Contacts of the helix formed by residues 381 - 386 (chain C) in PDB entry 4WCX
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 381 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C LYS* 4.1 3.8 - - + +
129C ARG* 3.5 33.9 - - + +
164C ARG* 3.2 45.5 - - + +
165C ARG* 4.1 14.6 - - + -
379C TYR 3.4 6.6 + - - +
380C CYS* 1.3 80.2 - - - +
382C ALA* 1.3 63.9 + - - +
383C CYS 3.2 3.8 + - - +
384C TYR* 3.3 6.4 + - - +
385C ARG* 3.0 22.5 + - - +
413C THR* 5.2 0.8 - - - +
465C TYR* 6.4 0.2 - - - -
502C SF4 4.4 1.8 - - - -
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Residues in contact with ALA 382 (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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380C CYS* 3.5 20.1 - - - -
381C THR* 1.3 78.5 - - - +
383C CYS* 1.3 62.2 + - - +
385C ARG* 4.4 6.5 - - - -
386C MET* 3.0 34.1 + - + +
388C ARG* 3.4 13.1 + - - +
409C ASN* 4.1 13.2 - - - +
465C TYR* 4.4 22.4 - - + -
466C PHE 4.9 1.3 - - - +
502C SF4 4.0 0.9 - - - -
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Residues in contact with CYS 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C ARG* 5.3 4.3 - - - +
381C THR 3.2 0.8 - - - -
382C ALA* 1.3 79.5 - - - +
384C TYR* 1.3 62.8 + - - +
386C MET 3.7 0.3 - - - -
387C GLY 3.1 3.8 + - - -
388C ARG* 2.8 68.1 + - - +
393C PHE* 3.7 20.4 - - + -
396C PHE* 4.0 4.9 - - - -
502C SF4 2.3 47.7 - - - -
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Residues in contact with TYR 384 (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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154C TYR* 3.5 11.3 + + - -
164C ARG 3.0 26.7 - - - -
165C ARG* 3.6 39.0 - - + +
185C GLY* 2.8 31.3 + - - -
186C ILE 3.5 24.2 - - - -
187C GLY* 4.2 9.0 - - - -
381C THR* 3.3 9.1 + - - +
383C CYS* 1.3 79.1 - - - +
385C ARG* 1.3 68.4 + - + +
386C MET 3.2 0.7 + - - -
387C GLY* 3.3 11.6 + - - -
389C THR* 4.9 15.8 - - + +
502C SF4 5.4 0.2 - - - -
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Residues in contact with ARG 385 (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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164C ARG* 6.0 6.3 - - + -
381C THR* 3.0 19.4 + - - +
382C ALA* 4.0 6.5 - - - +
384C TYR* 1.3 84.7 - - + +
386C MET* 1.3 80.1 + - + +
387C GLY 3.7 0.2 + - - -
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Residues in contact with MET 386 (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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382C ALA* 3.0 23.5 + - + +
385C ARG* 1.3 107.5 - - + +
387C GLY* 1.3 60.5 + - - +
388C ARG* 3.3 27.1 + - - +
392C ARG* 3.4 15.8 + - - -
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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