Contacts of the helix formed by residues 401 - 413 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381D LEU* 6.3 0.6 - - - +
387D HIS* 3.5 41.4 + - + +
388D ALA 4.5 1.6 + - - -
389D ILE* 4.0 3.6 - - - +
400D GLY* 1.3 67.6 - - - +
402D PRO* 1.4 74.9 - - - +
403D ALA* 3.6 12.9 + - - +
404D THR* 2.6 36.6 + - - +
405D VAL* 3.0 21.8 + - - +
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Residues in contact with PRO 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400D GLY 2.9 10.3 - - - +
401D ASP* 1.4 87.6 - - - +
403D ALA* 1.3 62.0 + - - +
405D VAL* 3.4 7.9 + - + +
406D LYS* 3.1 24.8 + - - +
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Residues in contact with ALA 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401D ASP* 3.3 12.9 + - - +
402D PRO* 1.3 79.0 - - - +
404D THR* 1.3 61.1 + - - +
406D LYS* 3.6 4.9 + - - +
407D ARG* 3.2 27.4 + - - +
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Residues in contact with THR 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D TYR* 4.1 15.7 - - + +
387D HIS* 3.5 22.0 - - + +
389D ILE* 3.8 21.3 - - + -
401D ASP* 2.6 29.2 + - - -
403D ALA* 1.3 73.8 - - - +
405D VAL* 1.3 55.7 + - - +
407D ARG* 3.4 27.9 + - - +
408D VAL* 2.8 44.4 + - + +
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Residues in contact with VAL 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D ILE* 3.9 20.6 - - + -
390D LYS 4.7 3.4 - - - +
391D ILE* 4.7 7.6 - - + +
398D ASN* 3.7 19.3 - - + +
399D MSE 3.8 24.9 - - - +
400D GLY 3.8 7.6 - - - +
401D ASP 3.0 18.1 + - - +
402D PRO* 3.6 9.9 - - + +
404D THR* 1.3 75.8 - - - +
406D LYS* 1.3 63.6 + - - +
408D VAL* 3.3 2.3 + - - +
409D LYS* 3.0 53.2 + - + +
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Residues in contact with LYS 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D PRO 3.1 16.9 + - - +
403D ALA* 4.1 4.9 - - - +
405D VAL* 1.3 76.6 - - - +
407D ARG* 1.3 61.6 + - - +
409D LYS* 3.4 12.6 + - + +
410D GLU* 3.0 46.3 + - + +
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Residues in contact with ARG 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D GLU* 5.2 11.1 - - - +
245D TYR* 4.8 8.7 - - - -
403D ALA* 3.2 17.4 + - - +
404D THR* 3.5 32.1 + - - +
406D LYS* 1.3 76.5 - - - +
408D VAL* 1.3 63.5 + - - +
410D GLU* 3.2 18.0 + - - +
411D GLU* 2.7 63.0 + - + +
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Residues in contact with VAL 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D TYR* 3.6 46.9 - - + -
273D PHE* 4.4 1.6 - - + -
389D ILE* 3.6 21.3 - - + -
391D ILE* 4.0 12.3 - - + -
404D THR* 2.8 28.8 + - + +
405D VAL 3.9 1.6 - - - +
407D ARG* 1.3 76.5 - - - +
409D LYS* 1.3 67.6 + - - +
411D GLU* 3.1 8.3 + - - +
412D LEU* 2.9 46.6 + - + +
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Residues in contact with LYS 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D ILE* 3.8 31.0 - - + -
395D LEU* 4.1 14.1 - - - +
398D ASN* 2.7 30.7 + - - +
405D VAL* 3.0 33.6 + - + +
406D LYS* 3.6 10.4 - - + +
408D VAL* 1.3 75.8 - - - +
410D GLU* 1.3 61.8 + - + +
412D LEU* 4.8 0.7 - - - -
413D GLY* 3.0 4.0 + - - -
414D TYR* 2.7 68.3 + - + +
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Residues in contact with GLU 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D LYS* 3.0 36.7 + - + +
407D ARG* 3.3 20.6 - - - +
409D LYS* 1.3 76.3 - - + +
411D GLU* 1.3 63.3 + - + +
413D GLY* 3.2 12.7 + - - -
414D TYR 5.6 0.2 - - - -
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Residues in contact with GLU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D GLU 4.8 4.9 - - - +
245D TYR* 4.2 23.0 + - - +
246D LEU* 4.4 28.1 + - + +
407D ARG* 2.7 61.2 + - + +
408D VAL* 3.1 9.1 + - - +
410D GLU* 1.3 74.3 - - + +
412D LEU* 1.3 67.2 + - + +
413D GLY 3.5 0.3 + - - -
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Residues in contact with LEU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D TYR* 3.8 25.1 - - + +
246D LEU* 3.8 20.9 - - + +
273D PHE* 3.5 40.2 - - + +
277D ASP* 3.6 28.9 - - + +
280D LYS* 3.9 19.8 + - - -
391D ILE* 4.7 3.1 - - + -
408D VAL* 2.9 35.0 + - + +
409D LYS* 4.2 3.4 - - - +
411D GLU* 1.3 79.1 - - + +
413D GLY* 1.3 62.6 + - - +
414D TYR* 4.6 5.8 - - + +
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Residues in contact with GLY 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D LYS* 5.8 0.4 + - - -
409D LYS 3.0 4.3 + - - -
410D GLU* 3.2 10.3 + - - -
411D GLU 3.3 1.2 + - - -
412D LEU* 1.3 79.3 - - - +
414D TYR* 1.3 60.6 - - - +
415D THR* 3.6 6.9 - - - -
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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