Contacts of the strand formed by residues 210 - 215 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183Q ASP* 2.8 30.8 + - - +
184Q SER* 3.3 4.3 - - - +
185Q ILE 2.9 22.4 + - - -
208Q ASP 3.5 9.6 - - - +
209Q ILE* 1.3 72.7 - - - +
211Q PRO* 1.3 64.5 - - + +
212Q VAL* 2.9 30.1 + - + +
247Q GLU* 2.4 41.5 + - + +
298Q GLU* 3.7 6.3 - - - +
299Q LEU* 3.2 46.4 + - - +
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Residues in contact with PRO 211 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185Q ILE* 3.8 7.4 - - + +
187Q VAL* 6.1 0.7 - - + -
195Q LEU* 4.7 4.3 - - + -
198Q LEU* 4.7 5.6 - - + -
199Q SER* 3.5 37.0 - - - +
202Q LEU* 3.3 32.3 - - + -
209Q ILE 3.4 8.1 - - - +
210Q ARG* 1.3 79.1 - - + +
212Q VAL* 1.3 60.1 + - - +
213Q GLY 4.0 0.4 - - - -
245Q ARG 5.4 3.1 - - - +
246Q PRO* 3.6 11.0 - - + +
247Q GLU* 2.9 24.0 + - + +
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Residues in contact with VAL 212 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184Q SER* 4.4 1.1 - - - -
185Q ILE 3.2 6.1 + - - -
186Q VAL* 3.0 38.0 - - + +
187Q VAL* 3.1 6.6 + - - -
210Q ARG* 2.9 46.8 + - + +
211Q PRO* 1.3 73.7 - - - +
213Q GLY* 1.3 59.0 + - - +
214Q ILE* 6.3 0.2 - - + -
247Q GLU* 3.4 12.8 - - + +
249Q TYR* 3.5 37.7 - - + -
293Q LEU* 4.8 5.6 - - + -
299Q LEU* 4.1 15.9 - - + -
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Residues in contact with GLY 213 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187Q VAL* 3.3 11.4 - - - -
189Q ALA* 4.6 0.7 - - - -
195Q LEU* 3.6 24.1 - - - +
211Q PRO 3.9 1.4 + - - -
212Q VAL* 1.3 77.8 - - - +
214Q ILE* 1.3 54.7 + - - +
247Q GLU 2.5 16.4 + - - +
248Q LEU* 3.0 8.9 - - - -
249Q TYR* 2.8 31.5 + - - -
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Residues in contact with ILE 214 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186Q VAL* 5.1 6.1 - - + -
187Q VAL 3.3 17.8 + - - +
188Q ALA* 3.7 0.7 - - - -
189Q ALA* 3.3 9.7 + - - +
212Q VAL* 5.2 0.7 - - + +
213Q GLY* 1.3 72.6 - - - -
215Q ALA* 1.3 63.9 + - - +
216Q VAL* 3.1 11.4 + - + +
249Q TYR* 3.1 18.6 - - + +
251Q TYR* 3.1 32.8 - - + -
285Q LYS 3.5 0.4 - - - +
286Q ALA* 2.8 63.3 - - + +
289Q GLY* 3.4 17.3 - - - +
293Q LEU* 6.2 2.0 - - + -
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Residues in contact with ALA 215 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Q ALA* 3.6 13.7 - - + +
213Q GLY 4.1 1.0 - - - -
214Q ILE* 1.3 68.4 - - - +
216Q VAL* 1.3 59.4 + - - +
217Q GLY 3.2 13.8 + - - +
219Q PHE* 4.5 7.2 - - + -
223Q MET* 3.6 31.2 - - + -
248Q LEU* 4.7 4.2 - - + +
249Q TYR 2.7 14.3 + - - +
250Q ASP* 4.2 8.7 - - - -
251Q TYR 2.9 28.6 + - - -
252Q SER* 3.2 5.9 + - - -
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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