Contacts of the helix formed by residues 199 - 206 (chain C) in PDB entry 1RIW
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 GLU 199 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B ALA* 3.5 27.3 - - + +
169B GLY 5.2 1.1 + - - -
197C ILE 4.8 0.6 - - - +
198C VAL* 1.3 81.5 - - - +
200C ARG* 1.3 65.1 + - - +
201C PRO* 4.0 11.9 - - + -
202C VAL* 3.0 16.3 + - + +
203C CYS* 3.0 18.2 + - - -
221C LYS* 3.2 29.7 + - - -
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Residues in contact with ARG 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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198C VAL 3.5 3.4 + - - +
199C GLU* 1.3 71.4 - - - +
201C PRO* 1.3 71.8 - - + +
203C CYS* 3.1 12.2 + - - +
204C LYS* 2.9 26.1 + - - +
211C ILE* 3.5 25.7 + - - +
212C THR 3.2 17.9 + - - -
213C ASP* 4.0 18.5 + - - +
215C MET 2.2 36.6 + - - -
216C PHE* 4.0 8.3 - - - +
272C HIS* 5.5 0.8 - - - -
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Residues in contact with PRO 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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199C GLU* 3.5 11.0 - - + -
200C ARG* 1.3 94.0 - - + +
202C VAL* 1.3 60.1 + - + +
204C LYS* 3.6 8.1 + - + +
205C ASP* 3.1 35.3 + - - +
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Residues in contact with VAL 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C VAL* 3.6 13.2 - - + -
199C GLU* 3.0 29.7 + - + +
201C PRO* 1.3 79.2 - - + +
203C CYS* 1.3 67.8 + - - +
205C ASP* 3.3 6.4 + - + +
206C SER* 3.2 19.3 + - - -
221C LYS* 4.4 13.5 - - + +
267C TYR* 3.7 27.6 - - + +
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Residues in contact with CYS 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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198C VAL* 3.5 15.5 - - - -
199C GLU 3.0 19.6 + - - -
200C ARG* 3.1 12.8 + - - +
202C VAL* 1.3 74.6 - - - +
204C LYS* 1.3 63.2 + - - +
206C SER* 2.6 25.5 + - - -
207C THR* 3.6 8.3 - - - +
211C ILE* 5.3 4.5 - - + -
216C PHE* 5.4 0.4 - - - -
217C CYS* 2.0 61.0 - - + -
269C PHE* 3.7 12.9 - - + -
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Residues in contact with LYS 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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200C ARG 2.9 16.0 + - - +
201C PRO* 3.7 8.5 - - + +
203C CYS* 1.3 77.3 - - - +
205C ASP* 1.3 62.9 + - - +
206C SER 3.3 0.3 + - - -
207C THR* 3.1 10.0 - - - +
209C ILE 5.4 0.5 - - - +
211C ILE* 4.2 21.4 - - + +
701C NA 2.4 29.6 - - - -
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Residues in contact with ASP 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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201C PRO* 3.1 22.5 + - - +
202C VAL* 3.7 6.5 - - - +
203C CYS 3.3 0.4 - - - -
204C LYS* 1.3 88.1 - - - +
206C SER* 1.3 58.2 + - - +
207C THR 3.4 0.7 - - - -
701C NA 4.0 4.3 - - - -
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Residues in contact with SER 206 (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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202C VAL* 3.2 10.2 + - - -
203C CYS* 2.6 22.1 + - - -
205C ASP* 1.3 78.4 - - - +
207C THR* 1.3 57.8 + - - +
259C GLU* 3.3 5.4 - - - +
265C GLY 3.3 23.3 - - - -
266C LYS* 3.0 31.9 + - - +
267C TYR* 3.6 20.6 + - - -
269C PHE* 4.1 10.7 - - - -
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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