Contacts of the strand formed by residues 210 - 215 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183H ASP* 3.1 22.0 + - - +
184H SER* 3.0 12.4 - - - -
185H ILE 3.0 26.3 + - - -
202H LEU* 5.1 0.7 - - - -
208H ASP 4.2 0.6 + - - -
209H ILE* 1.3 69.6 - - - +
211H PRO* 1.3 67.0 - - + +
212H VAL* 4.5 4.4 - - + +
247H GLU* 2.7 44.6 + - - +
249H TYR* 4.6 4.0 + - - -
298H GLU* 2.8 39.7 + - - +
299H LEU* 3.4 18.9 + - - -
300H GLY* 3.8 4.0 - - - +
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Residues in contact with PRO 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H ILE 4.0 0.9 - - - +
198H LEU* 3.7 18.4 - - + -
199H SER* 3.6 27.1 - - - +
202H LEU* 4.1 12.1 - - + -
209H ILE 3.3 11.4 - - - +
210H ARG* 1.3 82.7 - - + +
212H VAL* 1.3 59.6 + - - +
213H GLY 4.2 0.4 - - - -
244H VAL 5.7 2.0 - - - +
245H ARG 5.1 3.4 - - - +
246H PRO* 3.5 28.0 - - + -
247H GLU* 2.9 32.5 + - - +
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Residues in contact with VAL 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H SER* 4.1 15.0 - - - +
185H ILE 2.8 16.8 + - - +
186H VAL* 3.7 24.4 - - + +
187H VAL* 2.8 28.6 + - - +
195H LEU* 4.6 3.6 - - - +
198H LEU* 4.6 2.2 - - - +
210H ARG* 4.0 10.1 - - + +
211H PRO* 1.3 79.1 - - - +
213H GLY* 1.3 62.1 + - - +
214H ILE* 3.9 13.0 - - + -
247H GLU* 3.6 23.8 - - + +
249H TYR* 4.0 15.7 - - + -
293H LEU* 4.5 0.9 - - + -
299H LEU* 4.4 13.7 - - + -
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Residues in contact with GLY 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187H VAL 3.3 9.0 - - - -
189H ALA* 4.5 1.6 - - - -
195H LEU* 4.1 16.8 - - - +
211H PRO 4.2 0.2 - - - -
212H VAL* 1.3 70.3 - - - +
214H ILE* 1.3 60.2 + - - -
247H GLU 2.5 18.3 + - - -
248H LEU* 2.9 13.1 - - - +
249H TYR* 2.6 35.5 + - - -
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Residues in contact with ILE 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186H VAL* 3.2 33.2 - - + -
187H VAL 3.1 6.0 + - - +
188H ALA* 3.3 3.3 - - - -
189H ALA 2.7 25.8 + - - -
212H VAL* 3.9 5.8 - - + -
213H GLY* 1.3 73.2 - - - +
215H ALA* 1.3 60.8 + - - +
216H VAL* 3.7 3.5 - - - +
249H TYR* 3.2 2.0 - - + -
251H TYR* 3.4 26.0 - - + -
285H LYS 3.1 29.2 - - - +
286H ALA* 3.4 25.4 - - + +
289H GLY* 4.1 0.2 - - - -
290H LEU 4.3 6.1 - - - +
293H LEU* 3.8 28.9 - - + -
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Residues in contact with ALA 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H ALA* 3.7 11.9 - - + -
213H GLY 3.4 2.4 + - - -
214H ILE* 1.3 74.6 - - - +
216H VAL* 1.3 61.8 + - - +
217H GLY 3.7 2.2 - - - +
218H ARG 4.5 15.5 - - - +
219H PHE* 5.4 2.9 - - + -
223H MET* 4.6 3.4 - - - -
248H LEU* 3.4 23.3 - - + +
249H TYR 2.5 14.3 + - - +
250H ASP* 3.7 14.1 - - + +
251H TYR* 2.9 26.9 + - - +
252H SER* 3.5 1.3 + - - -
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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