Contacts of the strand formed by residues 234 - 239 (chain A) in PDB entry 5E63
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 TRP 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A THR* 5.2 2.9 - - + -
206A GLN 3.8 6.1 - - - +
207A HIS* 4.1 6.5 - + - -
208A ALA* 4.4 0.6 - - - +
228A LYS* 3.8 1.7 - - - +
229A ASP* 2.8 44.8 + - + +
231A ARG* 3.7 18.6 - - + -
232A GLY* 2.7 38.7 + - - -
233A PRO* 1.3 103.0 + - + +
235A LEU* 1.3 63.6 + - - +
236A TYR* 4.6 3.5 - - + +
13D T 4.1 11.9 - - + -
14D A 2.7 61.9 + + + -
15D T 3.6 29.4 - - + -
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Residues in contact with LEU 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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204A ILE 3.9 0.2 - - - +
205A THR* 3.6 1.4 - - - +
206A GLN 2.9 32.8 + - - +
207A HIS 4.6 0.2 - - - +
208A ALA* 3.7 26.9 - - + -
211A VAL* 3.7 41.7 - - + +
214A MET* 4.5 19.7 - - + -
226A ILE* 5.0 11.7 - - + -
227A GLU 3.3 13.9 - - - +
228A LYS* 3.8 21.1 - - + -
234A TRP* 1.3 79.5 - - - +
236A TYR* 1.3 75.0 + - - +
237A TYR 4.3 0.7 - - - -
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Residues in contact with TYR 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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203A GLN* 4.0 16.8 - - - +
204A ILE 3.4 3.4 - - - +
205A THR* 3.5 36.8 - - + -
225A PHE 3.5 1.0 - - - +
226A ILE* 3.2 7.8 - - - -
227A GLU* 2.8 64.2 + - + +
228A LYS 4.9 0.4 - - - -
229A ASP* 2.5 46.8 + - + -
234A TRP* 4.6 2.0 - - + -
235A LEU* 1.3 82.6 - - - +
237A TYR* 1.3 60.7 + - - +
238A THR* 3.8 10.4 + - - +
8B C 5.4 5.2 - - - -
9B T 4.8 3.4 - - - -
15D T 3.8 7.7 - - + +
16E C 3.1 27.6 + + - -
17E A 4.0 11.4 + - - -
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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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202A PHE* 3.9 19.3 - + - -
203A GLN* 3.2 4.7 - - - +
204A ILE* 2.8 52.4 + - + +
214A MET* 4.4 8.9 - - - -
217A LEU* 3.9 33.4 - - + -
218A ILE* 3.7 15.0 - - + -
221A LEU* 3.8 22.8 - - + +
223A CYS* 2.5 33.2 + - - -
224A GLY* 3.9 6.1 - - - -
225A PHE 3.5 3.1 - - - -
226A ILE* 3.7 23.3 - - + -
235A LEU 4.3 0.2 - - - -
236A TYR* 1.3 70.8 - - - +
238A THR* 1.3 57.1 + - - +
239A VAL* 3.6 25.0 - - + +
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Residues in contact with THR 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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201A VAL* 3.9 21.5 - - + -
202A PHE 3.5 4.3 - - - -
203A GLN* 3.1 20.5 + - - +
224A GLY* 3.1 3.9 - - - -
225A PHE* 2.9 70.1 + - + -
227A GLU* 3.4 14.8 + - - +
236A TYR* 3.8 5.6 - - - +
237A TYR* 1.3 71.5 - - - +
239A VAL* 1.3 64.6 + - - +
240A THR* 4.1 10.1 - - + -
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Residues in contact with VAL 239 (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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201A VAL* 3.3 6.4 - - - -
202A PHE* 3.0 36.8 + - + -
223A CYS* 3.9 12.6 - - + -
224A GLY* 3.8 8.3 - - - +
225A PHE* 4.8 1.1 - - - -
237A TYR* 3.6 30.3 - - + +
238A THR* 1.3 76.7 - - - +
240A THR* 1.3 60.3 + - - +
241A ASN* 4.0 4.5 - - + +
244A ASP* 3.8 27.4 - - + +
245A ILE* 3.5 26.1 - - + +
249A ILE* 4.1 9.2 - - + -
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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