Contacts of the helix formed by residues 203 - 214 (chain M) in PDB entry 3J8B
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 ASP 203 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199M GLN* 4.1 19.5 - - + -
200M ALA* 3.0 19.6 + - + +
202M VAL* 1.3 77.2 - - - +
204M ALA* 1.3 58.2 + - - +
205M HIS 3.5 0.9 - - - -
206M ARG* 3.7 9.8 + - + +
207M CYS* 3.0 27.6 + - - +
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Residues in contact with ALA 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M ASN* 6.4 3.6 - - + +
200M ALA 3.9 1.5 + - - +
201M ARG* 3.1 20.8 + - - +
203M ASP* 1.3 76.0 - - - +
205M HIS* 1.3 60.8 + - - +
207M CYS* 3.1 8.9 + - - +
208M ILE* 2.8 30.1 + - - +
228M PRO* 5.7 9.4 - - + +
229M VAL* 6.2 2.9 - - - -
237M ILE* 5.4 6.1 - - + -
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Residues in contact with HIS 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201M ARG 4.6 1.0 + - - -
202M VAL 4.4 7.3 + - - +
203M ASP 3.5 0.4 - - - -
204M ALA* 1.3 77.0 - - - +
206M ARG* 1.4 62.2 + - - +
208M ILE* 3.1 8.9 + - - +
209M VAL* 3.0 21.7 + - - +
237M ILE* 4.8 12.7 - - + +
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Residues in contact with ARG 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202M VAL 5.0 1.9 + - - +
203M ASP* 3.7 13.6 + - + +
204M ALA 3.4 0.2 - - - -
205M HIS* 1.4 78.6 - - - +
207M CYS* 1.3 57.5 + - - +
209M VAL* 3.2 7.9 + - - +
210M ARG* 2.9 29.2 + - - +
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Residues in contact with CYS 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192M TYR* 6.1 2.0 - - + +
195M ASP* 6.3 2.5 - - + -
196M ASN* 5.8 10.8 - - + +
203M ASP 3.0 19.5 + - - +
204M ALA* 3.1 9.4 + - - +
206M ARG* 1.3 74.8 - - - +
208M ILE* 1.3 57.8 + - - +
210M ARG* 3.3 8.6 + - - +
211M ALA* 2.8 30.1 + - - +
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Residues in contact with ILE 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204M ALA 2.8 13.1 + - - +
205M HIS* 3.1 11.0 + - - +
207M CYS* 1.3 74.5 - - - +
209M VAL* 1.3 64.8 + - - +
211M ALA* 3.3 6.3 + - - +
212M LEU* 3.0 26.2 + - - +
237M ILE* 4.7 21.3 - - + +
240M LEU* 5.2 9.2 - - + -
241M LEU 6.3 0.2 - - - +
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Residues in contact with VAL 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205M HIS 3.0 12.8 + - - +
206M ARG* 3.7 10.5 - - - +
208M ILE* 1.3 75.3 - - - +
210M ARG* 1.3 64.4 + - - +
212M LEU* 3.4 4.3 + - - +
213M LYS* 3.1 25.7 + - - +
269M LEU* 6.5 0.7 - - + -
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Residues in contact with ARG 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206M ARG 2.9 13.8 + - - +
207M CYS* 3.4 12.3 - - - +
209M VAL* 1.3 76.8 - - - +
211M ALA* 1.3 62.4 + - - +
213M LYS* 3.3 5.9 + - - +
214M ASP* 3.1 23.3 + - - +
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Residues in contact with ALA 211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192M TYR* 5.7 9.9 - - + -
207M CYS 2.8 19.9 + - - +
208M ILE* 3.7 7.2 - - - +
210M ARG* 1.3 72.0 - - - +
212M LEU* 1.3 62.8 + - + +
213M LYS 3.2 1.0 + - - -
214M ASP* 3.2 20.0 + - - +
217M ALA* 4.1 15.7 - - + +
223M LEU* 6.0 6.1 - - + -
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Residues in contact with LEU 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208M ILE 3.0 17.6 + - - +
209M VAL* 3.8 4.5 - - - +
211M ALA* 1.3 76.2 - - - +
213M LYS* 1.3 57.6 + - - +
214M ASP 3.5 0.7 - - - -
240M LEU* 6.1 4.5 - - + -
244M PHE* 4.7 19.3 - - + -
273M ASN* 4.0 24.5 - - + -
276M LYS* 4.1 14.0 - - - +
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Residues in contact with LYS 213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209M VAL 3.1 17.6 + - - +
210M ARG* 3.7 5.6 - - - +
212M LEU* 1.3 78.2 - - - +
214M ASP* 1.3 63.1 + - - +
215M PRO* 3.5 2.9 - - - +
269M LEU* 5.4 6.5 - - + +
272M GLN* 4.6 27.6 - - + +
273M ASN* 5.1 1.8 - - + +
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Residues in contact with ASP 214 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M LEU* 5.9 4.7 - - + -
210M ARG 3.1 15.4 + - - +
211M ALA* 3.2 14.6 + - - +
212M LEU 3.5 0.9 - - - -
213M LYS* 1.3 77.2 - - - +
215M PRO* 1.3 65.2 - - - +
216M ASN 3.1 4.3 + - - +
217M ALA* 3.3 26.7 + - + +
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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