Contacts of the helix formed by residues 202 - 209 (chain F) in PDB entry 3JCA
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 THR 202 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ARG* 5.9 0.5 + - - -
192F ASN 3.3 14.1 + - - -
193F HIS* 3.5 22.9 + - - +
194F VAL 4.5 0.7 - - - +
195F ASN 3.7 17.9 - - - +
196F MET* 4.3 14.6 - - + -
200F GLY 5.0 0.9 - - - +
201F HIS* 1.3 77.0 - - - +
203F ALA* 1.3 60.2 + - - +
204F ALA* 4.1 2.6 - - - +
205F GLU* 2.9 33.0 + - - +
206F ARG* 3.0 33.3 + - - +
208F TRP* 5.7 0.5 - - - -
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Residues in contact with ALA 203 (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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86F SER* 3.7 3.6 + - - +
87F HIS 4.5 3.4 - - - +
88F PHE* 3.9 14.8 - - - +
191F LEU 4.3 5.1 + - - +
192F ASN* 3.3 32.6 + - - +
195F ASN 4.8 1.8 + - - -
202F THR* 1.3 71.1 - - - +
204F ALA* 1.3 56.1 + - - +
206F ARG* 3.3 27.5 + - - +
207F HIS* 2.8 35.5 + - - +
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Residues in contact with ALA 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F PHE* 3.6 21.0 - - + -
192F ASN 2.9 17.3 + - - +
193F HIS* 3.5 31.9 - - + +
202F THR* 4.1 2.5 - - - +
203F ALA* 1.3 76.7 - - - +
205F GLU* 1.3 56.5 - - - +
207F HIS* 3.1 1.2 + - - +
208F TRP* 2.8 50.2 + - + -
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Residues in contact with GLU 205 (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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200F GLY 4.1 2.4 - - - +
201F HIS* 2.8 36.7 + - - -
202F THR* 2.9 36.9 + - - +
204F ALA* 1.3 79.3 - - - +
206F ARG* 1.3 62.0 + - - +
208F TRP* 3.9 13.6 - - + -
209F GLY 3.0 18.0 + - - -
210F PRO* 3.1 21.2 - - + +
211F ILE* 3.7 18.7 - - + +
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Residues in contact with ARG 206 (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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58F PRO* 4.0 0.3 - - - +
85F TYR* 3.6 21.6 - - + -
86F SER* 2.9 40.3 + - - +
87F HIS* 4.5 10.2 - - - +
197F ASP* 2.9 44.8 + - - +
201F HIS* 3.7 22.7 + - + -
202F THR* 3.0 14.6 + - - +
203F ALA* 3.5 23.2 - - - +
205F GLU* 1.3 76.9 - - - +
207F HIS* 1.3 63.6 + - - +
209F GLY* 3.2 13.8 + - - +
211F ILE* 4.9 10.8 - - + -
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Residues in contact with HIS 207 (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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58F PRO* 3.0 21.8 - - - +
59F ARG* 3.0 32.2 + - + +
62F TRP* 4.0 1.6 - + - -
83F ASP* 3.5 28.3 - - - +
86F SER* 3.3 12.3 - - - +
88F PHE* 3.7 19.7 - + + +
112F TYR 5.0 1.8 - - - -
113F MET* 3.0 56.1 + - + -
203F ALA 2.8 20.6 + - - +
204F ALA 3.3 4.9 - - - +
206F ARG* 1.3 72.4 - - - +
208F TRP* 1.3 80.0 + + - +
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Residues in contact with TRP 208 (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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59E ARG* 3.4 34.1 - - - -
88E PHE* 6.0 1.5 - + - -
112E TYR 4.7 8.3 - - - -
113E MET 4.2 6.7 - - - -
193E HIS* 6.1 2.9 - + - -
207E HIS* 4.4 11.2 - + - -
208E TRP* 3.1 77.9 - + + -
58F PRO* 4.4 0.5 - - - +
59F ARG* 3.0 22.7 + - - +
88F PHE* 5.8 2.3 - + - -
112F TYR 5.0 7.9 + - - -
193F HIS* 3.9 17.5 - + - -
202F THR* 5.7 0.2 - - - -
204F ALA* 2.8 32.5 + - + +
205F GLU* 3.4 13.5 - - + +
207F HIS* 1.3 94.0 - + - +
209F GLY* 1.3 57.7 + - - +
210F PRO* 3.5 5.6 - - + -
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Residues in contact with GLY 209 (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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208E TRP* 4.2 2.7 - - - -
58F PRO* 4.4 11.2 - - - -
85F TYR* 5.7 1.8 - - - -
205F GLU 3.0 4.0 + - - -
206F ARG* 3.2 13.4 + - - -
208F TRP* 1.3 77.5 - - - +
210F PRO* 1.4 67.3 - - - +
211F ILE* 3.1 15.3 + - - +
212F SER* 5.4 0.9 - - - -
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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