Contacts of the strand formed by residues 232 - 236 (chain W) in PDB entry 6NE3
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 HIS 232 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219W LEU* 3.5 46.7 - - + +
228W ILE* 3.5 32.9 + - + +
229W PRO 4.8 0.7 - - - -
230W GLY* 3.4 25.4 + - - -
231W PRO* 1.3 73.7 - - - +
233W MET* 1.3 65.5 + - - +
234W VAL* 4.3 1.5 - - + +
255W LEU* 5.3 1.1 - - + -
280W TRP* 5.1 0.2 - - - +
281W ASP 3.3 9.9 + - - -
282W VAL* 3.3 22.9 - - - +
283W CYS* 3.6 4.5 + - - -
303W ARG* 3.6 13.9 - - + -
304W TYR* 3.4 42.7 + + + +
306W VAL* 6.5 0.4 - - + -
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Residues in contact with MET 233 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232W HIS* 1.3 78.3 - - - +
234W VAL* 1.3 66.2 + - - +
235W LEU* 4.5 16.2 - - + -
283W CYS* 3.3 18.8 - - - +
285W THR* 5.6 4.7 - - - +
290W LEU* 4.7 10.1 - - - -
297W PHE* 4.9 4.7 - - + -
302W TRP* 3.5 56.5 - - + -
304W TYR 4.4 3.0 + - - +
305W LEU* 3.7 30.1 - - + -
306W VAL* 3.4 20.6 + - - +
327W PHE* 3.6 31.6 - - + -
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Residues in contact with VAL 234 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215W THR* 5.3 3.4 - - - +
219W LEU* 6.5 0.2 - - + -
232W HIS* 4.3 8.1 - - + +
233W MET* 1.3 79.9 - - - +
235W LEU* 1.3 63.9 + - - +
236W VAL* 3.8 16.8 + - + +
244W TRP* 3.8 39.7 - - + -
248W PHE* 4.7 5.2 - - + -
282W VAL* 4.3 12.6 - - + -
283W CYS 3.1 5.5 + - - -
284W VAL* 3.4 16.2 - - + +
285W THR* 2.9 28.6 + - - +
306W VAL* 3.3 19.1 - - + +
308W ASP* 5.0 1.1 - - + -
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Residues in contact with LEU 235 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233W MET* 4.5 13.2 - - + -
234W VAL* 1.3 73.9 - - - +
236W VAL* 1.3 60.4 + - - +
285W THR* 3.3 18.6 - - + +
286W SER 3.8 13.9 - - - +
287W TYR* 3.9 20.0 - - + -
290W LEU* 3.7 36.1 - - + -
305W LEU* 4.5 9.2 - - + -
306W VAL 3.0 8.2 + - - +
307W ILE* 4.0 33.9 - - + -
308W ASP* 2.7 35.3 + - - +
320W LEU* 5.7 5.8 - - + -
324W VAL* 4.5 7.0 - - + -
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Residues in contact with VAL 236 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234W VAL* 3.8 12.6 - - + +
235W LEU* 1.3 78.8 - - - +
237W PRO* 1.3 84.3 - - + +
240W THR* 4.3 4.5 - - - -
241W LEU* 3.7 37.2 - - + +
244W TRP* 3.5 36.1 - - + +
284W VAL* 5.2 1.1 - - + -
285W THR 3.4 7.4 + - - +
286W SER* 3.3 20.8 + - - -
287W TYR* 3.5 13.2 + - - -
308W ASP* 3.7 9.6 - - + -
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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