Contacts of the strand formed by residues 200 - 205 (chain F) in PDB entry 4OA5
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLN* 5.9 0.2 + - - -
146F LEU* 4.5 1.2 - - + +
150F LYS* 3.3 26.5 - - + +
159F ILE* 4.1 14.1 - - + -
193F GLU* 2.8 55.9 + - + +
194F LEU* 3.6 28.9 - - + +
196F ASN 3.0 15.8 + - - +
197F LYS* 3.5 17.3 - - - +
199F LYS* 1.3 105.9 - - + +
201F LEU* 1.3 59.7 + - - +
202F SER* 3.4 9.2 + - - +
214F SER* 3.3 17.5 - - - +
215F ILE 3.2 5.8 - - - -
216F LYS* 4.0 19.7 - - + -
217F LEU* 3.6 7.9 - - - +
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Residues in contact with LEU 201 (chain F).
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* 3.9 31.6 - - + +
49A GLN* 3.8 19.3 - - + +
50A LEU* 3.4 33.0 - - + +
53A ARG* 3.5 34.5 - - + +
305A IOD 4.4 13.5 - - + -
197F LYS* 6.3 2.9 - - + -
200F TYR* 1.3 72.9 - - - +
202F SER* 1.3 60.5 + - - +
214F SER* 3.4 0.2 - - - -
215F ILE* 2.9 37.5 + - + +
217F LEU* 3.9 15.1 - - + +
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Residues in contact with SER 202 (chain F).
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 22.5 - - - +
46A GLN* 2.8 30.2 + - - +
50A LEU* 4.9 1.3 - - - -
194F LEU* 2.7 29.2 + - - +
200F TYR* 3.4 2.7 + - - +
201F LEU* 1.3 75.6 - - - +
203F THR* 1.3 65.1 + - - +
212F MET* 4.0 7.4 - - - -
213F VAL 3.4 4.3 - - - -
214F SER* 2.7 28.7 + - - -
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Residues in contact with THR 203 (chain F).
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* 4.5 8.4 + - + +
43A VAL* 5.0 7.8 + - + +
46A GLN* 4.1 3.8 + - - +
47A MET* 3.5 31.3 + - + +
50A LEU* 3.8 17.7 - - - +
304A IOD 4.1 25.4 - - + -
202F SER* 1.3 76.1 + - - +
204F ILE* 1.3 78.0 + - - +
205F ILE* 3.7 8.0 + - + +
211F MET 3.7 0.2 - - - +
212F MET* 3.6 2.4 - - - +
213F VAL* 2.9 31.7 + - - +
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Residues in contact with ILE 204 (chain F).
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 2.5 - - + -
13A LEU* 4.1 23.7 - - + +
17A PHE* 3.6 31.8 - - + +
43A VAL* 5.9 0.9 - - - +
164F THR* 3.3 26.2 - - - +
165F PHE* 3.4 29.6 - - + -
191F ASN* 3.9 15.7 - - - +
203F THR* 1.3 80.4 - - - +
205F ILE* 1.3 64.1 + - - +
206F PRO* 3.2 10.0 - - - +
210F GLY* 3.6 16.6 - - - -
211F MET 3.6 3.8 - - - +
212F MET* 3.6 26.0 - - + -
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Residues in contact with ILE 205 (chain F).
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* 4.1 26.5 - - + -
50A LEU* 5.6 2.7 - - + -
205A ILE* 4.0 22.4 - - + -
206A PRO* 4.0 11.2 - - + -
47F MET* 3.7 29.8 - - - -
51F LEU* 6.3 2.0 - - + -
203F THR* 3.7 10.5 + - + +
204F ILE* 1.3 70.1 - - - +
206F PRO* 1.4 63.1 - - + +
207F THR* 2.8 21.9 + - + -
210F GLY* 3.6 2.9 - - - -
211F MET* 2.8 42.7 + - + +
213F VAL* 4.0 20.9 - - + -
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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