Contacts of the strand formed by residues 210 - 215 (chain M) in PDB entry 1J0B
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 ARG 210 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183M ASP* 2.9 19.7 + - - +
184M SER* 4.1 2.9 - - - -
185M ILE* 3.3 20.8 + - - +
202M LEU* 4.3 1.6 - - - -
208M ASP* 5.5 3.1 - - - +
209M ILE* 1.3 73.9 - - - +
211M PRO* 1.3 64.1 - - - +
212M VAL* 2.9 15.3 + - + +
247M GLU* 2.8 43.2 + - - +
249M TYR* 4.5 0.4 + - - -
298M GLU 2.4 32.1 + - - -
299M LEU* 3.0 32.1 + - - +
300M GLY* 3.5 3.2 - - - +
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Residues in contact with PRO 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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185M ILE* 4.4 3.8 - - + +
195M LEU* 3.6 6.4 - - + +
198M LEU* 4.9 4.7 - - + -
199M SER* 3.3 40.4 - - - +
202M LEU* 3.5 24.0 - - + -
203M SER 5.8 0.2 - - - +
209M ILE 3.0 10.1 - - - +
210M ARG* 1.3 80.4 - - + +
212M VAL* 1.3 61.6 + - - +
213M GLY 3.5 0.5 + - - -
244M VAL 5.7 2.5 - - - +
245M ARG 5.1 5.4 - - - +
246M PRO* 3.2 16.4 - - + +
247M GLU* 3.2 21.6 + - + +
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Residues in contact with VAL 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184M SER* 4.1 6.1 - - - -
185M ILE 3.4 6.4 + - - +
186M VAL* 3.2 17.4 - - + +
187M VAL* 3.2 23.2 + - - +
195M LEU* 4.1 2.2 - - - -
210M ARG* 2.9 31.0 + - + +
211M PRO* 1.3 71.4 - - - +
213M GLY* 1.3 61.3 + - - +
214M ILE* 5.6 0.7 - - + -
247M GLU* 3.5 13.0 - - - +
249M TYR* 3.3 35.4 - - + -
293M LEU* 4.3 6.1 - - + -
299M LEU* 3.8 28.0 - - + -
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Residues in contact with GLY 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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187M VAL* 3.3 8.3 - - - -
189M ALA* 4.4 1.3 - - - -
195M LEU* 3.4 31.0 - - - +
211M PRO 3.5 4.8 + - - -
212M VAL* 1.3 76.3 - - - +
214M ILE* 1.3 61.3 + - - +
247M GLU 3.0 18.8 + - - +
248M LEU* 3.7 6.7 - - - -
249M TYR* 3.4 15.1 + - - -
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Residues in contact with ILE 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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186M VAL* 4.7 7.9 - - + -
187M VAL 2.8 32.2 + - - +
188M ALA* 3.5 4.0 - - - -
189M ALA* 2.9 19.1 + - - +
212M VAL* 4.5 2.0 - - + +
213M GLY* 1.3 76.2 - - - +
215M ALA* 1.3 59.6 + - - +
216M VAL* 3.4 4.2 + - - +
249M TYR* 3.5 8.5 - - + +
251M TYR* 3.5 25.1 - - + -
285M LYS 3.4 5.2 - - - +
286M ALA* 3.0 43.0 - - + +
289M GLY* 3.1 28.0 - - - -
290M LEU 5.7 0.2 - - - +
293M LEU* 5.4 4.5 - - + -
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Residues in contact with ALA 215 (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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189M ALA* 3.2 13.7 - - - +
214M ILE* 1.3 72.0 - - - +
216M VAL* 1.3 60.3 + - - +
217M GLY 3.8 11.2 - - - +
219M PHE* 4.2 14.6 - - + -
223M MET* 3.4 26.9 - - + -
248M LEU* 4.0 3.4 - - + +
249M TYR 2.9 17.2 + - - +
250M ASP* 4.4 2.0 - - - -
251M TYR* 3.2 9.5 + - - +
252M SER 3.1 21.0 + - - -
285M LYS* 5.4 0.2 - - - +
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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