Contacts of the strand formed by residues 229 - 237 (chain A) in PDB entry 1EGA
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 TYR 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLN* 2.8 29.1 + - - -
221A PHE* 3.6 23.3 - + - -
222A VAL 3.3 15.9 - - - -
223A SER* 5.3 4.9 - - - -
224A ASN* 4.8 0.2 - - - -
228A GLY* 1.3 74.4 - - - -
230A ASP* 1.3 61.6 + - - +
231A ILE* 3.6 6.5 + - + -
269A PHE* 4.1 22.4 - + + -
270A GLU* 4.9 3.6 - - + -
271A ALA* 3.7 28.3 - - + -
272A PRO 3.4 7.8 + - - +
273A VAL* 3.2 25.1 - - + +
274A HIS* 3.1 25.6 + - - +
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Residues in contact with ASP 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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220A ARG* 3.0 43.5 + - - +
221A PHE* 3.3 0.2 - - - -
222A VAL* 2.8 38.5 + - + +
223A SER 4.6 0.3 - - - +
224A ASN* 2.7 28.9 - - - +
228A GLY 4.1 0.6 + - - -
229A TYR* 1.3 69.2 - - - +
231A ILE* 1.3 60.3 + - - +
232A ASN* 4.2 1.8 - - - +
274A HIS* 3.7 30.3 + - - +
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Residues in contact with ILE 231 (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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194A ALA* 4.4 0.7 - - + -
218A ILE* 4.3 19.1 - - + -
220A ARG 3.2 5.4 - - - +
221A PHE* 3.2 44.6 - - + -
229A TYR* 3.6 11.5 + - + -
230A ASP* 1.3 76.3 - - - +
232A ASN* 1.3 65.1 + - - +
265A MET* 3.1 41.5 - - + -
269A PHE* 4.5 0.4 - - + -
273A VAL* 3.7 24.5 - - + -
274A HIS 3.2 11.9 + - - +
275A LEU* 3.2 15.4 - - + +
276A GLU 2.9 24.3 + - - -
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Residues in contact with ASN 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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218A ILE* 3.4 4.9 - - - -
219A GLU* 2.9 60.7 + - + +
220A ARG* 2.8 43.3 + - + +
230A ASP* 4.8 0.9 - - - +
231A ILE* 1.3 78.8 + - - +
233A GLY* 1.3 61.3 + - - +
274A HIS 5.3 0.7 - - - +
276A GLU* 3.2 41.1 + - - +
278A TRP* 3.7 3.2 - - - +
293A ARG* 4.2 4.0 - - - +
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Residues in contact with GLY 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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198A ILE* 4.2 13.5 - - - -
217A GLU 3.8 3.4 - - - -
218A ILE* 4.2 2.7 - - - -
219A GLU* 4.7 0.4 - - - -
231A ILE 4.1 1.6 + - - -
232A ASN* 1.3 74.2 - - - +
234A LEU* 1.3 61.2 + - - +
235A ILE* 4.2 0.4 - - - -
275A LEU* 4.4 1.4 - - - +
276A GLU 2.8 14.3 + - - +
277A LEU* 3.9 20.0 - - - +
278A TRP* 2.8 31.5 + - - +
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Residues in contact with LEU 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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198A ILE* 5.3 0.6 - - - +
215A THR 3.4 5.7 - - - +
216A VAL* 3.6 1.1 - - - -
217A GLU* 2.8 55.4 + - + +
219A GLU* 4.4 20.9 - - + +
233A GLY* 1.3 73.7 - - - +
235A ILE* 1.3 61.9 + - - +
236A LEU* 3.6 28.7 + - + +
278A TRP* 3.5 27.6 - - + +
280A LYS* 4.7 11.2 - - + +
285A TRP* 3.9 22.0 - - + -
293A ARG* 4.2 5.4 - - - +
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Residues in contact with ILE 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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198A ILE* 4.0 24.7 - - + -
202A LEU* 3.8 31.9 - - + -
214A VAL* 3.9 24.2 - - + -
215A THR 3.6 3.4 - - - +
216A VAL* 4.9 2.5 - - + -
233A GLY 5.3 0.2 - - - -
234A LEU* 1.3 73.3 - - - +
236A LEU* 1.3 60.7 + - - +
237A VAL* 5.5 0.7 - - + -
246A VAL* 4.2 15.5 - - + -
254A ILE* 4.1 25.4 - - + -
257A ILE* 4.8 1.8 - - + -
277A LEU* 4.3 14.1 - - + -
278A TRP 2.9 13.8 + - - +
279A VAL* 3.4 8.7 - - + +
280A LYS 2.9 23.4 + - - +
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Residues in contact with LEU 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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213A SER 4.1 1.6 - - - +
214A VAL* 3.6 7.0 - - - +
215A THR* 2.8 55.3 + - + +
217A GLU* 3.9 22.4 - - + +
234A LEU* 4.1 22.4 - - + +
235A ILE* 1.3 73.0 - - - +
237A VAL* 1.3 60.1 + - - +
280A LYS* 3.0 43.5 - - + +
282A LYS* 3.9 29.8 - - + +
303A SO4 5.7 0.4 - - - +
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Residues in contact with VAL 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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211A PRO* 5.1 3.6 - - + -
213A SER 4.7 2.5 - - - -
214A VAL* 4.9 10.3 - - + +
235A ILE* 4.1 0.9 - - + +
236A LEU* 1.3 75.6 - - - +
238A GLU* 1.3 65.7 + - - +
239A ARG 3.2 9.0 - - - +
242A GLN* 2.9 41.5 - - + +
243A LYS* 4.0 13.0 - - + +
246A VAL* 5.0 7.6 - - + -
279A VAL* 3.9 21.3 - - + -
280A LYS 2.8 20.9 + - - +
281A VAL* 3.4 3.9 - - - +
282A LYS* 3.0 30.9 + - - +
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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