Contacts of the helix formed by residues 401 - 412 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A VAL 5.1 4.2 - - - +
148A ASP* 5.0 4.2 - - - +
149A ILE* 5.3 3.5 + - - +
150A ASP* 4.7 10.3 + - - +
387B HIS* 3.5 46.4 + - + +
388B ALA 4.7 0.8 + - - -
389B ILE* 3.9 4.2 - - - +
400B GLY* 1.3 69.6 - - - +
402B PRO* 1.3 74.2 - - - +
403B ALA* 3.5 13.0 + - - +
404B THR* 2.7 37.3 + - - +
405B VAL* 2.9 19.8 + - - +
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Residues in contact with PRO 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 6.3 1.1 - - + -
150A ASP* 3.3 37.9 - - + +
364A LYS* 5.9 0.7 - - + -
365A SER* 3.6 24.5 - - - -
400B GLY 3.0 8.5 - - - +
401B ASP* 1.3 83.1 - - - +
403B ALA* 1.3 57.9 + - - +
405B VAL* 3.3 8.5 + - + +
406B LYS* 2.9 30.6 + - - +
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 4.0 26.7 - - + +
401B ASP* 3.2 11.9 + - - +
402B PRO* 1.3 75.7 - - - +
404B THR* 1.3 64.4 + - - +
406B LYS* 3.5 11.4 + - - +
407B ARG* 3.1 25.0 + - - +
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Residues in contact with THR 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B GLU* 4.8 1.3 + - - +
245B TYR* 4.1 11.2 - - - +
387B HIS* 3.3 26.9 - - + +
389B ILE* 3.8 19.3 - - + -
401B ASP* 2.7 27.0 + - - -
403B ALA* 1.3 72.8 - - - +
405B VAL* 1.3 68.1 + - - +
407B ARG* 3.1 34.5 + - - +
408B VAL* 2.9 34.9 + - + +
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B ILE* 3.8 32.5 - - + -
391B ILE* 5.1 4.7 - - + +
398B ASN* 3.6 35.7 - - + +
399B MSE 4.0 10.5 - - - +
400B GLY 4.1 7.2 - - - +
401B ASP 2.9 15.8 + - - +
402B PRO* 3.6 9.9 - - + +
404B THR* 1.3 77.9 - - - +
406B LYS* 1.3 63.4 + - - +
408B VAL* 3.9 1.6 - - - +
409B LYS* 3.0 39.9 + - + +
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Residues in contact with LYS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B PRO 2.9 17.6 + - - +
403B ALA* 3.6 10.1 - - - +
404B THR 3.1 0.2 - - - -
405B VAL* 1.3 80.2 - - - +
407B ARG* 1.3 62.7 + - - +
409B LYS* 3.4 8.2 + - - +
410B GLU* 3.1 20.6 + - - +
415B THR* 4.2 3.8 + - - +
67C GLU* 5.6 3.6 + - - -
71C GLU* 3.0 31.9 + - - -
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Residues in contact with ARG 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B GLU* 2.8 50.2 + - - +
245B TYR* 4.2 5.3 - - - -
403B ALA 3.1 16.1 + - - +
404B THR* 3.2 41.5 + - - +
406B LYS* 1.3 77.0 - - - +
408B VAL* 1.3 61.2 + - - +
410B GLU* 3.3 8.2 + - - +
411B GLU* 2.9 64.3 + - - +
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Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B TYR* 3.5 58.8 - - + -
273B PHE* 4.8 0.7 - - + -
389B ILE* 4.2 9.2 - - + -
391B ILE* 4.1 11.9 - - + -
404B THR* 2.9 28.1 + - + +
405B VAL 3.9 3.1 - - - +
407B ARG* 1.3 81.1 - - + +
409B LYS* 1.3 64.6 + - - +
411B GLU* 3.1 8.0 + - - +
412B LEU* 2.9 43.1 + - + +
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Residues in contact with LYS 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B ILE* 4.1 22.2 - - + -
395B LEU* 2.8 22.6 + - - +
396B GLY* 4.8 2.2 - - - -
398B ASN* 2.8 31.1 + - - +
405B VAL* 3.0 31.4 + - + +
406B LYS* 3.4 6.3 + - - +
408B VAL* 1.3 75.8 - - - +
410B GLU* 1.3 60.6 + - - +
413B GLY 3.2 1.4 + - - -
414B TYR* 2.8 52.9 + - + -
415B THR* 3.1 14.5 + - - +
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B LYS* 3.1 13.5 + - + +
407B ARG* 3.3 12.8 - - - +
408B VAL 3.1 0.4 - - - -
409B LYS* 1.3 74.8 - - - +
411B GLU* 1.3 69.4 + - + +
413B GLY* 3.2 13.0 + - - -
415B THR* 3.1 16.6 + - - +
418B SER* 3.3 10.6 - - - +
419B TRP* 4.0 10.2 + - - -
67C GLU* 2.5 45.7 - - - +
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Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B GLU 4.3 5.1 - - - +
245B TYR* 4.1 18.7 + - + +
246B LEU* 3.4 13.3 + - + +
407B ARG* 2.9 65.1 + - + +
408B VAL* 3.1 5.7 + - - +
410B GLU* 1.3 76.2 - - + +
412B LEU* 1.3 65.7 + - + +
419B TRP* 3.0 24.5 - - - -
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B TYR* 3.7 12.6 - - + +
246B LEU* 3.6 39.9 - - + +
273B PHE* 3.7 40.4 - - + +
277B ASP* 3.8 22.8 - - - +
280B LYS* 4.0 11.4 + - - -
391B ILE* 4.3 1.3 - - + -
408B VAL* 2.9 34.1 + - + +
411B GLU* 1.3 77.7 - - + +
413B GLY* 1.3 62.3 + - - +
414B TYR* 3.4 22.3 + - + -
419B TRP* 3.9 11.6 - - - -
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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