Contacts of the helix formed by residues 416 - 422 (chain B) in PDB entry 6VSB
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 GLY 416 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B GLN* 5.0 4.5 - - - -
415B THR* 1.3 78.0 - - - +
417B LYS* 1.3 58.8 + - - -
418B ILE 3.2 3.1 - - - -
419B ALA* 3.2 1.9 + - - -
420B ASP* 2.7 41.5 + - - +
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Residues in contact with LYS 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLY* 1.3 70.1 - - - -
418B ILE* 1.3 63.0 + - + +
420B ASP* 4.9 2.2 - - - -
421B TYR* 2.9 26.0 + - + +
422B ASN* 2.5 26.7 + - - +
453B TYR* 5.7 6.3 - - + -
454B ARG 5.0 5.4 - - - +
370C ASN 5.7 4.7 - - - +
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Residues in contact with ILE 418 (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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350B VAL* 4.2 14.8 - - + -
402B ILE* 5.0 5.4 - - + -
406B GLU* 3.6 30.7 - - + +
409B GLN* 4.9 9.6 - - + -
410B ILE* 3.8 28.3 - - + -
416B GLY 3.2 0.4 - - - -
417B LYS* 1.3 84.9 - - + +
419B ALA* 1.3 61.8 + - - +
422B ASN* 2.8 31.7 + - + +
423B TYR* 2.6 33.5 + - + +
453B TYR* 5.7 1.8 - - + -
495B TYR* 4.3 18.2 - - - +
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLN* 4.1 18.8 - - + +
411B ALA 5.8 0.2 - - - +
414B GLN* 3.6 28.7 - - + +
415B THR* 3.7 19.5 - - - +
416B GLY 3.2 2.2 + - - -
418B ILE* 1.3 80.0 - - - +
420B ASP* 1.3 58.9 + - - +
423B TYR 3.4 10.5 - - - -
424B LYS* 3.4 27.9 - - - +
461B LEU 5.1 0.9 - - - +
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Residues in contact with ASP 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B THR* 5.8 1.3 - - - -
416B GLY 2.7 27.3 + - - +
417B LYS* 4.5 1.3 - - - +
419B ALA* 1.3 76.8 - - - +
421B TYR* 1.3 66.1 + - + +
460B ASN* 3.2 22.6 - - + +
461B LEU* 3.1 31.5 + - - +
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Residues in contact with TYR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B TYR* 5.5 0.3 - - - +
417B LYS* 2.9 18.5 + - + +
420B ASP* 1.3 91.6 - - + +
422B ASN* 1.3 64.2 + - - +
454B ARG* 3.7 25.4 - - + +
460B ASN* 3.3 29.9 + - - -
461B LEU* 3.7 14.8 - - + +
370C ASN* 5.7 11.4 + - + -
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Residues in contact with ASN 422 (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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350B VAL* 3.9 22.3 - - + +
351B TYR* 4.0 12.7 - - - +
353B TRP* 4.2 6.6 + - - -
417B LYS* 2.5 33.5 + - - +
418B ILE* 2.8 31.9 + - + +
421B TYR* 1.3 78.6 - - - +
423B TYR* 1.3 62.6 + - - +
453B TYR* 3.3 14.5 - - - +
454B ARG* 2.4 49.3 + - - +
461B LEU* 4.7 5.3 - - - +
465B GLU 4.7 5.0 - - - +
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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