Contacts of the strand formed by residues 229 - 234 (chain A) in PDB entry 3MZ2
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 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR 4.6 6.2 - - - +
205A MSE 3.4 10.6 - - - +
206A PHE* 3.7 6.7 - - + -
208A ALA* 3.8 17.7 - - + -
219A TYR* 4.1 17.7 - - + -
224A ILE* 3.7 31.0 - - + +
225A PRO 3.8 7.4 - - - +
226A TRP* 3.0 55.6 + - + +
227A SER 3.4 1.1 - - - -
228A HIS* 1.3 82.4 - - - +
230A MSE 1.3 75.9 + - - +
231A ALA* 4.2 2.9 - - + +
253A VAL* 3.9 18.0 - - + +
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Residues in contact with MSE 230 (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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48A TYR* 3.8 27.8 - - + +
59A SER* 6.1 0.2 - - - -
87A THR* 5.9 0.4 - - - +
160A ILE* 4.0 12.3 - - + -
185A MSE 3.9 23.3 - - + -
205A MSE 3.6 0.6 - - + +
206A PHE 2.9 11.3 + - - +
207A GLU* 3.3 29.2 - - + +
208A ALA 2.9 24.9 + - - -
229A ILE* 1.3 76.4 - - - +
231A ALA* 1.3 74.1 + - - +
253A VAL* 4.4 0.4 - - - -
254A MSE 3.7 11.0 - - + +
256A MSE 3.9 20.2 - - - +
286A ILE* 3.4 33.7 - - + -
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA 3.4 4.3 - - - -
210A VAL* 3.6 25.1 - - + -
229A ILE* 4.5 1.1 - - + -
230A MSE 1.3 77.4 - - - +
232A TYR* 1.3 55.5 + - - +
233A VAL* 3.7 3.2 + - + +
248A LEU* 3.7 16.6 - - + -
253A VAL* 3.7 19.9 - - + +
254A MSE 2.9 11.9 + - - +
255A CYS* 3.3 2.6 - - - -
256A MSE 2.8 33.1 + - - +
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Residues in contact with TYR 232 (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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207A GLU* 3.8 23.3 - - + +
208A ALA 2.9 12.0 + - - +
209A PHE* 3.6 46.4 - + + -
210A VAL 2.7 31.5 + - - +
211A LYS* 4.3 8.0 - - + +
230A MSE 4.0 1.6 + - - -
231A ALA* 1.3 70.6 - - - +
233A VAL* 1.3 56.1 + - - +
234A GLY* 3.3 41.8 - - - -
235A PRO* 3.6 9.0 - - - +
256A MSE 3.6 27.6 - - + -
258A SER* 3.5 27.0 - - - -
261A PRO* 5.4 2.4 - - - +
288A GLU* 5.0 0.9 - - - -
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A VAL 3.4 20.9 - - - +
211A LYS* 4.1 13.4 - - - +
231A ALA* 4.2 3.4 - - + +
232A TYR* 1.3 74.4 - - - +
234A GLY* 1.3 56.9 + - - +
236A LYS 4.7 0.7 - - - +
241A VAL* 3.9 34.7 - - + +
244A VAL* 4.5 4.0 - - + -
245A ILE* 4.2 15.0 - - + -
248A LEU* 3.9 22.4 - - + -
255A CYS* 4.0 16.6 - - + -
256A MSE 2.9 25.6 + - - +
257A ILE* 3.8 20.2 - - + -
284A VAL* 5.4 0.2 - - + -
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Residues in contact with GLY 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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211A LYS* 4.2 7.6 - - - -
232A TYR* 3.3 24.6 - - - -
233A VAL* 1.3 80.1 - - - +
235A PRO* 1.3 71.4 - - - +
236A LYS 3.4 3.6 - - - -
257A ILE* 3.3 10.8 - - - +
258A SER 3.0 21.7 + - - -
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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