Contacts of the helix formed by residues 401 - 412 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A HIS* 3.5 47.4 + - + +
388A ALA 4.8 0.8 + - - -
389A ILE* 3.9 3.8 - - - +
400A GLY* 1.3 67.9 - - - -
402A PRO* 1.4 73.3 - - - +
403A ALA* 3.5 13.9 + - - +
404A THR* 2.7 34.7 + - - +
405A VAL* 3.0 22.7 + - - +
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Residues in contact with PRO 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLY 3.2 10.3 - - - +
401A ASP* 1.4 86.9 - - - +
403A ALA* 1.3 58.7 + - - +
405A VAL* 3.3 7.1 + - + +
406A LYS* 2.9 30.1 + - - +
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A ASP* 3.3 12.6 + - - +
402A PRO* 1.3 79.6 - - - +
404A THR* 1.3 57.7 + - - +
406A LYS* 3.5 8.3 + - - +
407A ARG* 3.0 36.4 + - + +
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Residues in contact with THR 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLU* 4.8 4.1 + - - +
245A TYR* 4.2 14.8 - - - +
387A HIS* 3.4 23.8 - - + +
389A ILE* 3.8 21.1 - - + -
401A ASP* 2.7 31.3 + - - -
403A ALA* 1.3 75.6 - - - +
405A VAL* 1.3 60.8 + - - +
407A ARG* 3.3 29.1 + - - +
408A VAL* 2.9 36.0 + - + +
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Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A ILE* 3.8 28.5 - - + -
390A LYS 4.8 1.3 - - - +
391A ILE* 4.8 6.2 - - + +
398A ASN* 3.5 35.4 - - + +
399A MSE 3.9 15.0 - - - +
400A GLY 4.1 7.4 - - - +
401A ASP 3.0 18.6 + - - +
402A PRO* 3.6 9.6 - - + +
404A THR* 1.3 76.7 - - - +
406A LYS* 1.3 58.0 + - - +
408A VAL* 3.8 1.4 - - - +
409A LYS* 2.9 43.8 + - + +
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A PRO 2.9 17.8 + - - +
403A ALA* 3.5 8.5 - - - +
405A VAL* 1.3 79.1 - - - +
407A ARG* 1.3 62.1 + - + +
409A LYS* 3.5 8.9 + - - +
410A GLU* 3.2 49.9 + - + +
415A THR* 5.4 1.9 - - + -
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Residues in contact with ARG 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLU* 3.4 35.6 + - - +
245A TYR* 4.4 11.5 - - - -
403A ALA* 3.0 23.8 + - + +
404A THR* 3.5 27.4 + - - +
406A LYS* 1.3 76.7 - - + +
408A VAL* 1.3 59.7 + - - +
410A GLU* 3.4 16.0 + - - +
411A GLU* 2.6 67.9 + - - +
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A TYR* 3.7 45.1 - - + -
273A PHE* 4.7 0.7 - - + -
389A ILE* 3.6 20.4 - - + -
391A ILE* 3.7 14.8 - - + -
404A THR* 2.9 23.3 + - + +
405A VAL 3.8 1.3 - - - +
407A ARG* 1.3 78.2 - - - +
409A LYS* 1.3 60.4 + - - +
410A GLU 3.1 1.8 - - - -
411A GLU* 3.1 8.2 + - - +
412A LEU* 2.9 53.6 + - + +
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Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ILE* 4.2 20.4 - - + -
395A LEU 3.5 16.7 + - - -
396A GLY* 4.9 2.8 - - - -
398A ASN* 2.9 30.9 + - - +
405A VAL* 2.9 31.1 + - + +
406A LYS* 3.7 7.9 - - - +
408A VAL* 1.3 76.2 - - - +
410A GLU* 1.3 60.5 + - - +
412A LEU 3.6 0.7 + - - -
413A GLY 3.2 2.8 + - - -
414A TYR* 2.8 47.6 + - + -
415A THR* 3.3 22.5 + - + +
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Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A LYS* 3.2 44.9 + - - +
407A ARG* 3.4 14.2 - - - +
408A VAL 3.1 0.4 - - - -
409A LYS* 1.3 75.4 - - - +
411A GLU* 1.3 60.4 + - + +
413A GLY* 3.0 20.3 + - - -
415A THR* 4.0 32.7 - - + +
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLU 4.5 5.5 - - - +
245A TYR* 4.3 23.7 + - + +
246A LEU* 3.8 23.9 + - + +
407A ARG* 2.6 51.2 + - - +
408A VAL* 3.7 6.2 - - - +
410A GLU* 1.3 76.4 - - + +
412A LEU* 1.3 65.5 + - + +
413A GLY 3.3 1.4 + - - -
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Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A TYR* 3.8 13.2 - - + +
246A LEU* 3.8 31.9 - - + +
273A PHE* 3.7 35.9 - - + +
277A ASP* 3.6 29.5 - - - +
280A LYS* 4.3 17.9 + - - +
391A ILE* 4.5 0.2 - - + -
408A VAL* 2.9 34.5 + - + +
411A GLU* 1.3 81.7 - - + +
413A GLY* 1.3 61.2 + - - +
414A TYR* 3.3 25.0 + - + -
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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