Contacts of the helix formed by residues 197 - 205 (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 HIS 197 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C ASP* 4.5 5.2 + - - -
195C THR* 3.1 8.2 + - - +
196C TYR* 1.3 77.2 - - - +
198C ARG* 1.3 60.6 + - - +
199C PRO* 3.6 33.2 - - + +
200C THR* 2.7 29.6 + - - +
201C TYR* 2.8 27.9 + - - +
213C TYR* 4.3 0.9 - - - -
240C TYR* 3.4 54.4 + + + -
244C TYR* 3.8 27.0 - + + -
245C GLU* 3.9 0.4 + - - -
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Residues in contact with ARG 198 (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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196C TYR 3.4 4.8 + - - -
197C HIS* 1.3 71.6 - - - +
199C PRO* 1.3 72.9 - - + +
201C TYR* 3.2 1.0 + - - +
202C GLU* 2.9 51.7 + - - +
212C ASP* 5.3 0.8 + - - -
213C TYR* 3.3 49.1 - - + +
214C ASP* 3.1 41.8 + - - +
244C TYR* 5.1 1.4 + - - -
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Residues in contact with PRO 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C HIS* 3.6 31.6 - - + +
198C ARG* 1.3 94.4 - - + +
200C THR* 1.3 60.3 + - - +
202C GLU* 3.4 7.7 + - + +
203C TYR* 3.1 23.7 + - - +
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Residues in contact with THR 200 (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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195C THR* 4.0 12.3 - - + -
197C HIS* 2.7 30.7 + - - -
199C PRO* 1.3 75.7 - - - +
201C TYR* 1.3 67.0 + - - +
203C TYR* 3.2 6.9 + - + +
204C MET* 2.9 41.8 + - + +
239C LEU 3.5 29.2 - - - +
240C TYR* 3.4 14.8 - - + -
285C TYR* 5.6 0.3 - - - -
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Residues in contact with TYR 201 (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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193C GLN* 3.5 27.8 - - - -
194C GLU* 4.8 0.7 - - + -
195C THR* 3.4 28.6 - - + +
197C HIS 2.8 20.4 + - - +
198C ARG 3.5 4.7 - - - +
200C THR* 1.3 74.3 - - - +
202C GLU* 1.3 63.6 + - - +
205C HIS* 2.9 54.4 + + - +
210C LYS* 2.7 36.7 + - - +
211C HIS 3.5 16.4 - - - -
213C TYR* 3.6 31.4 - + + -
216C HIS* 3.0 30.4 - + + +
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Residues in contact with GLU 202 (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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198C ARG* 2.9 58.5 + - + +
199C PRO* 4.0 6.5 - - + +
200C THR 3.2 0.2 - - - -
201C TYR* 1.3 81.3 - - + +
203C TYR* 1.3 61.5 + - - +
205C HIS 3.5 5.2 - - - +
206C PRO* 3.9 3.3 - - - +
211C HIS* 3.4 52.0 + - + +
213C TYR* 4.4 4.0 + - + +
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Residues in contact with TYR 203 (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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95C ARG* 2.8 68.7 + - - -
199C PRO 3.1 17.1 + - - +
200C THR* 3.7 6.5 - - + +
202C GLU* 1.3 79.4 - - - +
204C MET* 1.3 85.1 + - + +
205C HIS 3.4 0.5 + - - -
206C PRO* 3.7 6.2 - - - +
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Residues in contact with MET 204 (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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94C CYS* 3.4 3.8 - - - -
95C ARG* 2.9 43.8 + - - -
96C TYR* 4.3 7.6 - - + -
195C THR* 5.3 0.2 - - + -
200C THR* 2.9 32.1 + - + +
201C TYR* 5.2 0.2 - - - -
203C TYR* 1.3 98.8 - - + +
205C HIS* 1.3 74.2 + - + +
206C PRO* 3.2 5.1 - - - +
239C LEU* 4.0 36.1 - - + +
283C PHE* 3.8 34.3 - - + -
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Residues in contact with HIS 205 (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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93C ASN 6.1 0.2 - - - +
94C CYS* 3.6 17.0 - - - +
96C TYR* 2.6 33.0 + + - -
194C GLU* 3.8 12.3 - - + +
195C THR* 4.5 2.9 - - + -
201C TYR* 2.9 58.9 + + + +
202C GLU 3.5 2.1 - - - +
204C MET* 1.3 90.4 - - + +
206C PRO* 1.3 55.9 - - - +
207C GLN 3.4 4.0 - - - -
210C LYS* 3.5 38.8 - - + +
211C HIS* 2.7 36.9 + - - +
239C LEU* 5.0 0.2 - - + -
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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