO* 1.3 78.5 - - - +
404C THR* 1.3 57.2 + - - +
406C LYS* 3.5 6.2 + - - +
407C ARG* 2.9 28.8 + - - +
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Residues in contact with THR 404 (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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243C GLU* 4.6 4.5 + - - +
245C TYR* 4.2 14.4 - - - +
387C HIS* 3.6 19.3 - - + -
389C ILE* 3.9 22.4 - - + -
401C ASP* 2.7 31.3 + - - -
403C ALA* 1.3 73.8 - - - +
405C VAL* 1.3 65.1 + - - +
407C ARG* 3.1 27.8 + - - +
408C VAL* 2.9 31.4 + - + +
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Residues in contact with VAL 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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389C ILE* 3.8 21.8 - - + -
390C LYS 4.5 4.5 - - - +
391C ILE* 4.4 7.8 - - + +
398C ASN* 3.8 19.3 - - + +
399C MSE 3.7 26.0 - - - +
400C GLY 3.9 6.5 - - - +
401C ASP 3.0 17.0 + - - +
402C PRO* 3.5 10.1 - - + +
404C THR* 1.3 76.7 - - - +
406C LYS* 1.3 58.3 + - + +
408C VAL* 3.9 1.0 - - - +
409C LYS* 3.0 54.6 + - - +
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Residues in contact with LYS 406 (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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402C PRO 2.9 17.1 + - - +
403C ALA* 3.9 6.1 - - - +
405C VAL* 1.3 76.2 - - + +
407C ARG* 1.3 67.2 + - - +
409C LYS* 3.5 11.4 + - + +
410C GLU* 2.7 57.6 + - + +
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Residues in contact with ARG 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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243C GLU* 3.4 37.1 + - - +
245C TYR* 4.3 7.7 - - - -
403C ALA 2.9 18.8 + - - +
404C THR* 3.1 22.5 + - - +
406C LYS* 1.3 77.6 - - - +
408C VAL* 1.3 67.3 + - - +
410C GLU* 3.4 11.7 + - - +
411C GLU* 2.7 83.8 + - + +
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Residues in contact with VAL 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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245C TYR* 3.7 49.4 - - + -
273C PHE* 4.6 0.9 - - + -
389C ILE* 3.9 15.7 - - + -
391C ILE* 4.0 12.1 - - + -
404C THR* 2.9 19.6 + - + +
405C VAL 4.0 0.9 - - - +
407C ARG* 1.3 83.4 - - - +
409C LYS* 1.3 67.6 + - - +
411C GLU* 3.3 11.9 + - - +
412C LEU* 3.0 41.8 + - + +
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Residues in contact with LYS 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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391C ILE* 3.6 29.6 - - + +
395C LEU* 3.9 6.1 - - - +
398C ASN* 2.9 30.2 + - - +
405C VAL* 3.0 30.2 + - + +
406C LYS* 3.5 11.0 - - + +
408C VAL* 1.3 77.3 - - - +
410C GLU* 1.3 59.2 + - + +
412C LEU* 3.3 0.8 + - - -
413C GLY 3.0 9.2 + - - -
414C TYR* 2.9 57.8 + - + +
416C GLU* 2.8 29.7 + - - +
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Residues in contact with GLU 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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406C LYS* 2.7 54.0 + - + +
407C ARG* 3.7 11.0 - - - +
409C LYS* 1.3 76.2 - - + +
411C GLU* 1.3 63.0 + - + +
413C GLY* 3.2 13.6 + - - +
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Residues in contact with GLU 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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243C GLU 5.5 0.9 - - - +
245C TYR* 4.5 9.5 - - - +
246C LEU* 4.7 9.9 + - + +
407C ARG* 2.7 63.3 + - + +
408C VAL* 3.3 14.8 + - - +
410C GLU* 1.3 77.9 - - + +
412C LEU* 1.3 66.2 + - + +
413C GLY 3.9 0.2 + - - -
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Residues in contact with LEU 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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245C TYR* 4.0 11.0 - - + +
246C LEU* 3.9 34.3 - - + +
273C PHE* 3.6 37.5 - - + +
277C ASP* 3.6 35.8 + - + +
280C LYS* 5.4 5.7 - - - +
391C ILE* 5.0 1.3 - - + -
408C VAL* 3.0 30.9 + - + +
409C LYS* 4.0 2.9 - - - +
411C GLU* 1.3 82.5 - - + +
413C GLY* 1.4 63.2 - - - +
414C TYR* 3.3 5.0 + - + +
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Residues in contact with GLY 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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276C ASP* 5.5 2.3 - - - +
409C LYS 3.0 4.7 + - - -
410C GLU* 3.2 13.4 + - - -
411C GLU 3.4 1.0 + - - -
412C LEU* 1.4 78.4 - - - +
414C TYR* 1.3 64.6 + - - +
415C THR* 3.5 10.2 + - - -
502C EDO 4.7 0.9 + - - -
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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