Contacts of the strand formed by residues 199 - 206 (chain B) in PDB entry 2ORY
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 199 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ILE* 3.5 30.1 - - + -
164B GLY 4.0 5.2 - - - +
166B ALA 3.1 11.7 - - - +
168B ILE* 3.7 29.8 - - + -
191B GLN* 2.8 27.4 + - - +
195B LEU* 3.7 35.9 - - + -
196B SER* 3.6 21.5 - - - +
197B GLN 3.2 3.6 - - - +
198B ASN* 1.3 80.7 - - - +
200B ASP* 1.3 66.6 + - - +
201B ILE* 3.6 17.0 + - + -
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Residues in contact with ASP 200 (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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166B ALA 2.7 14.6 + - - +
167B LYS* 3.3 30.3 - - + +
168B ILE 2.7 33.5 + - - +
198B ASN 4.9 5.4 - - - +
199B ILE* 1.3 74.0 - - - +
201B ILE* 1.3 58.3 + - - +
202B SER* 3.9 1.1 + - - -
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ILE* 3.4 11.4 - - + +
170B VAL* 4.7 4.9 - - + -
184B ALA* 3.9 25.4 - - + +
187B LEU* 3.8 16.2 - - + -
188B LYS* 3.8 25.6 + - + +
191B GLN* 3.5 33.8 + - + +
195B LEU* 4.3 6.5 - - + -
199B ILE* 3.6 16.9 + - + +
200B ASP* 1.3 74.9 - - - +
202B SER* 1.3 70.2 + - - +
224B LEU* 3.5 18.4 - - + +
227B GLN* 3.5 20.8 - - - +
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Residues in contact with SER 202 (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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5B LYS* 2.9 30.0 + - - -
168B ILE 2.8 9.7 + - - +
169B CYS* 3.4 12.9 - - - +
170B VAL* 2.9 25.8 + - - +
200B ASP 5.0 0.8 + - - -
201B ILE* 1.3 79.2 - - - +
203B THR* 1.3 65.9 + - - +
204B ILE* 5.9 0.9 - - - -
224B LEU* 4.7 0.7 - - - -
227B GLN* 3.2 20.4 - - - -
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Residues in contact with THR 203 (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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169B CYS* 4.2 1.1 - - - -
170B VAL* 2.7 21.7 + - - +
181B SER* 3.7 16.2 + - - -
184B ALA* 3.9 12.3 - - + -
202B SER* 1.3 78.7 - - - +
204B ILE* 1.3 64.7 + - - +
205B PRO* 3.5 11.0 - - - +
220B PHE* 4.0 6.1 - - + -
224B LEU* 3.9 23.1 - - + -
227B GLN 2.9 5.7 + - - +
228B CYS* 3.1 31.2 - - + -
229B THR 3.1 22.7 + - - -
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Residues in contact with ILE 204 (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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5B LYS* 4.0 26.7 - - + +
6B GLU* 4.2 19.1 - - - +
9B MET* 3.8 26.7 - - + -
169B CYS* 4.0 7.9 - - - -
170B VAL 3.1 10.2 + - - -
171B THR* 2.7 27.3 + - - +
202B SER* 5.9 0.4 - - - -
203B THR* 1.3 80.1 - - - +
205B PRO* 1.3 56.6 - - - +
206B PHE* 3.3 29.5 - - + -
227B GLN 5.8 0.2 - - - +
229B THR* 3.4 27.4 - - - +
231B ILE* 4.0 12.3 - - + -
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Residues in contact with PRO 205 (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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172B GLY 3.6 6.1 - - - +
177B GLY 3.1 29.6 - - - +
180B SER* 3.6 8.5 - - - +
181B SER* 4.0 14.4 - - - -
203B THR* 3.5 13.2 - - - +
204B ILE* 1.3 88.9 - - - +
206B PHE* 1.3 59.8 + - - +
208B GLY* 5.3 1.7 + - - +
228B CYS* 3.9 10.5 - - - -
229B THR 3.6 7.0 - - - +
230B ARG* 3.7 18.9 - - + +
231B ILE 3.1 25.1 + - - +
286B ILE* 4.6 3.4 - - + -
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Residues in contact with PHE 206 (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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6B GLU 3.4 22.7 - - - -
9B MET 3.9 0.7 - - - -
10B LEU* 3.6 37.5 - - + -
13B SER* 3.8 9.0 - - - -
171B THR* 3.3 14.6 - - - -
172B GLY 2.8 16.9 + - - +
173B HIS* 3.3 19.0 - - + -
174B SER 2.9 23.6 + - - -
177B GLY* 3.7 2.3 - - - -
204B ILE* 3.3 33.2 - - + -
205B PRO* 1.3 71.9 - - - +
207B ALA* 1.3 65.0 + - + +
208B GLY 3.0 4.1 + - - -
231B ILE* 3.4 42.6 - - + +
316B TYR* 4.3 4.0 - + + -
320B MET* 3.8 11.0 - - + -
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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