Contacts of the helix formed by residues 189 - 195 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I ASN 3.4 7.5 - - - +
188I CYS* 1.3 87.8 - - - +
190I ARG* 1.3 58.2 + - + +
191I LEU* 2.9 9.3 + - + -
192I LYS* 3.6 28.1 + - - +
229I PRO* 4.3 6.1 - - + +
238I TRP* 3.7 22.7 - - + +
240I VAL* 5.9 0.2 - - + -
241I GLN* 6.4 1.3 - - + +
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Residues in contact with ARG 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I CYS* 3.3 11.3 - - - -
189I PRO* 1.3 76.2 - - + +
191I LEU* 1.3 59.0 + - - +
192I LYS 3.1 3.1 - - - -
193I HIS* 3.0 27.3 + - + +
194I PHE* 3.1 11.4 + - - +
208I ALA 4.6 6.5 + - - -
211I GLY* 3.4 34.0 + - - +
212I TYR 3.0 33.8 + - - +
213I CYS* 4.1 5.3 - - - +
214I LEU* 3.4 18.6 - - - +
240I VAL* 3.0 46.7 + - + +
241I GLN* 4.0 9.5 + - - +
243I GLY* 3.5 14.8 - - - +
265I SF4 3.8 15.1 - - - -
232J ASP* 5.8 1.0 - - - +
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Residues in contact with LEU 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I HIS* 2.9 62.8 - - + +
186I ASP* 4.7 11.9 - - - +
188I CYS 3.0 14.4 + - - +
189I PRO* 2.9 1.5 - - + -
190I ARG* 1.3 75.4 - - - +
192I LYS* 1.3 60.6 + - - +
194I PHE* 3.4 5.3 - - + +
195I GLU* 2.9 68.4 + - - +
265I SF4 3.7 5.0 - - - -
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Residues in contact with LYS 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I PRO* 3.6 20.7 + - - +
190I ARG* 3.1 0.4 - - - +
191I LEU* 1.3 79.8 - - - +
193I HIS* 1.3 91.2 + - + +
195I GLU* 3.3 6.9 + - - +
196I ALA* 3.0 24.0 + - - +
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Residues in contact with HIS 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190I ARG* 3.0 21.7 + - + +
192I LYS* 1.3 101.8 - - + +
194I PHE* 1.3 60.4 + - - +
196I ALA* 3.2 1.4 + - - +
197I GLY 3.0 4.5 + - - -
198I GLU* 2.8 64.1 + - - +
210I LYS 3.9 8.9 + - - -
211I GLY 2.7 30.0 + - - -
212I TYR* 3.8 18.7 - + - -
213I CYS 3.7 7.2 - - - +
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Residues in contact with PHE 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C HIS* 4.5 18.8 - + - -
88C GLY 4.6 2.8 - - - +
90C ARG* 6.3 0.4 - - - -
185I HIS* 3.7 35.2 - + - -
190I ARG 3.1 8.6 + - - +
191I LEU* 3.4 13.0 - - - +
193I HIS* 1.3 76.0 - - - +
195I GLU* 1.3 85.4 + - - +
197I GLY* 3.0 12.8 + - - -
199I PHE* 3.5 28.9 - + - -
213I CYS* 3.3 28.2 - - - +
215I TYR* 4.4 15.5 - + + -
222I PRO* 5.6 2.2 - - + -
265I SF4 4.0 4.7 - - - -
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Residues in contact with GLU 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C HIS* 3.7 30.3 + - - +
88C GLY 5.5 0.5 - - - +
10D VAL* 3.6 24.8 - - + +
22D ARG* 3.5 12.5 + - - -
185I HIS* 5.1 0.3 + - - -
191I LEU* 2.9 55.0 + - - +
192I LYS* 3.8 6.0 - - - +
194I PHE* 1.3 91.8 - - - +
196I ALA* 1.3 54.8 + - - +
197I GLY 3.2 3.0 + - - -
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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