Contacts of the strand formed by residues 200 - 204 (chain A) in PDB entry 5E9W
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 THR 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LYS* 5.2 1.1 + - - -
198A ASP 4.4 4.7 + - - -
199A ILE* 1.3 73.2 + - - +
201A VAL* 1.3 65.6 + - - +
221A ASN* 5.6 1.2 - - - +
222A LYS* 3.4 40.3 + - + +
276A MET* 4.4 2.0 - - + -
277A CYS 3.2 26.9 + - - +
278A PHE* 3.6 16.3 - - + -
279A ASP* 2.8 42.7 + - - +
280A ILE 3.5 4.5 + - - -
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Residues in contact with VAL 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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199A ILE* 3.8 20.2 - - + -
200A THR* 1.3 81.1 - - - +
202A LEU* 1.3 69.5 + - - +
215A TRP* 3.8 37.0 - - + -
220A ILE* 4.0 19.3 - - + -
222A LYS 2.8 10.7 + - - +
223A LEU* 3.3 20.6 - - + +
224A VAL 2.9 26.5 + - - -
278A PHE* 3.6 7.3 - - - -
280A ILE* 3.3 20.6 - - + +
282A SER 4.8 0.2 - - - +
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Residues in contact with LEU 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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201A VAL* 1.3 73.6 - - - +
203A ASP* 1.3 53.9 + - - +
204A LEU* 4.3 6.5 - - + +
224A VAL* 3.7 31.2 - - + +
226A THR* 4.2 9.2 - - + -
267A LEU* 4.1 24.7 - - + -
271A PHE* 4.4 2.2 - - + -
278A PHE* 3.4 35.7 - - + -
280A ILE 2.9 11.5 + - - +
281A CYS* 3.2 22.9 - - + -
282A SER 2.7 32.9 + - - +
303A ASN 3.4 25.6 - - - +
304A ALA 4.6 0.9 - - - +
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Residues in contact with ASP 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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201A VAL 4.0 1.0 + - - -
202A LEU* 1.3 71.0 - - - +
204A LEU* 1.3 63.3 + - - +
205A GLY 3.7 0.2 + - - -
206A CYS* 3.7 29.7 - - + +
209A GLY* 6.0 0.9 - - - -
211A ASP* 4.1 17.6 + - - +
212A LEU* 6.1 0.7 - - - +
215A TRP* 3.8 20.2 + - - +
223A LEU* 3.9 15.7 - - + +
224A VAL 2.9 15.0 + - - +
225A CYS* 4.7 5.5 - - - -
226A THR* 3.2 25.5 + - - +
282A SER* 3.4 17.5 + - - +
284A GLN* 5.2 1.4 + - - +
500A SAH 4.5 6.8 + - - -
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Residues in contact with LEU 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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202A LEU* 3.7 5.6 + - + -
203A ASP* 1.3 70.2 - - - +
205A GLY* 1.3 66.6 + - - +
226A THR* 3.9 9.9 - - + -
262A SER* 3.6 30.1 - - - +
267A LEU* 4.6 1.3 - - + -
281A CYS* 4.1 10.5 - - - -
282A SER 2.9 19.9 + - - +
283A CYS* 3.8 12.3 - - - -
284A GLN 4.4 0.5 + - - -
286A VAL* 3.4 19.1 - - + +
300A MET* 4.1 28.0 - - + +
303A ASN* 4.1 13.0 - - + +
304A ALA* 3.9 39.3 - - + +
500A SAH 4.5 1.6 - - + -
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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