Contacts of the helix formed by residues 189 - 198 (chain C) in PDB entry 1R4N
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 PHE 189 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ARG* 3.7 31.9 - - + +
187C LYS 5.1 0.7 - - - +
188C PRO* 1.3 75.6 - - - +
190C PRO* 1.3 81.5 - - + +
191C GLU* 3.5 15.3 - - + -
192C LEU* 3.1 51.2 + - + +
193C ARG* 2.8 20.0 + - - +
325C VAL* 4.2 9.0 - - + -
345C VAL* 4.0 14.4 - - + -
346C TYR* 4.3 17.9 - + - -
349C LYS* 3.5 53.4 - - + +
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Residues in contact with PRO 190 (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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188C PRO 4.7 0.4 - - - +
189C PHE* 1.3 85.8 - - + -
191C GLU* 1.3 77.9 + - - +
193C ARG* 2.6 25.8 + - + +
194C GLU* 2.6 26.3 + - + +
349C LYS* 5.3 3.6 - - - +
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Residues in contact with GLU 191 (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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189C PHE* 3.5 22.1 - - + -
190C PRO* 1.3 86.5 - - - +
192C LEU* 1.3 51.7 + - - +
194C GLU* 3.2 14.7 + - - +
195C HIS* 2.7 34.8 + - - +
345C VAL* 4.0 13.5 - - + +
348C GLU* 6.4 1.8 - - + -
349C LYS* 4.2 15.1 + - + +
352C LYS* 3.3 33.1 + - - +
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Residues in contact with LEU 192 (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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183C LEU 3.9 10.3 - - - +
184C ARG 3.7 23.8 - - - +
185C LEU* 5.0 1.3 - - + -
188C PRO* 3.9 11.2 - - + -
189C PHE* 3.1 33.2 + - + +
190C PRO 2.9 1.8 + - - -
191C GLU* 1.3 75.0 - - - +
193C ARG* 1.3 57.0 + - - +
195C HIS* 2.8 23.6 + - + +
196C PHE* 2.9 52.2 + - + -
342C LEU* 4.4 3.1 - - + -
345C VAL* 3.7 14.8 - - + -
346C TYR* 3.6 29.8 - - + +
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Residues in contact with ARG 193 (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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188C PRO* 5.0 12.5 - - + +
189C PHE 2.8 13.3 + - - +
190C PRO* 2.6 18.2 + - + +
192C LEU* 1.3 72.8 - - - +
194C GLU* 1.3 65.2 + - - +
196C PHE* 3.0 16.2 + - + +
197C GLN* 2.9 46.6 + - + +
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Residues in contact with GLU 194 (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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190C PRO* 2.6 23.2 + - + +
191C GLU* 3.5 20.6 + - - +
193C ARG* 1.3 75.5 - - + +
195C HIS* 1.3 63.8 + - - +
197C GLN* 3.4 22.9 + - - +
198C SER* 3.3 16.6 + - - -
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Residues in contact with HIS 195 (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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191C GLU 2.7 13.2 + - - +
192C LEU* 2.8 16.7 + - + +
194C GLU* 1.3 77.1 - - - +
196C PHE* 1.3 73.7 + + - +
198C SER* 2.9 25.2 + - - -
199C TYR* 3.8 35.3 + + - -
216C VAL* 4.7 2.5 - - + +
341C LYS* 3.9 38.6 - - + -
342C LEU* 3.8 37.2 - - + +
345C VAL* 3.8 20.3 - - + +
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Residues in contact with PHE 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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185C LEU* 3.6 21.1 - - + -
188C PRO* 5.0 4.9 - - + -
192C LEU* 2.9 53.9 + - + -
193C ARG* 3.0 13.4 + - + +
195C HIS* 1.3 86.2 - + - +
197C GLN* 1.3 57.0 + - - +
198C SER 2.9 1.4 + - - -
199C TYR* 3.0 15.2 + - - +
215C ILE* 3.7 28.0 - - + -
216C VAL* 4.2 20.0 - - + -
219C ALA* 3.7 24.5 - - + -
220C LYS* 2.7 31.5 + - + +
342C LEU* 4.9 2.2 - - + -
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Residues in contact with GLN 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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193C ARG* 2.9 48.6 + - + +
194C GLU* 3.5 24.5 + - - +
195C HIS 3.2 0.2 - - - -
196C PHE* 1.3 75.7 - - + +
198C SER* 1.3 57.7 - - - +
199C TYR 3.1 10.2 + - - +
220C LYS* 3.8 10.9 + - - +
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Residues in contact with SER 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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194C GLU 3.3 8.7 + - - -
195C HIS* 2.9 20.7 + - - -
197C GLN* 1.3 78.0 - - - +
199C TYR* 1.3 67.9 + - - +
341C LYS* 4.6 13.1 + - - -
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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