Contacts of the strand formed by residues 200 - 205 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A LEU* 4.5 0.9 - - + +
150A LYS* 3.3 26.9 - - + +
159A ILE* 4.1 14.4 - - + -
193A GLU* 2.8 57.9 + - + +
194A LEU* 3.6 29.1 - - + +
195A ALA 5.4 0.2 - - - -
196A ASN 2.9 15.9 + - - +
197A LYS* 3.5 17.5 - - - +
199A LYS* 1.3 107.0 - - + +
201A LEU* 1.3 60.8 + - - +
202A SER* 3.4 9.4 + - - +
214A SER* 3.3 17.3 - - - +
215A ILE 3.2 5.8 - - - -
216A LYS* 4.0 20.0 - - + -
217A LEU* 3.7 7.9 - - - +
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LYS* 6.2 3.1 - - + -
200A TYR* 1.3 72.8 - - - +
202A SER* 1.3 60.6 + - - +
215A ILE* 2.9 34.6 + - + +
217A LEU* 4.0 13.8 - - + +
46F GLN* 3.9 32.3 - - + +
49F GLN* 3.8 16.2 - - + +
50F LEU* 3.3 37.6 - - + +
53F ARG* 3.6 37.5 - - + +
77F ALA* 5.4 0.9 - - + -
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Residues in contact with SER 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LEU* 2.7 29.0 + - - +
200A TYR* 3.4 3.1 + - - +
201A LEU* 1.3 75.9 - - - +
203A THR* 1.3 64.2 + - - +
212A MET* 4.0 7.2 - - - -
213A VAL 3.4 4.7 - - - -
214A SER* 2.7 28.7 + - - -
17F PHE* 3.7 22.0 - - - +
46F GLN* 2.8 32.3 + - - +
50F LEU* 4.8 1.1 - - - -
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Residues in contact with THR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A SER* 1.3 76.8 + - - +
204A ILE* 1.3 78.3 + - - +
205A ILE* 3.7 7.0 + - + +
206A PRO* 5.7 0.7 - - + -
212A MET* 3.6 3.4 - - - +
213A VAL* 2.9 32.4 + - - +
17F PHE* 4.4 7.7 + - + +
43F VAL* 5.0 13.2 + - + +
46F GLN* 4.2 4.2 + - - +
47F MET* 3.5 48.1 + - + +
50F LEU* 3.7 18.0 - - - +
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A THR* 3.3 26.5 - - - +
165A PHE* 3.4 26.0 - - + -
191A ASN* 3.9 15.5 - - - +
203A THR* 1.3 80.7 - - - +
205A ILE* 1.3 65.5 + - - +
206A PRO* 3.2 9.2 - - - +
210A GLY* 3.6 16.2 - - - -
211A MET 3.6 3.6 - - - +
212A MET* 3.6 26.0 - - + -
12F TYR* 4.4 3.8 - - + -
13F LEU* 4.0 26.8 - - + +
17F PHE* 3.5 31.7 - - + +
43F VAL* 5.9 0.7 - - - +
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Residues in contact with ILE 205 (chain A).
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* 3.4 43.7 - - + -
51A LEU* 5.0 6.3 - - + -
203A THR* 3.7 9.4 + - + -
204A ILE* 1.3 71.1 - - - +
206A PRO* 1.3 64.2 - - + +
207A THR* 2.7 27.9 + - + -
210A GLY* 3.6 2.9 - - - -
211A MET* 2.8 35.6 + - + +
213A VAL* 3.6 28.3 - - + -
47F MET* 5.3 4.0 - - + -
50F LEU* 6.4 0.7 - - + -
205F ILE* 4.0 25.6 - - + -
206F PRO* 4.1 4.9 - - + -
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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