Contacts of the strand formed by residues 194 - 201 (chain B) in PDB entry 2ANL
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 GLN 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B LEU* 3.0 12.9 - - - +
188B ASN* 2.9 32.7 + - - +
189B HIS* 3.3 24.8 + - - +
191B LEU* 3.2 30.3 - - - +
192B PHE* 3.2 24.0 + - + +
193B TRP* 1.3 70.9 - - - +
195B VAL* 1.3 61.3 - - - +
210B ASN* 3.1 37.1 + - - +
211B VAL 3.3 6.1 - - - +
212B ILE* 3.9 9.4 - - + +
298B THR* 6.0 0.4 - - - +
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Residues in contact with VAL 195 (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 GLU* 3.9 18.4 - - + -
186B LYS 3.9 13.2 - - - +
187B LEU* 3.7 6.7 - - + -
188B ASN* 3.1 12.1 + - - +
193B TRP 4.4 2.0 - - - +
194B GLN* 1.3 78.3 - - - +
196B ASP* 1.3 62.0 + - - +
197B LEU* 3.6 27.1 + - + -
211B VAL* 3.0 38.1 + - + +
213B VAL* 5.5 2.7 - - + -
320B ILE* 3.7 29.2 - - + -
322B PHE* 5.0 7.0 - - + -
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Residues in contact with ASP 196 (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 GLU* 4.5 5.0 - - - +
186B LYS 4.7 2.8 + - - -
188B ASN* 3.2 32.0 + - + +
195B VAL* 1.3 72.4 - - - +
197B LEU* 1.3 72.3 + - - +
208B LYS* 4.0 32.8 + - + +
209B ALA 3.6 12.2 - - - +
210B ASN* 4.8 1.4 - - - +
260B LYS 4.7 0.3 - - - +
261B SER* 5.1 1.7 - - - -
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Residues in contact with LEU 197 (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 GLU* 4.1 20.0 - - + +
195B VAL* 3.6 20.1 + - + +
196B ASP* 1.3 84.5 - - - +
198B ASP* 1.3 65.1 + - - +
199B VAL* 4.0 3.7 + - + +
208B LYS* 4.4 2.2 - - - +
209B ALA* 2.9 36.0 + - - +
211B VAL* 4.3 25.1 - - + -
259B PHE* 4.1 23.3 - - + -
260B LYS 3.4 22.4 - - - +
261B SER* 4.0 9.4 - - - +
266B TYR* 4.7 10.8 - - + -
301B LEU* 5.8 2.0 - - + -
305B PHE* 6.4 1.6 - - + -
322B PHE* 5.8 5.2 - - + -
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Residues in contact with ASP 198 (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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184A TYR* 4.9 11.4 - - + +
186A LYS* 5.3 5.0 + - - -
197B LEU* 1.3 71.9 - - - +
199B VAL* 1.3 59.6 + - - +
200B ASN* 4.8 2.2 - - - +
207B GLU* 2.6 41.9 - - - +
208B LYS* 2.6 17.9 + - - +
259B PHE* 3.5 0.7 - - - -
260B LYS* 2.6 60.0 + - + +
261B SER 6.1 0.2 - - - -
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Residues in contact with VAL 199 (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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197B LEU 4.5 6.3 - - - +
198B ASP* 1.3 75.8 - - - +
200B ASN* 1.3 56.7 + - - +
201B PHE* 4.0 6.3 - - + -
205B SER* 2.2 25.1 + - - -
206B MET 3.1 21.9 + - - +
209B ALA* 4.7 3.6 - - + -
211B VAL* 4.4 8.7 - - + -
226B PHE* 3.6 16.8 - - + -
258B GLU 3.2 2.2 - - - -
259B PHE* 3.2 37.9 - - + -
299B PHE* 3.2 37.5 - - + -
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Residues in contact with ASN 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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181A GLU* 2.6 55.1 + - + +
182A LEU 3.6 18.7 + - - +
183A THR* 5.9 0.8 - - - +
184A TYR* 5.3 2.1 - - - -
198B ASP* 4.8 2.6 - - - +
199B VAL* 1.3 78.2 + - - +
201B PHE* 1.3 70.0 + - - +
202B GLY 3.4 4.1 + - - +
205B SER* 2.3 31.9 + - - +
257B LEU* 3.6 0.3 - - - -
258B GLU* 2.8 43.3 + - + +
260B LYS* 5.0 9.1 - - - +
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Residues in contact with PHE 201 (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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199B VAL* 4.0 3.1 - - + -
200B ASN* 1.3 80.7 - - - +
202B GLY* 1.3 51.5 + - - +
203B LYS 2.8 17.3 + - - -
204B THR* 3.0 19.8 + - + +
220B ILE* 4.5 12.6 - - + -
222B ALA* 4.9 6.3 - - + -
226B PHE* 3.5 36.0 - + + -
227B ILE* 5.8 2.2 - - + -
230B PHE* 3.4 42.3 - + + -
257B LEU* 3.3 36.1 - - + -
259B PHE* 4.0 25.1 - + - -
289B ILE* 4.3 23.3 - - + -
299B PHE* 4.0 14.4 - + - -
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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