Contacts of the strand formed by residues 225 - 230 (chain A) in PDB entry 3L81
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 GLU 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLY 3.5 4.2 + - - +
224A SER* 1.3 74.7 - - - +
226A MET* 1.3 62.2 + - - +
227A ARG* 4.6 15.8 + - - +
271A ARG* 3.7 43.9 + - + +
272A LEU 3.7 8.1 - - - +
273A GLN* 3.2 30.0 + - + +
274A PRO* 5.2 0.2 - - - -
425A ARG 4.0 0.5 - - - +
426A LEU* 3.6 4.3 - - - +
427A ALA* 2.9 39.6 + - + +
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Residues in contact with MET 226 (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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187A VAL* 4.0 10.3 - - + -
216A LEU* 3.6 46.7 - - + -
218A SER* 4.4 1.3 - - - +
220A LEU* 3.9 14.4 - - + -
225A GLU* 1.3 74.7 - - - +
227A ARG* 1.3 65.3 + - - +
228A ILE* 4.1 11.2 - - + -
271A ARG* 3.4 5.2 - - - +
272A LEU* 2.9 47.7 + - + +
274A PRO* 4.1 9.6 - - + +
424A LEU* 3.7 22.2 - - + -
425A ARG 3.5 4.9 - - - +
426A LEU* 3.5 25.6 - - + -
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Residues in contact with ARG 227 (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 GLU* 4.6 20.2 + - - +
226A MET* 1.3 75.5 - - - +
228A ILE* 1.3 62.8 + - - +
263A GLU* 6.1 3.4 - - - +
269A ILE* 4.2 13.6 - - + +
270A LEU 3.2 8.1 - - - +
271A ARG* 3.3 39.5 - - + +
423A PHE* 3.7 15.8 - - + -
424A LEU* 3.6 3.8 - - - +
425A ARG* 2.8 50.4 + - + +
427A ALA* 4.8 13.1 - - - +
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Residues in contact with ILE 228 (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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189A LEU* 3.9 27.4 - - + -
214A ILE* 5.0 4.0 - - + -
226A MET* 4.1 9.0 - - + -
227A ARG* 1.3 78.6 - - - +
229A GLY* 1.3 59.0 + - - +
230A LEU* 4.0 22.8 + - + +
268A ARG 3.9 0.9 - - - +
269A ILE* 3.3 2.6 - - - -
270A LEU* 2.8 46.8 + - + +
272A LEU* 4.2 15.9 - - + -
281A VAL* 4.1 27.1 - - + -
421A VAL* 4.0 13.0 - - + -
423A PHE* 3.5 11.2 - - - +
424A LEU* 4.0 16.4 - - + -
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Residues in contact with GLY 229 (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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228A ILE* 1.3 71.3 - - - +
230A LEU* 1.3 59.6 + - - -
267A HIS 5.4 0.9 - - - -
268A ARG 3.6 6.3 - - - -
269A ILE* 4.2 3.4 - - - -
421A VAL* 3.6 5.7 - - - +
422A ARG* 2.7 31.8 + - - -
423A PHE* 3.0 42.0 + - - +
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Residues in contact with LEU 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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214A ILE* 3.9 21.8 - - + -
228A ILE* 4.0 17.3 - - + +
229A GLY* 1.3 82.0 - - - +
231A THR* 1.3 67.5 + - - +
232A GLU* 3.1 6.6 + - - +
234A PHE* 3.7 31.0 - - + -
264A PHE* 4.3 10.1 - - + -
267A HIS 4.7 1.2 - - - +
268A ARG* 2.9 18.8 + - - +
270A LEU* 4.6 7.6 - - + -
282A MET* 3.8 28.0 - - + -
419A LEU* 4.2 7.2 - - + -
420A GLN 3.3 13.9 - - - +
421A VAL* 4.1 6.7 - - + -
422A ARG* 3.6 12.6 + - - +
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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