Contacts of the helix formed by residues 194 - 202 (chain F) in PDB entry 5B6N
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 194 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192F THR 3.5 8.5 - - - +
193F ILE* 1.3 95.1 - - + +
195F GLU* 1.3 63.6 + - - +
196F GLU* 3.1 12.4 + - + +
197F GLU* 3.5 20.7 + - + +
198F ALA* 3.3 19.2 + - - +
219F ARG* 4.2 2.9 - - - +
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Residues in contact with GLU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F PRO* 1.3 74.4 - - - +
196F GLU* 1.3 60.8 + - - +
198F ALA* 3.6 14.1 - - - +
199F LYS* 4.0 8.3 + - - +
206F VAL* 4.2 10.4 - - - +
208F THR* 3.4 28.0 - - - +
216F LYS* 4.4 26.8 + - + +
219F ARG* 3.7 29.3 + - - +
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Residues in contact with GLU 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F PRO* 3.1 8.4 - - + +
195F GLU* 1.3 78.1 - - - +
197F GLU* 1.3 64.3 + - - +
198F ALA 3.0 5.2 + - - -
199F LYS* 3.7 15.6 + - - +
200F LYS* 3.8 17.6 + - - +
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Residues in contact with GLU 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F ARG* 3.4 27.0 + - - -
193F ILE* 3.8 17.8 - - + +
194F PRO* 3.5 16.4 + - + +
196F GLU* 1.3 80.6 - - - +
198F ALA* 1.3 58.9 + - - +
200F LYS* 3.8 22.6 + - + +
201F LEU* 3.0 46.1 + - + +
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Residues in contact with ALA 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F VAL* 4.8 4.0 - - + -
193F ILE* 4.8 2.5 - - - -
194F PRO 3.3 17.6 + - - +
195F GLU* 3.6 15.7 - - + +
196F GLU 3.0 0.4 - - - -
197F GLU* 1.3 79.4 - - - +
199F LYS* 1.3 57.9 + - - +
200F LYS 3.1 0.2 - - - -
201F LEU* 4.7 0.2 - - - -
202F PHE* 2.8 43.9 + - - +
206F VAL* 3.8 24.4 - - + +
219F ARG* 4.5 10.5 - - - +
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Residues in contact with LYS 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F GLU 4.0 6.8 + - - +
196F GLU* 3.7 11.8 + - - +
197F GLU 3.5 0.2 - - - -
198F ALA* 1.3 78.6 - - - +
200F LYS* 1.3 62.9 + - - +
201F LEU 3.3 0.4 + - - -
202F PHE 4.0 18.9 - - - +
203F PRO* 4.4 5.7 - - - +
206F VAL* 4.4 6.9 - - + +
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Residues in contact with LYS 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F GLU* 3.8 16.8 + - - +
197F GLU* 3.7 25.7 + - + +
198F ALA 3.1 0.2 - - - -
199F LYS* 1.3 84.9 - - + +
201F LEU* 1.3 60.2 + - + +
203F PRO* 5.3 1.9 - - - +
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Residues in contact with LEU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F ARG* 3.5 44.6 - - + +
193F ILE* 4.6 5.4 - - + -
197F GLU* 3.0 30.5 + - + +
200F LYS* 1.3 85.3 - - + +
202F PHE* 1.3 88.4 + - + +
203F PRO* 3.7 8.8 - - - +
224F PRO* 6.1 0.3 - - - +
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Residues in contact with PHE 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F LYS* 5.5 2.0 - - + -
174F ARG* 4.1 18.2 - - + -
175F VAL* 3.5 31.0 - - + -
189F VAL* 3.9 25.1 - - + -
193F ILE* 5.1 3.1 - - + -
198F ALA* 2.8 33.0 + - - +
199F LYS* 4.0 8.4 - - - +
201F LEU* 1.3 111.0 - - + +
203F PRO* 1.3 67.0 - - - +
204F LYS* 3.4 3.2 + - + +
205F GLY* 3.7 6.5 + - - +
206F VAL* 3.8 14.6 - - + +
221F THR* 3.7 26.2 - - + +
222F PRO 5.4 0.4 - - - -
224F PRO* 4.1 20.6 - - + -
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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