Contacts of the helix formed by residues 455 - 463 (chain B) in PDB entry 3VF1
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 455 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B PHE 3.6 4.1 + - - +
452B ASP* 3.2 15.2 + - - +
454B TYR* 1.3 73.9 - - - +
456B LEU* 1.3 66.5 + - - +
457B VAL* 3.4 9.7 + - - +
458B LYS* 3.2 48.9 + - + +
459B ASP* 2.9 23.1 + - - +
481B TRP* 4.4 9.7 + - - -
543B HIS* 3.6 29.6 + - + +
547B VAL* 5.0 0.2 - - - +
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Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B SER 5.7 0.2 - - - -
454B TYR 3.0 9.4 + - - +
455B ASP* 1.3 70.8 + - - +
457B VAL* 1.3 64.7 + - - +
459B ASP* 3.1 6.3 + - + +
460B LEU* 3.0 50.0 + - + +
473B TYR* 3.7 24.0 - - + +
477B ALA* 3.4 35.0 - - + +
478B LEU* 3.8 9.4 - - + -
481B TRP* 3.8 31.4 - - + -
550B PHE* 3.7 21.5 - - + -
555B GLN* 5.3 0.7 - - - +
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Residues in contact with VAL 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ASP* 3.3 7.3 + - - +
456B LEU* 1.3 75.3 - - - +
458B LYS* 1.3 64.5 + - + +
460B LEU* 3.8 3.0 + - - +
461B ARG* 3.2 52.6 + - - +
466B ASP* 5.1 1.2 - - - +
478B LEU* 4.1 22.4 - - + -
481B TRP* 3.9 29.4 - - + +
482B ASN* 4.9 7.2 - - - +
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Residues in contact with LYS 458 (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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452B ASP 5.4 2.2 - - - +
455B ASP* 3.2 33.5 + - + +
457B VAL* 1.3 78.8 - - + +
459B ASP* 1.3 59.8 + - - +
461B ARG* 3.7 20.9 - - - +
462B GLN* 3.0 31.8 + - - +
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Residues in contact with ASP 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B GLU* 6.1 0.5 - - - +
452B ASP 4.8 3.5 + - - +
453B SER* 4.1 32.7 - - - +
455B ASP 2.9 18.2 + - - +
456B LEU* 3.1 6.6 + - + +
458B LYS* 1.3 74.6 - - - +
460B LEU* 1.3 68.5 + - + +
461B ARG 3.1 1.3 + - - -
462B GLN* 3.3 21.9 + - - +
463B ARG* 3.1 52.1 + - - +
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Residues in contact with LEU 460 (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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456B LEU* 3.0 33.4 + - + +
457B VAL 4.2 2.5 - - - +
459B ASP* 1.3 78.8 - - - +
461B ARG* 1.3 61.2 + - - +
463B ARG* 3.5 26.3 + - - +
464B GLY 3.2 15.6 + - - -
465B VAL* 3.2 28.0 + - + +
466B ASP* 3.5 16.2 + - + -
471B PHE* 4.4 12.6 - - + -
473B TYR* 4.7 10.1 - - + -
474B LYS* 3.7 26.0 - - + -
478B LEU* 3.9 27.8 - - + -
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Residues in contact with ARG 461 (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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457B VAL* 3.2 43.9 + - - +
458B LYS* 3.7 19.9 - - - +
459B ASP 3.1 0.4 - - - -
460B LEU* 1.3 76.2 - - - +
462B GLN* 1.3 58.9 + - - +
463B ARG 3.1 2.0 - - - -
464B GLY* 3.1 17.3 + - - -
466B ASP* 3.8 23.1 + - - +
1D GLC 5.1 13.3 + - - -
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Residues in contact with GLN 462 (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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252B ARG* 2.9 48.2 + - - +
458B LYS 3.0 18.0 + - - +
459B ASP* 3.3 24.7 + - - +
461B ARG* 1.3 76.3 - - - +
463B ARG* 1.3 69.3 + - - +
464B GLY* 3.6 0.3 + - - -
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Residues in contact with ARG 463 (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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248B PRO 2.9 29.4 + - - -
249B GLU* 3.3 29.7 + - - +
250B VAL 3.6 2.4 - - - +
251B ILE* 2.7 36.4 + - - +
252B ARG* 3.6 24.4 - - + +
253B ARG* 2.9 31.7 + - - +
459B ASP* 3.1 37.0 + - - +
460B LEU* 3.5 30.5 - - - +
462B GLN* 1.3 94.1 - - - +
464B GLY* 1.3 59.6 + - - +
465B VAL* 3.2 16.1 + - + +
471B PHE* 4.9 1.0 - - - -
473B TYR* 5.6 1.2 - - - -
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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
------------------------------------------------------------
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