Contacts of the helix formed by residues 405 - 410 (chain C) in PDB entry 2VGB
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 SER 405 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C THR* 3.4 10.3 + - - -
116C ARG* 3.8 7.0 + - - -
371C THR* 4.8 14.5 + - - +
372C GLN 5.8 2.1 - - - +
375C GLU* 6.0 0.2 - - - -
403C MET* 3.5 22.2 - - - +
404C LEU* 1.3 78.4 + - - +
406C GLY* 1.3 69.7 + - - -
407C GLU* 2.7 12.5 + - - -
408C THR* 3.0 4.3 + - - -
409C ALA* 2.8 28.0 + - - +
581C PGA 4.9 5.2 + - - -
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Residues in contact with GLY 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C GLU* 4.8 3.4 + - - -
378C ILE* 3.4 23.6 - - - +
405C SER* 1.3 77.8 - - - +
407C GLU* 1.3 65.2 + - - +
408C THR 3.1 1.2 + - - -
409C ALA 4.5 0.4 - - - -
410C LYS* 3.1 29.5 + - - +
411C GLY 3.1 22.3 + - - -
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Residues in contact with GLU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C GLN* 4.0 4.4 + - - -
373C MET 3.6 8.5 + - - -
374C LEU* 3.0 56.4 + - + +
375C GLU* 3.6 13.4 + - - +
377C MET* 4.8 1.4 - - + +
378C ILE* 3.6 15.7 - - + +
404C LEU* 3.8 15.3 - - + +
405C SER* 2.7 25.2 + - - -
406C GLY* 1.3 76.5 + - - +
408C THR* 1.3 58.0 + - - +
411C GLY* 4.3 7.6 + - - -
413C PHE 4.1 4.0 + - - -
414C PRO* 3.3 21.5 - - - +
417C ALA* 3.8 19.0 - - + +
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Residues in contact with THR 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA* 3.8 4.7 - - + +
93C THR 2.7 36.6 + - - -
97C ALA* 3.6 7.0 - - - +
98C SER* 3.1 21.8 + - - -
107C MET* 4.1 10.5 - - + -
404C LEU* 3.6 33.1 + - + +
405C SER 3.0 4.0 + - - -
407C GLU* 1.3 79.7 - - - +
409C ALA* 1.3 64.7 + - - +
410C LYS 3.6 0.4 - - - -
414C PRO* 3.6 29.1 - - + +
417C ALA* 4.5 0.2 - - + -
418C VAL* 3.8 9.4 - - + -
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Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C THR* 3.7 20.4 - - + +
94C ILE 4.2 4.5 - - - +
95C GLY* 3.7 14.8 - - - +
96C PRO* 3.1 14.9 - - + +
97C ALA* 2.9 22.0 + - - -
405C SER 2.8 25.1 + - - +
406C GLY* 4.7 0.2 - - - -
408C THR* 1.3 75.8 + - - +
410C LYS* 1.3 69.9 + - + +
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Residues in contact with LYS 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C PRO* 4.9 12.1 - - + -
97C ALA* 3.8 7.2 - - - +
121C HIS* 6.3 1.2 - - - -
378C ILE* 5.3 10.5 - - + -
406C GLY* 3.1 26.9 + - - +
409C ALA* 1.3 87.6 - - + +
411C GLY* 1.3 69.1 + - - +
412C ASN* 4.4 4.3 - - - +
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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