Contacts of the helix formed by residues 404 - 409 (chain C) in PDB entry 6VVT
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 THR 404 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C GLN* 3.4 19.6 + - - +
403C ILE* 1.3 75.3 - - - +
405C PRO* 1.3 82.5 - - - +
406C GLN* 3.2 24.0 - - + +
407C THR* 2.7 39.6 + - + +
408C LEU* 2.9 13.8 + - - +
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Residues in contact with PRO 405 (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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98C PHE* 5.7 2.5 - - + -
140C SER* 3.8 20.2 - - - +
141C GLN* 3.3 29.8 - - + +
143C VAL* 4.4 1.3 - - + -
404C THR* 1.3 94.7 - - - +
406C GLN* 1.3 56.6 + - - +
408C LEU* 4.5 6.0 - - + +
409C ILE* 2.8 53.5 + - + +
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Residues in contact with GLN 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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141C GLN* 3.4 21.9 - - + +
142C THR 5.1 1.1 - - - +
143C VAL* 4.6 6.5 - - - -
404C THR* 3.1 13.9 - - + +
405C PRO* 1.3 78.9 - - - +
407C THR* 1.3 62.5 + - + +
409C ILE* 3.2 18.3 - - - +
326F GLN* 4.6 21.0 - - + +
327F ASP* 5.6 4.5 - - - +
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Residues in contact with THR 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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394C ARG* 5.3 2.8 - - - +
402C ALA 5.2 2.9 - - - +
403C ILE* 3.4 15.2 - - - +
404C THR* 2.7 45.5 + - + +
406C GLN* 1.3 80.4 - - + +
408C LEU* 1.3 62.6 + - - +
409C ILE 3.8 1.4 + - - +
410C ASN* 6.1 0.2 - - - +
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Residues in contact with LEU 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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390C VAL* 4.7 5.0 - - - +
391C VAL* 3.2 33.4 + - + +
394C ARG* 3.8 17.7 - - + +
395C MET* 3.7 54.7 - - + +
398C GLN* 4.7 2.9 - - + -
403C ILE* 4.1 22.4 - - + -
404C THR 2.9 20.4 + - - +
405C PRO* 4.1 5.8 - - + +
407C THR* 1.3 80.0 + - - +
409C ILE* 1.3 63.0 + - + +
410C ASN* 3.5 2.6 + - - +
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Residues in contact with ILE 409 (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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98C PHE* 3.3 41.7 - - + -
143C VAL* 3.6 27.8 - - + -
145C MET* 4.8 4.3 - - + -
387C MET* 6.0 5.2 - - + -
391C VAL* 4.3 12.8 - - + -
405C PRO* 2.8 34.0 + - + +
406C GLN* 3.2 14.5 - - - +
407C THR 4.7 1.5 - - - -
408C LEU* 1.3 78.1 - - + +
410C ASN* 1.3 60.9 + - - +
411C ILE* 3.4 31.4 + - + +
326F GLN* 4.7 7.8 + - - +
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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