Contacts of the helix formed by residues 195 - 206 (chain C) in PDB entry 1RZR
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 LYS 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C ILE* 4.9 12.1 - - + -
149C GLU 5.9 1.0 + - - -
160C ASP* 4.5 9.1 + - - +
161C TYR* 3.5 18.3 - - + +
162C GLU* 3.4 41.2 - - + +
165C ALA* 3.8 0.2 - - - +
190C PRO 3.2 4.0 + - - +
191C ILE* 3.9 4.3 - - - +
194C ALA* 1.3 96.6 - - + +
196C LYS* 1.3 67.1 + - - +
197C VAL 3.6 0.4 - - - -
198C LYS* 3.9 12.3 - - - +
199C GLY 3.0 18.0 + - - -
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Residues in contact with LYS 196 (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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161C TYR* 4.1 6.9 + - - +
165C ALA* 3.5 7.1 - - + +
182C PHE* 4.3 21.3 - - + -
184C SER* 6.1 0.2 - - - -
191C ILE* 2.7 64.4 + - + +
192C ASN* 2.8 21.6 + - - +
195C LYS* 1.3 74.0 - - - +
197C VAL* 1.3 63.6 + - - +
199C GLY 3.3 0.2 + - - -
200C TYR* 3.1 21.1 + - - +
221C TYR* 5.8 2.4 + - - -
244C PHE* 4.8 5.5 - - + -
246C GLY* 3.3 30.2 + - - -
247C THR* 5.1 1.6 - - - +
274C PHE* 3.8 42.5 - - + -
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Residues in contact with VAL 197 (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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182C PHE* 3.8 21.7 - - + -
184C SER* 5.5 0.2 - - - +
187C LEU* 5.5 7.2 - - + -
192C ASN* 3.2 20.2 + - + +
193C HIS* 4.0 13.9 - - + +
196C LYS* 1.3 72.6 - - - +
198C LYS* 1.3 67.5 + - - +
200C TYR* 4.1 10.5 - - + -
201C LYS* 2.7 53.8 + - + +
216C ILE* 4.4 24.9 - - + -
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Residues in contact with LYS 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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162C GLU* 3.2 26.0 - - - +
193C HIS 3.9 6.0 + - - +
194C ALA* 2.8 31.0 + - - +
195C LYS* 3.7 15.5 - - - +
196C LYS 3.2 0.4 - - - -
197C VAL* 1.3 79.7 - - - +
199C GLY* 1.3 65.5 + - - +
201C LYS* 3.5 15.1 - - - +
202C ARG* 3.0 22.7 + - - +
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Residues in contact with GLY 199 (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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162C GLU* 2.7 25.6 + - - -
165C ALA* 3.4 20.6 - - - -
166C PHE* 3.8 8.2 - - - -
195C LYS 3.0 9.5 + - - -
198C LYS* 1.3 75.0 - - - +
200C TYR* 1.3 62.9 + - - +
202C ARG* 3.6 4.0 + - - +
203C ALA* 3.0 23.9 + - - +
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Residues in contact with TYR 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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165C ALA* 3.8 4.5 - - + +
169C VAL* 4.2 20.6 - - + -
180C ILE* 3.1 30.8 + - + -
181C ALA 4.0 3.8 - - - -
182C PHE* 3.5 43.6 - + + +
196C LYS 3.1 13.5 + - - +
197C VAL* 3.4 17.5 - - + +
199C GLY* 1.3 72.1 - - - +
201C LYS* 1.3 72.0 + - + +
203C ALA* 2.9 22.9 - - - +
204C LEU* 3.5 13.7 + - + +
211C VAL* 3.5 28.5 - - + +
215C TYR* 3.6 17.8 + - - +
216C ILE* 4.1 19.7 - - + -
244C PHE* 5.5 9.2 - + + -
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Residues in contact with LYS 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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197C VAL* 2.7 41.4 + - + +
198C LYS* 3.5 13.8 - - - +
200C TYR* 1.3 77.6 - - + +
202C ARG* 1.3 70.2 + - - +
203C ALA 2.8 1.1 - - - -
204C LEU* 2.6 18.9 + - - +
205C THR* 3.3 16.2 + - + +
211C VAL* 4.5 17.5 - - + -
216C ILE* 5.3 6.5 - - + -
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Residues in contact with ARG 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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162C GLU* 3.8 26.4 + - - +
163C GLN* 3.7 24.9 + - - -
166C PHE* 3.4 43.7 - - - -
198C LYS 3.0 14.0 + - - +
199C GLY 3.6 9.2 - - - +
201C LYS* 1.3 76.6 - - - +
203C ALA* 1.3 65.0 + - - +
205C THR* 3.2 12.9 + - - +
206C GLU* 2.8 39.3 + - + +
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Residues in contact with ALA 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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166C PHE* 3.5 18.2 - - + -
169C VAL* 3.1 39.3 - - + -
170C GLN* 4.4 1.8 - - - +
173C ILE* 3.1 20.4 - - + +
199C GLY 3.0 9.8 + - - +
200C TYR 2.9 16.8 - - - +
201C LYS 2.6 4.2 + - - -
202C ARG* 1.3 76.0 - - - +
204C LEU* 1.3 57.3 + - - +
206C GLU* 3.4 11.6 - - - +
207C SER* 3.5 2.9 + - - -
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Residues in contact with LEU 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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169C VAL* 4.6 1.1 - - + -
173C ILE* 4.3 12.6 - - + -
178C LYS 5.6 0.7 - - - +
180C ILE* 3.3 35.2 - - + -
200C TYR* 3.8 26.7 - - + +
201C LYS 2.6 11.3 + - - +
203C ALA* 1.3 68.9 - - + +
205C THR* 1.3 54.2 + - - +
206C GLU 2.9 1.6 - - - -
207C SER* 2.6 6.6 + - - +
208C GLY 2.6 33.1 + - - -
209C LEU* 3.2 34.9 + - + +
211C VAL* 2.9 48.0 - - + -
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Residues in contact with THR 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 LYS* 3.3 14.3 + - + +
202C ARG* 3.2 18.8 + - - +
204C LEU* 1.3 77.6 - - + +
206C GLU* 1.3 62.2 + - - +
207C SER 3.3 0.5 + - - -
208C GLY* 3.4 10.7 + - - +
209C LEU 4.6 3.1 - - - +
210C PRO* 4.8 19.5 - - + -
211C VAL* 5.3 4.5 - - + -
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Residues in contact with GLU 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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166C PHE* 4.2 14.8 - - + -
170C GLN* 3.4 18.2 - - - +
202C ARG* 2.8 31.9 + - - +
203C ALA* 3.4 9.2 - - - +
205C THR* 1.3 78.3 + - - +
207C SER* 1.3 57.8 + - - +
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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