Contacts of the strand formed by residues 230 - 237 (chain A) in PDB entry 4C02
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A THR* 3.3 20.2 + - - -
180A LEU* 2.9 48.9 + - + +
181A ALA 4.9 0.3 + - - -
226A SER* 3.5 4.1 + - - -
227A TRP* 2.9 48.3 + - + +
228A GLN 4.7 3.4 - - - +
229A GLY* 1.3 79.3 - - - +
231A ASN* 1.3 69.4 + - - +
232A VAL* 4.1 1.4 - - - +
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Residues in contact with ASN 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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180A LEU* 5.2 0.3 - - - +
211A LEU* 4.8 2.4 - - - +
224A ARG* 2.9 32.3 + - - +
225A GLY 3.3 7.4 - - - +
226A SER* 5.2 1.6 - - - -
229A GLY 4.3 0.4 + - - -
230A GLU* 1.3 79.5 - - - +
232A VAL* 1.3 67.2 + - - +
284A HIS* 5.9 0.2 - - - -
285A TYR* 3.8 29.5 + - + +
1516A EDO 3.0 40.0 + - - -
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 3.5 30.7 - - + -
204A VAL* 6.3 0.4 - - + -
208A ILE* 4.0 30.3 - - + -
224A ARG* 3.7 4.5 - - - +
225A GLY* 2.9 46.4 + - - +
226A SER 4.3 0.4 - - - +
227A TRP* 4.6 5.6 - - + +
230A GLU 4.1 4.5 - - - +
231A ASN* 1.3 79.5 - - - +
233A ALA* 1.3 59.5 + - - +
234A VAL* 4.4 3.4 - - + -
266A ILE* 3.9 10.8 - - + -
282A ILE* 4.1 9.2 - - + -
283A THR 3.7 8.5 - - - +
285A TYR* 3.7 11.8 - - - +
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Residues in contact with ALA 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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222A VAL* 4.4 3.4 - - + -
223A TRP 3.4 6.7 - - - +
232A VAL* 1.3 74.6 - - - +
234A VAL* 1.3 62.9 + - - +
235A LYS 4.1 0.4 - - - -
281A LEU 3.7 0.3 - - - +
282A ILE* 3.2 6.4 - - - +
283A THR* 2.9 43.6 + - - +
284A HIS 3.9 1.3 - - - +
285A TYR* 3.8 8.2 - - + +
1507A TAK 3.4 44.4 - - + +
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Residues in contact with VAL 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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208A ILE* 4.2 19.7 - - + -
210A LEU* 3.9 25.4 - - + -
221A GLU 3.8 0.7 - - - +
222A VAL* 3.4 3.4 - - - -
223A TRP* 2.7 42.1 + - + +
225A GLY* 4.9 2.2 - - - -
232A VAL* 4.4 5.6 - - + -
233A ALA* 1.3 78.3 - - - +
235A LYS* 1.3 60.5 + - - +
236A ILE* 3.8 16.4 + - + +
280A TRP* 3.7 37.7 - - + -
281A LEU 3.5 4.0 - - - +
282A ILE* 4.3 11.9 - - + -
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Residues in contact with LYS 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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219A TYR* 3.8 34.9 - - - +
221A GLU 3.3 10.8 - - - +
222A VAL* 4.2 11.0 - - + +
233A ALA 4.1 0.6 - - - -
234A VAL* 1.3 71.0 - - - +
236A ILE* 1.3 63.6 + - - +
237A PHE* 3.7 43.1 - - + -
241A ASP* 5.7 0.4 + - - -
248A GLU* 4.7 6.1 + - - +
279A LEU 3.5 1.4 - - - +
280A TRP* 3.3 5.0 - - - -
281A LEU* 2.8 44.8 + - + +
354A ASP* 2.9 26.5 + - - +
1507A TAK 3.8 29.0 + - + +
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Residues in contact with ILE 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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210A LEU* 4.1 18.2 - - + -
219A TYR 4.2 0.2 - - - +
220A GLY* 3.3 0.7 - - - -
221A GLU* 2.8 45.8 + - + +
223A TRP* 3.8 27.1 - - + +
234A VAL* 3.9 14.1 - - + +
235A LYS* 1.3 76.3 - - - +
237A PHE* 1.3 67.9 + - - +
278A GLN* 3.8 37.2 - - + +
279A LEU 3.4 8.7 - - - +
280A TRP* 3.8 20.2 - - + +
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Residues in contact with PHE 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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219A TYR 3.5 7.6 - - - -
220A GLY* 4.2 0.2 - - - -
235A LYS* 3.7 36.1 - - + -
236A ILE* 1.3 79.9 - - - +
238A SER* 1.3 69.8 - - - +
239A SER 3.9 0.3 + - - -
241A ASP* 3.6 28.3 - - + +
244A SER* 4.0 11.9 - - - -
245A TRP* 3.5 42.4 - + + -
248A GLU* 3.7 20.9 - - + -
278A GLN* 5.8 0.5 - - - -
279A LEU* 3.0 34.8 + - + +
281A LEU* 3.8 25.8 - - + -
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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