Contacts of the strand formed by residues 232 - 238 (chain A) in PDB entry 1MK2
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 CYS 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A PHE* 4.6 1.2 - - - +
231A TRP* 1.3 107.3 - - + +
233A SER* 1.3 58.9 + - - +
234A ILE* 3.9 21.8 - - - -
248A HIS* 3.7 2.3 + - - +
249A ALA* 2.7 50.5 + - - +
397A LEU* 4.5 7.9 - - - -
398A HIS 2.8 23.1 - - - +
399A LEU* 4.2 5.2 - - + -
400A ASN* 2.8 11.8 + - - +
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Residues in contact with SER 233 (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 CYS* 1.3 75.7 - - - +
234A ILE* 1.3 64.7 + - - +
235A SER* 5.5 0.4 + - - -
246A THR* 3.8 11.9 - - - +
247A PHE 3.2 4.9 - - - -
248A HIS* 3.5 26.9 - - - +
396A GLU 3.4 1.2 - - - +
397A LEU* 3.1 6.6 - - - -
398A HIS* 3.0 46.7 + - - +
400A ASN* 3.9 6.2 + - - -
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Residues in contact with ILE 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 CYS* 3.9 13.5 - - - -
233A SER* 1.3 79.0 - - - +
235A SER* 1.3 65.9 + - - +
242A ARG* 4.2 0.2 + - - -
245A GLU 4.2 0.2 - - - +
246A THR* 3.5 4.4 - - - -
247A PHE* 2.5 48.2 + - + +
249A ALA* 5.1 0.2 - - + -
254A MET* 3.3 34.3 - - + -
256A VAL* 3.7 11.7 - - + -
268A PHE* 3.8 22.5 - - + -
295A LEU* 3.8 15.0 - - + -
395A ILE* 3.7 31.6 - - + -
396A GLU 3.3 4.9 - - - +
397A LEU* 4.2 6.3 - - + -
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Residues in contact with SER 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 SER* 5.7 0.2 + - - -
234A ILE* 1.3 75.9 - - - +
236A TYR* 1.3 59.5 + - - +
237A TYR* 3.7 20.3 + - - -
242A ARG* 3.3 32.4 + - - +
246A THR* 3.5 11.8 + - - +
395A ILE* 2.9 8.6 - - - +
396A GLU* 2.9 38.1 + - - -
398A HIS* 5.2 8.0 + - - -
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Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A ILE 4.3 0.4 + - - -
235A SER* 1.3 72.0 - - - +
237A TYR* 1.3 88.9 + - - +
238A GLU* 2.8 41.4 + - + +
242A ARG* 3.4 8.5 - - - +
243A VAL* 2.9 58.9 + - + +
268A PHE* 4.2 19.5 - - + -
270A LEU* 3.9 29.3 - - + +
273A LEU* 4.3 12.6 - - + -
286A ARG* 2.9 30.8 + - - +
289A ILE* 5.7 0.5 - - - +
375A PHE* 4.9 0.7 - + - -
393A CYS* 3.6 16.5 - - + -
394A TRP 3.2 10.8 - - - -
395A ILE* 4.0 7.4 - - + -
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Residues in contact with TYR 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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235A SER* 3.7 30.7 + - - -
236A TYR* 1.3 83.7 - - - +
238A GLU* 1.3 64.3 + - - +
239A LEU 3.9 2.5 - - - +
240A ASN 5.0 5.4 - - - -
241A GLN 3.4 8.5 - - - +
242A ARG* 3.3 49.8 - - + -
243A VAL 4.2 1.6 - - - +
393A CYS* 3.4 0.9 - - - -
394A TRP* 2.8 92.8 + + + +
396A GLU* 4.1 15.8 + - + -
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Residues in contact with GLU 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 TYR* 2.8 31.6 + - + +
237A TYR* 1.3 71.0 - - - +
239A LEU* 1.3 71.1 + - - +
241A GLN* 3.0 23.9 + - - +
243A VAL* 3.4 19.3 - - + +
275A ASN* 2.7 40.8 - - - +
278A ARG* 2.7 29.2 + - - -
282A VAL* 3.3 20.0 - - + -
286A ARG* 2.9 11.4 + - - -
392A PRO 3.1 11.0 - - - +
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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