Contacts of the strand formed by residues 226 - 235 (chain A) in PDB entry 2IBS
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 GLY 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLU* 4.6 19.5 - - - -
29A ASP* 6.5 0.9 - - - -
221A GLN 3.7 1.0 - - - +
222A GLU* 3.7 1.8 - - - -
223A SER* 2.8 36.4 + - - -
224A GLU 3.2 1.6 - - - -
225A SER* 1.3 82.1 + - - +
227A PHE* 1.3 65.5 + - - -
228A THR* 4.1 1.9 + - - -
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Residues in contact with PHE 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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26A GLU* 3.4 46.5 + - + -
27A VAL* 4.0 11.9 - - + -
30A PHE* 3.6 38.6 - - + +
192A LEU* 3.7 27.6 - - + -
195A VAL* 3.9 25.1 - - + -
220A THR* 4.1 14.4 - - - -
221A GLN 3.5 2.9 - - - -
222A GLU* 3.7 41.7 - - + -
226A GLY* 1.3 73.8 - - - -
228A THR* 1.3 61.2 + - - +
229A PRO* 4.0 1.9 - - - +
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Residues in contact with THR 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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220A THR* 3.3 5.4 - - - -
221A GLN* 2.9 53.6 + - + +
223A SER* 5.3 2.6 + - - -
225A SER* 5.5 2.9 + - - -
226A GLY 4.8 2.8 + - - -
227A PHE* 1.3 74.4 + - - +
229A PRO* 1.3 78.3 - - + +
230A ILE* 3.7 11.3 + - + +
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Residues in contact with PRO 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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30A PHE* 3.9 18.1 - - + -
34A LEU* 5.5 4.7 - - + -
190A TYR* 4.0 20.9 - - + -
218A TRP* 3.7 27.3 - - + -
219A ASP 3.6 5.4 - - - +
220A THR* 4.3 4.5 - - + -
227A PHE 4.0 1.8 - - - +
228A THR* 1.3 92.6 - - + +
230A ILE* 1.3 67.5 + - - +
231A LEU 4.4 0.3 + - - -
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Residues in contact with ILE 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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218A TRP* 3.4 4.1 - - - -
219A ASP* 2.6 57.7 + - + +
220A THR 4.6 0.9 - - - -
221A GLN* 4.5 22.7 - - + +
228A THR* 3.9 20.9 - - + +
229A PRO* 1.3 82.8 - - - +
231A LEU* 1.3 72.7 + - - +
232A TRP* 3.4 2.4 + - + -
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Residues in contact with LEU 231 (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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216A SER* 4.6 3.4 - - - +
217A LEU 3.8 11.4 - - - +
218A TRP* 3.4 48.6 - - + +
230A ILE* 1.3 79.8 - - - +
232A TRP* 1.3 61.0 + - - +
233A ALA 4.3 5.6 - - - +
234A GLU* 3.4 40.8 - - + +
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Residues in contact with TRP 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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217A LEU* 2.9 22.9 + - + +
219A ASP* 3.9 21.8 - - + +
230A ILE* 3.4 2.8 + - + -
231A LEU* 1.3 77.7 - - - +
233A ALA* 1.3 74.3 + - + +
245A PHE* 3.4 46.7 - + + -
246A GLU 2.9 25.9 + - - +
247A THR* 3.6 27.4 - - + -
386A THR* 5.1 4.3 - - + -
389A ARG* 3.6 21.3 - - - -
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Residues in contact with ALA 233 (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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215A LEU 4.4 0.2 - - - +
216A SER* 3.7 0.2 - - - -
217A LEU* 2.9 31.9 + - + +
231A LEU* 4.3 3.0 - - - +
232A TRP* 1.3 95.2 - - + +
234A GLU* 1.3 68.7 + - - +
235A TYR* 3.8 29.1 + - + +
246A GLU* 5.5 2.7 - - + +
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Residues in contact with GLU 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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215A LEU 3.6 4.7 - - - +
216A SER* 4.2 14.6 - - - +
231A LEU* 3.4 32.2 - - + +
233A ALA* 1.3 79.1 - - - +
235A TYR* 1.3 71.4 + - - +
236A PRO* 3.5 12.6 - - + +
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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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215A LEU* 2.7 59.7 + - + +
217A LEU* 5.0 7.4 - - + -
233A ALA* 3.8 29.1 - - + +
234A GLU* 1.3 79.2 - - - +
236A PRO* 1.3 63.0 - - - +
237A HIS 3.2 3.5 + - - -
238A TRP* 3.3 23.9 + + + +
243A ILE* 5.7 2.0 - - + -
244A ARG 4.0 14.4 + - - -
246A GLU* 2.6 40.3 + - - +
251A ARG* 4.5 9.7 + - - -
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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