Contacts of the strand formed by residues 210 - 215 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ASP* 2.8 22.4 + - - +
184B SER* 3.3 7.1 - - - -
185B ILE 2.9 27.9 + - - -
202B LEU* 4.8 0.2 - - - -
208B ASP 5.0 2.9 - - - +
209B ILE* 1.3 75.4 - - - +
211B PRO* 1.3 62.6 - - + +
212B VAL* 3.3 8.4 + - - +
247B GLU* 2.4 58.2 + - - +
298B GLU 2.6 29.3 + - - -
299B LEU* 3.1 26.5 + - - +
300B GLY* 3.9 1.6 - - - +
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Residues in contact with PRO 211 (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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185B ILE* 4.2 3.4 - - + +
195B LEU* 3.9 5.8 - - + -
198B LEU* 4.8 7.2 - - + -
199B SER* 3.5 18.2 - - - +
202B LEU* 3.3 28.9 - - + -
209B ILE 3.0 7.9 - - - +
210B ARG* 1.3 81.9 - - + +
212B VAL* 1.3 59.9 + - - +
246B PRO* 2.9 27.9 - - + +
247B GLU* 2.8 27.8 + - + +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B SER* 4.0 6.5 - - - -
185B ILE 3.0 15.4 + - - +
186B VAL* 3.3 26.3 - - + +
187B VAL* 3.4 6.8 + - - +
195B LEU* 4.9 1.3 - - - -
198B LEU* 5.6 0.2 - - - +
210B ARG* 3.6 12.3 - - - +
211B PRO* 1.3 73.9 - - - +
213B GLY* 1.3 59.7 + - - +
214B ILE* 4.4 6.1 - - + -
247B GLU* 3.7 25.1 - - - +
249B TYR* 3.3 37.9 - - + -
293B LEU* 4.1 11.7 - - + -
299B LEU* 4.0 21.5 - - + -
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Residues in contact with GLY 213 (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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187B VAL* 3.5 9.0 - - - -
189B ALA* 4.5 1.8 - - - -
195B LEU* 3.6 26.9 - - - +
211B PRO 3.7 1.2 + - - -
212B VAL* 1.3 73.2 - - - +
214B ILE* 1.3 63.1 + - - +
215B ALA 3.6 1.3 - - - -
247B GLU 3.3 11.1 + - - -
248B LEU* 3.1 9.1 - - - -
249B TYR* 2.9 26.9 + - - -
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Residues in contact with ILE 214 (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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186B VAL* 3.2 31.9 - - + -
187B VAL 3.1 9.2 + - - +
188B ALA* 3.6 0.5 - - - -
189B ALA 3.2 15.0 + - - +
212B VAL* 4.4 11.2 - - + -
213B GLY* 1.3 75.0 - - - +
215B ALA* 1.3 72.7 + - - +
216B VAL* 3.3 7.4 - - + +
249B TYR* 3.3 12.3 - - + +
251B TYR* 3.6 34.5 - - + -
285B LYS 3.8 2.5 - - - +
286B ALA* 3.7 33.7 - - + +
289B GLY* 3.6 22.2 - - - +
293B LEU* 4.4 2.2 - - + -
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Residues in contact with ALA 215 (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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189B ALA* 3.7 13.8 - - - +
213B GLY 3.5 5.1 + - - -
214B ILE* 1.3 81.4 - - - +
216B VAL* 1.3 62.3 + - - +
217B GLY 3.7 1.1 - - - +
219B PHE* 4.3 4.7 - - + -
223B MET* 3.5 27.4 - - + -
248B LEU* 4.4 5.8 - - + -
249B TYR 2.9 7.6 + - - +
250B ASP* 3.7 28.0 - - + +
251B TYR 3.3 19.7 + - - -
252B SER 4.6 0.4 - - - -
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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