Contacts of the strand formed by residues 207 - 213 (chain B) in PDB entry 3ORH
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 ILE 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B PHE* 4.2 17.9 - - + -
194B VAL* 4.6 7.2 - - + -
197B LEU* 3.8 39.7 - - + -
198B LEU* 4.0 20.6 - - + -
202B PHE* 4.5 5.6 - - + -
203B ARG 3.6 13.7 - - - +
204B ARG* 2.8 48.1 + - - +
205B GLU* 3.4 1.8 - - - +
206B ASN* 1.4 83.6 - - - +
208B ARG* 1.3 71.1 + - - +
209B THR* 6.2 0.2 - - - -
232B LEU 3.7 2.5 - - - -
233B VAL* 4.1 20.9 - - + -
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Residues in contact with ARG 208 (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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205B GLU 4.3 17.7 + - - +
206B ASN* 4.1 1.3 - - - +
207B ILE* 1.3 83.4 - - - +
209B THR* 1.3 64.4 + - - +
210B GLU* 6.4 0.2 - - + -
231B PRO* 3.6 2.8 - - - +
232B LEU* 2.9 45.2 + - + +
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Residues in contact with THR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B THR* 4.7 17.0 - - + +
189B PHE* 5.0 13.6 - - + -
204B ARG* 6.3 1.1 - - - +
207B ILE* 6.2 0.2 - - - -
208B ARG* 1.3 77.6 - - - +
210B GLU* 1.3 72.2 + - - +
211B VAL* 5.4 1.8 - - + -
229B ILE* 2.6 44.6 - - + +
230B THR 3.3 11.1 + - - -
231B PRO* 4.5 2.4 - - - +
232B LEU* 4.7 0.2 - - - -
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Residues in contact with GLU 210 (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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52B ALA* 5.1 6.9 - - - +
56B ALA* 5.6 0.5 - - - +
208B ARG* 6.4 0.2 - - + -
209B THR* 1.3 81.3 + - - +
211B VAL* 1.3 68.0 + - - +
212B MET* 4.0 1.0 + - - +
228B MET 3.8 0.5 - - - +
229B ILE* 3.4 2.3 - - - -
230B THR* 2.8 50.1 + - - +
232B LEU* 3.5 31.6 - - + +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 3.8 14.4 - - + -
186B THR* 3.6 24.5 - - - +
209B THR* 4.3 2.4 - - + +
210B GLU* 1.3 77.6 - - - +
212B MET* 1.3 65.6 + - - +
227B GLN* 3.7 38.1 - - + +
228B MET 3.4 7.4 - - - +
229B ILE* 4.1 10.3 - - + -
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Residues in contact with MET 212 (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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48B PRO* 3.8 17.9 - - + +
49B TYR* 3.8 34.3 - - + -
52B ALA* 3.7 25.1 - - + -
210B GLU 5.3 0.9 - - - +
211B VAL* 1.3 79.3 - - - +
213B ALA* 1.3 68.3 + - - +
214B LEU* 5.0 1.8 - - - -
227B GLN* 3.3 6.7 - - - +
228B MET* 2.9 50.4 + - + +
230B THR* 5.2 3.6 - - - +
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Residues in contact with ALA 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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48B PRO* 6.1 0.3 - - - +
212B MET* 1.3 77.5 - - - +
214B LEU* 1.3 62.4 + - - +
215B VAL* 5.9 1.1 - - + -
226B PRO 3.8 8.1 - - - +
227B GLN* 4.6 4.3 - - + +
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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