Contacts of the helix formed by residues 189 - 195 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187G ASN 3.4 7.4 - - - +
188G CYS* 1.3 88.4 - - - +
190G ARG* 1.3 56.6 + - + +
191G LEU* 2.9 8.5 + - - -
192G LYS* 3.6 28.9 + - - +
229G PRO* 4.3 5.4 - - + +
238G TRP* 3.7 23.1 - - + +
241G GLN* 6.4 1.3 - - + +
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Residues in contact with ARG 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G CYS* 3.3 11.2 - - - -
189G PRO* 1.3 77.0 - - + +
191G LEU* 1.3 58.5 + - - +
192G LYS 3.1 2.9 - - - -
193G HIS* 3.0 28.3 + - + +
194G PHE* 3.1 11.4 + - - +
208G ALA* 4.6 5.9 + - - +
211G GLY* 3.4 33.3 + - - +
212G TYR 3.0 28.3 + - - +
213G CYS* 4.1 4.3 - - - +
214G LEU* 3.4 19.3 - - - +
240G VAL* 3.0 46.7 + - + +
241G GLN* 4.0 8.9 + - - +
243G GLY* 3.5 16.0 - - - +
265G SF4 3.8 15.7 - - - -
232H ASP* 5.8 1.4 - - - +
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Residues in contact with LEU 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G HIS* 2.9 63.7 - - + +
186G ASP* 4.7 10.8 - - - +
188G CYS 3.0 15.1 + - - +
189G PRO 2.9 1.0 - - - -
190G ARG* 1.3 75.8 - - - +
192G LYS* 1.3 60.0 + - - +
193G HIS 3.3 0.2 - - - -
194G PHE* 3.4 4.9 - - + +
195G GLU* 2.8 68.3 + - - +
265G SF4 3.7 5.4 - - - -
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Residues in contact with LYS 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G PRO* 3.6 20.7 + - - +
190G ARG 3.1 0.6 - - - -
191G LEU* 1.3 78.4 - - - +
193G HIS* 1.3 90.8 + - + +
195G GLU* 3.3 7.3 + - - +
196G ALA* 3.0 23.8 + - - +
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Residues in contact with HIS 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G ARG* 3.0 21.5 + - + +
192G LYS* 1.3 100.5 + - + +
194G PHE* 1.3 60.1 + - - +
196G ALA* 3.2 1.4 + - - +
197G GLY 3.0 4.9 + - - -
198G GLU* 2.8 64.7 + - - +
210G LYS 3.9 9.2 + - - -
211G GLY 2.7 29.2 + - - -
212G TYR* 3.8 19.2 - + - -
213G CYS 3.7 6.5 - - - +
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Residues in contact with PHE 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G HIS* 3.7 34.8 - + - -
190G ARG 3.1 8.0 + - - +
191G LEU* 3.4 13.5 - - + +
193G HIS* 1.3 75.8 - - - +
195G GLU* 1.3 86.2 + - - +
197G GLY* 3.0 12.8 + - - -
199G PHE* 3.5 27.2 - + - -
213G CYS* 3.3 28.2 - - - +
215G TYR* 4.4 15.7 - + + -
222G PRO* 5.8 2.2 - - + -
265G SF4 4.0 5.4 - - - -
54S HIS* 4.5 17.1 - + - -
88S GLY 4.5 3.3 - - - +
90S ARG* 6.2 1.1 - - - -
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Residues in contact with GLU 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G HIS* 5.1 0.3 + - - -
191G LEU* 2.8 55.0 + - - +
192G LYS* 3.8 6.6 - - - +
194G PHE* 1.3 92.3 - - - +
196G ALA* 1.3 55.4 + - - +
197G GLY 3.2 3.3 + - - -
10L VAL* 3.7 24.5 - - + +
22L ARG* 3.5 12.3 + - - -
54S HIS* 3.6 32.6 + - - +
88S GLY 5.4 0.3 - - - +
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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