Contacts of the helix formed by residues 202 - 209 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ARG* 5.9 0.7 + - - -
192B ASN 3.3 13.5 + - - -
193B HIS* 3.5 23.6 + - - +
194B VAL 4.5 0.7 - - - +
195B ASN 3.6 18.6 - - - +
196B MET* 4.3 14.4 - - + -
200B GLY 5.0 1.3 - - - +
201B HIS* 1.3 75.7 - - - +
203B ALA* 1.3 59.7 - - - +
204B ALA* 4.1 2.6 - - - +
205B GLU* 2.9 34.3 + - - +
206B ARG* 3.0 34.2 + - - +
208B TRP* 5.7 0.5 - - - -
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B SER* 3.7 3.1 - - - -
87B HIS 4.5 2.9 - - - +
88B PHE* 3.9 14.8 - - - +
191B LEU 4.3 6.0 + - - +
192B ASN* 3.3 32.0 + - - +
195B ASN 4.8 1.8 + - - -
202B THR* 1.3 71.6 - - - +
204B ALA* 1.3 56.3 + - - +
206B ARG* 3.3 27.5 + - - +
207B HIS* 2.8 35.0 + - - +
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PHE* 3.6 21.2 - - + -
192B ASN 2.9 17.5 + - - +
193B HIS* 3.5 31.9 - - + +
202B THR* 4.1 2.5 - - - +
203B ALA* 1.3 77.5 - - - +
205B GLU* 1.3 56.3 + - - +
207B HIS* 3.1 1.7 + - - +
208B TRP* 2.8 50.3 + - + -
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Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B GLY 4.1 2.4 - - - +
201B HIS* 2.8 36.9 + - - -
202B THR* 2.9 35.5 + - - +
204B ALA* 1.3 79.4 - - - +
206B ARG* 1.3 62.5 + - - +
208B TRP* 3.3 15.1 + - + -
209B GLY 3.0 17.2 + - - -
210B PRO* 3.1 19.6 - - + +
211B ILE* 3.7 17.5 - - + +
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Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B TYR* 3.6 21.8 - - + -
86B SER* 2.9 39.8 + - - +
87B HIS* 4.5 10.1 - - - +
197B ASP* 2.9 45.2 + - - +
201B HIS* 3.7 22.5 + - + -
202B THR 3.0 13.5 + - - +
203B ALA* 3.5 25.2 - - - +
205B GLU* 1.3 76.0 - - - +
207B HIS* 1.3 63.8 + - - +
209B GLY* 3.1 14.9 + - - -
211B ILE* 4.7 11.9 - - + -
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Residues in contact with HIS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PRO* 3.0 21.5 - - - +
59B ARG* 3.1 31.9 + - + +
62B TRP* 3.9 1.8 - + - -
83B ASP* 3.4 28.2 - - - +
86B SER* 3.3 11.6 - - - +
88B PHE* 3.7 19.2 - + + +
112B TYR 5.0 1.3 - - - -
113B MET* 3.0 57.4 + - + -
203B ALA 2.8 21.1 + - - +
204B ALA 3.1 4.7 + - - +
206B ARG* 1.3 72.2 - - - +
208B TRP* 1.3 81.6 + + - +
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Residues in contact with TRP 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.4 33.7 - - - -
88A PHE* 6.2 0.9 - + - -
112A TYR 4.8 6.7 - - - -
113A MET 4.3 5.8 - - - -
193A HIS* 6.2 2.8 - + - -
207A HIS* 4.5 8.1 - + - -
208A TRP* 3.3 83.2 - + + +
58B PRO* 4.3 0.5 - - - +
59B ARG* 3.0 23.7 + - - +
88B PHE* 5.7 2.4 - + - -
112B TYR 4.9 7.7 + - - -
193B HIS* 4.0 18.2 - + - -
202B THR* 5.7 0.4 - - - -
204B ALA* 2.8 31.8 + - + +
205B GLU* 3.4 13.9 - - + +
207B HIS* 1.3 93.6 - + - +
209B GLY* 1.3 59.1 + - - +
210B PRO* 3.4 3.6 - - + -
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Residues in contact with GLY 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A TRP* 4.8 1.3 - - - -
58B PRO* 4.3 11.9 - - - -
85B TYR* 5.6 1.8 - - - -
205B GLU 3.0 4.4 + - - -
206B ARG* 3.1 14.1 + - - -
208B TRP* 1.3 77.7 - - - +
210B PRO* 1.4 66.6 - - - +
211B ILE* 3.1 16.0 + - - +
212B SER* 5.4 1.2 - - - -
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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