Contacts of the strand formed by residues 200 - 205 (chain B) in PDB entry 4OA8
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 TYR 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLN* 5.8 0.2 + - - -
146B LEU* 4.1 4.5 - - + +
150B LYS* 3.6 35.1 - - + +
159B ILE* 4.0 15.7 - - + -
193B GLU* 3.4 39.4 + - + +
194B LEU* 3.6 31.4 - - + +
195B ALA 5.4 0.2 - - - -
196B ASN 2.9 14.9 + - - +
197B LYS* 3.4 17.7 - - - +
199B LYS* 1.3 109.5 - - + +
201B LEU* 1.3 60.9 + - - +
202B SER* 3.4 9.5 + - - +
214B SER* 3.4 16.8 - - - +
215B ILE 3.3 5.6 - - - -
216B LYS* 4.0 21.1 - - + -
217B LEU* 3.8 6.7 - - - +
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Residues in contact with LEU 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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46A GLN* 3.8 32.8 - - + +
49A GLN* 3.8 39.0 - - + +
50A LEU* 3.4 27.0 - - + +
53A ARG* 3.9 23.3 - - + +
77A ALA* 5.6 0.4 - - + -
197B LYS* 6.2 3.1 - - + -
200B TYR* 1.3 73.7 - - - +
202B SER* 1.3 58.9 + - - +
215B ILE* 2.9 37.0 + - + -
217B LEU* 3.9 17.6 - - + +
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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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17A PHE* 3.7 19.1 - - - +
46A GLN* 2.7 33.7 + - - +
50A LEU* 4.6 3.1 - - - -
194B LEU 2.6 29.1 + - - -
200B TYR* 3.4 3.1 + - - +
201B LEU* 1.3 74.2 - - - +
203B THR* 1.3 63.7 + - - +
212B MET* 4.0 6.7 - - - -
213B VAL 3.3 5.8 - - - -
214B SER* 2.8 29.0 + - - -
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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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17A PHE* 4.2 13.8 + - - +
43A VAL* 4.7 6.6 + - - +
46A GLN* 5.5 0.7 - - - -
47A MET* 3.6 40.6 - - + +
50A LEU* 3.2 26.2 - - + +
202B SER* 1.3 76.2 - - - +
204B ILE* 1.3 64.1 + - - +
205B ILE* 4.4 18.8 - - + +
211B MET 3.8 0.2 - - - +
212B MET* 3.6 3.8 - - - +
213B VAL* 2.9 33.5 + - + +
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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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12A TYR* 4.5 2.9 - - + -
13A LEU* 4.0 21.0 - - + +
17A PHE* 3.6 34.0 - - + +
47A MET* 4.6 2.1 - - - +
164B THR* 3.4 26.9 - - - +
165B PHE* 3.4 33.6 - - + -
191B ASN* 3.9 20.0 - - - +
203B THR* 1.3 77.7 + - - +
205B ILE* 1.3 64.0 + - - +
206B PRO* 3.1 10.4 - - - +
210B GLY* 3.6 13.0 - - - -
211B MET 3.6 3.8 - - - +
212B MET* 3.7 18.4 - - + -
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Residues in contact with ILE 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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47A MET* 5.1 1.3 - - + -
203A THR* 6.5 0.4 - - + -
205A ILE* 4.2 23.8 - - + -
206A PRO* 4.0 10.3 - - + -
47B MET* 3.9 41.5 - - + -
51B LEU* 5.3 9.2 - - + -
203B THR* 3.9 12.3 - - + -
204B ILE* 1.3 68.5 - - - +
206B PRO* 1.3 68.4 - - + +
207B THR* 2.7 13.6 + - + -
210B GLY* 3.6 2.6 - - - -
211B MET* 2.8 39.9 + - + +
213B VAL* 3.7 26.5 - - + -
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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