Contacts of the strand formed by residues 200 - 204 (chain A) in PDB entry 3P9K
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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198A LEU* 3.9 3.6 - - - +
199A GLY* 1.3 73.7 - - - +
201A LEU* 1.3 61.8 + - - +
202A VAL* 4.0 9.2 - - + -
223A LYS* 3.2 20.2 - - + +
225A VAL* 4.2 11.9 - - + -
255A SER 3.9 9.0 - - - +
256A GLY* 3.8 21.1 - - - -
257A ASP* 2.8 43.1 + - - +
258A THR 3.3 7.6 + - - +
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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
----------------------------------------------------------
195A PHE* 4.0 18.6 - - + -
198A LEU* 4.5 9.0 - - + -
199A GLY 3.9 0.8 + - - -
200A THR* 1.3 72.4 - - - +
202A VAL* 1.3 63.0 + - - +
212A VAL* 4.0 15.7 - - + +
215A ILE* 3.7 44.4 - - + -
216A ALA 5.9 0.2 - - - +
222A ILE* 4.1 17.9 - - + -
223A LYS 2.9 6.9 + - - +
224A GLY* 3.4 2.2 - - - -
225A VAL 2.8 27.7 + - - +
258A THR* 3.6 33.2 - - + +
260A LEU* 4.1 17.7 - - + -
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A THR* 4.0 2.9 - - + -
201A LEU* 1.3 77.8 - - - +
203A ASP* 1.3 59.3 + - - +
204A VAL* 3.6 15.1 + - + -
225A VAL* 3.6 20.6 - - + +
227A PHE* 4.3 5.6 - - + -
254A PRO* 4.0 32.3 - - + +
255A SER 3.4 27.8 - - - +
256A GLY* 4.0 11.9 - - - -
258A THR 2.9 9.9 + - - +
259A ILE* 3.2 10.7 - - + +
260A LEU 2.7 31.2 + - - -
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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 LEU* 4.0 0.8 + - + -
202A VAL* 1.3 72.7 - - - +
204A VAL* 1.3 63.5 + - - +
205A GLY 4.0 0.9 - - - +
206A GLY* 3.4 25.6 + - - -
211A THR* 3.7 20.8 - - - +
212A VAL* 4.1 17.8 + - + -
225A VAL 2.9 16.5 + - - +
226A ASN* 4.4 2.5 - - - +
227A PHE 3.0 28.9 + - - +
260A LEU* 3.3 38.4 - - + +
261A MET* 4.7 1.4 - - - -
262A LYS* 4.8 2.3 + - - +
401A SAH 4.6 5.4 + - - -
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Residues in contact with VAL 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 VAL* 4.3 10.8 - - + -
203A ASP* 1.3 72.9 - - - +
205A GLY* 1.3 66.9 + - - +
227A PHE* 3.9 8.7 - - + -
249A MET* 3.6 37.9 - - + -
253A VAL* 4.0 26.5 - - + -
259A ILE* 3.5 25.4 - - + -
260A LEU 2.8 11.3 + - - +
261A MET* 3.7 22.1 - - + +
264A ILE* 3.3 20.3 - - - +
276A LEU* 4.2 1.6 - - + -
280A CYS* 4.7 1.1 - - - -
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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