Contacts of the strand formed by residues 401 - 404 (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 CYS 401 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C THR* 4.0 0.7 - - - -
89C SER* 3.1 14.8 - - - +
91C ILE* 3.7 25.4 - - + -
114C ILE* 4.6 1.8 - - - -
366C PRO* 5.8 0.4 - - - -
367C VAL 3.2 4.1 + - - +
368C VAL* 3.5 10.0 - - + -
369C CYS 3.0 24.8 + - - -
399C ALA* 4.0 3.3 - - - +
400C ASP* 1.3 83.4 - - - +
402C ILE* 1.3 67.8 + - - +
507C HIS 3.6 24.2 - - - -
508C LEU* 3.8 29.2 - - - -
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Residues in contact with ILE 402 (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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88C THR* 3.9 19.0 - - + +
89C SER 3.0 8.5 + - - +
90C ILE* 3.4 7.0 - - + -
91C ILE* 2.9 25.4 + - - +
369C CYS* 3.5 4.5 - - + -
373C MET* 3.8 25.8 - - + -
391C VAL* 3.7 18.6 - - + -
394C ALA* 4.1 15.3 - - + -
395C VAL* 4.8 5.2 - - + -
399C ALA* 4.9 2.2 - - + -
401C CYS* 1.3 80.8 - - - +
403C MET* 1.3 59.5 + - - +
421C GLN* 3.1 51.0 + - + +
425C ALA* 4.4 5.8 - - + -
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Residues in contact with MET 403 (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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91C ILE* 3.5 26.2 - - + -
116C ARG* 3.6 35.0 - - - +
284C PHE* 4.5 0.9 - - - -
334C MET* 3.6 28.0 - - + -
368C VAL* 4.6 5.8 - - + -
369C CYS 3.1 17.2 + - - +
370C ALA* 3.8 23.6 - - + -
371C THR* 4.7 8.8 + - - +
373C MET* 3.9 14.0 + - - +
402C ILE* 1.3 75.3 - - - +
404C LEU* 1.3 76.1 + - - +
405C SER* 3.5 20.6 - - - +
407C GLU* 5.0 0.5 - - - +
421C GLN* 3.1 17.0 - - - +
581C PGA 5.0 3.1 - - - +
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Residues in contact with LEU 404 (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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90C ILE* 4.4 6.1 - - + -
91C ILE 3.0 9.8 + - - +
92C ALA* 4.9 0.4 - - + -
93C THR* 2.5 34.0 + - - -
371C THR* 6.0 1.3 - - - +
372C GLN 6.4 0.2 - - - +
374C LEU* 3.9 17.7 - - + +
403C MET* 1.3 78.4 - - - +
405C SER* 1.3 57.9 + - - +
407C GLU* 3.8 29.4 - - + +
408C THR* 3.6 34.1 - - + +
417C ALA* 3.9 15.5 - - + +
418C VAL* 3.7 20.4 - - + -
421C GLN* 3.4 31.2 - - - +
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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
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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