Contacts of the strand formed by residues 233 - 238 (chain A) in PDB entry 1MKP
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 ILE 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A PRO* 5.0 1.8 - - + -
215A TYR* 3.7 46.0 - - + -
228A LEU* 2.9 41.8 + - + +
229A GLU* 4.6 2.8 + - - -
231A PHE* 3.9 22.7 - - + -
232A GLY* 1.3 76.6 - - - +
234A LYS* 1.3 62.6 + - - +
235A TYR 3.5 22.2 - - - +
236A ILE* 4.8 5.4 - - + -
253A PHE* 3.3 19.8 - - + -
288A GLY* 3.4 10.3 - - - +
290A LEU* 4.0 15.9 - - + -
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Residues in contact with LYS 234 (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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232A GLY 3.6 3.2 + - - +
233A ILE* 1.3 75.0 - - - +
235A TYR* 1.3 77.0 + - + +
252A GLU 4.4 9.6 - - - +
253A PHE* 3.2 15.4 - - - +
254A LYS* 2.8 26.3 + - - +
287A CYS* 4.4 17.3 - - + -
288A GLY 2.9 4.2 + - - -
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Residues in contact with TYR 235 (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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233A ILE* 3.5 6.8 - - - +
234A LYS* 1.3 93.5 - - + +
236A ILE* 1.3 62.9 + - - +
247A PHE* 5.3 1.8 - + - -
254A LYS* 3.5 38.6 - - + +
278A PHE* 3.4 32.8 - + + -
281A GLU* 2.8 33.6 + - - -
282A ALA* 3.6 30.1 - - + -
285A LYS* 3.9 12.0 + - + +
287A CYS* 4.2 17.9 - - + -
288A GLY 3.1 5.3 + - - +
289A VAL* 3.3 20.6 - - + -
290A LEU 2.8 25.2 + - - -
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Residues in contact with ILE 236 (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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225A LEU* 5.3 4.3 - - + -
228A LEU* 3.9 27.8 - - + -
233A ILE* 4.8 1.1 - - + -
235A TYR* 1.3 79.2 - - - +
237A LEU* 1.3 68.5 + - - +
238A ASN* 4.5 2.9 - - + +
253A PHE* 4.0 29.4 - - + -
254A LYS 3.0 8.9 + - - +
255A TYR* 4.0 30.7 - - + -
256A LYS* 2.8 30.0 + - - +
278A PHE* 3.6 5.3 - - - -
290A LEU* 3.7 20.2 - - + +
292A HIS* 5.5 3.6 - - + -
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Residues in contact with LEU 237 (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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236A ILE* 1.3 73.4 - - - +
238A ASN* 1.3 73.4 + - - +
239A VAL* 3.7 14.7 + - + -
256A LYS* 3.8 26.2 - - + +
258A ILE* 4.4 12.1 - - + -
275A ALA* 4.0 31.2 - - + +
278A PHE* 3.8 21.9 - - + -
279A ILE* 4.7 2.7 - - + -
289A VAL* 4.9 1.1 - - + -
290A LEU 2.7 15.8 + - - +
291A VAL* 3.5 15.1 - - + +
292A HIS* 3.0 27.0 + - - +
303A VAL* 4.1 16.2 - - + -
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Residues in contact with ASN 238 (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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236A ILE* 3.9 3.5 - - + -
237A LEU* 1.3 73.2 - - - +
239A VAL* 1.3 74.2 + - - +
240A THR* 2.7 33.1 + - - +
243A LEU* 3.8 16.5 - - - +
255A TYR* 3.1 33.3 + - + +
256A LYS 2.8 17.3 + - - +
257A GLN* 3.7 4.6 - - - +
258A ILE* 3.4 25.1 + - - +
292A HIS* 3.2 13.6 + - - +
293A SER* 4.2 0.2 - - - +
294A LEU* 5.6 3.7 - - - +
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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