Contacts of the helix formed by residues 189 - 195 (chain S) in PDB entry 2FRV
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 PRO 189 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187S ASN 3.4 7.7 - - - +
188S CYS* 1.3 88.0 - - - +
190S ARG* 1.3 58.2 + - + +
191S LEU 2.9 9.3 + - - -
192S LYS* 3.6 28.6 + - - +
229S PRO* 4.3 5.2 - - + +
238S TRP* 3.7 23.6 - - + +
241S GLN* 6.4 1.8 - - + +
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Residues in contact with ARG 190 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232L ASP* 5.8 1.8 - - - +
188S CYS* 3.3 10.6 - - - -
189S PRO* 1.3 76.2 - - + +
191S LEU* 1.3 59.2 + - - +
192S LYS 3.1 2.9 - - - -
193S HIS* 3.0 27.1 + - + +
194S PHE* 3.1 11.8 + - - +
208S ALA* 4.6 5.9 + - - +
211S GLY* 3.4 35.8 + - - +
212S TYR 3.0 27.5 + - - -
213S CYS* 4.1 3.8 - - - +
214S LEU* 3.4 18.8 - - - +
240S VAL* 3.0 45.4 + - + +
241S GLN* 4.0 9.1 + - - +
243S GLY* 3.5 16.1 - - - +
265S SF4 3.8 15.7 - - - -
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Residues in contact with LEU 191 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185S HIS* 2.9 62.8 - - + +
186S ASP* 4.7 11.0 - - - +
188S CYS 3.0 14.6 + - - +
189S PRO 2.9 1.2 - - - -
190S ARG* 1.3 75.4 - - - +
192S LYS* 1.3 61.8 + - - +
194S PHE* 3.4 5.1 - - + +
195S GLU* 2.8 68.3 + - - +
265S SF4 3.7 4.9 - - - -
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Residues in contact with LYS 192 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189S PRO* 3.6 20.9 + - - +
190S ARG 3.1 0.4 - - - -
191S LEU* 1.3 79.2 - - - +
193S HIS* 1.3 93.2 + - + +
195S GLU* 3.3 7.8 + - - +
196S ALA* 3.0 23.7 + - - +
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Residues in contact with HIS 193 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190S ARG* 3.0 21.7 + - + +
192S LYS* 1.3 101.8 - - + +
194S PHE* 1.3 59.8 + - - +
196S ALA* 3.2 1.9 + - - +
197S GLY 3.0 4.3 + - - -
198S GLU* 2.8 64.9 + - - +
210S LYS 3.9 9.6 + - - -
211S GLY 2.7 29.4 + - - -
212S TYR* 3.8 19.0 - + - -
213S CYS 3.7 6.7 - - - +
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Residues in contact with PHE 194 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185S HIS* 3.7 34.3 - + - -
190S ARG 3.1 8.0 + - - +
191S LEU* 3.4 13.0 - - - +
193S HIS* 1.3 77.0 - - - +
195S GLU* 1.3 86.2 + - - +
197S GLY* 3.0 13.3 + - - -
199S PHE* 3.5 27.3 - + - -
213S CYS* 3.3 29.8 - - - +
215S TYR* 4.4 15.9 - + + -
222S PRO* 5.6 2.0 - - + -
265S SF4 4.0 4.5 - - - -
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Residues in contact with GLU 195 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185S HIS* 5.1 0.5 + - - -
191S LEU* 2.8 56.8 + - - +
192S LYS* 3.8 6.2 - - - +
194S PHE* 1.3 92.0 - - + +
196S ALA* 1.3 55.0 + - - +
197S GLY 3.4 3.1 + - - -
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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