Contacts of the strand formed by residues 232 - 240 (chain A) in PDB entry 4NAK
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A GLY 3.5 24.7 - - - -
207A VAL 3.4 20.4 - - - -
208A PRO* 3.6 20.9 - - + -
209A ALA* 4.5 3.4 - - - -
230A THR* 3.7 32.0 + - + +
231A LEU* 1.3 84.2 - - - +
233A GLU* 1.3 61.3 + - - +
234A MET* 3.7 24.7 + - + +
275A VAL* 3.8 21.8 - - + -
277A GLN* 3.6 39.9 - - + -
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Residues in contact with GLU 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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182A ARG* 5.2 8.5 + - - -
206A GLY* 3.2 5.0 - - - -
207A VAL* 2.8 52.1 + - + +
208A PRO 5.4 0.2 - - - +
209A ALA* 4.1 15.9 - - + +
210A LYS 5.6 1.2 + - - -
232A TRP* 1.3 70.6 - - - +
234A MET* 1.3 72.0 + - - +
235A GLN* 4.3 5.2 - - + +
280A TYR* 5.5 2.9 - - - -
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Residues in contact with MET 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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182A ARG* 3.7 12.8 + - - -
204A VAL* 3.6 32.3 - - + -
205A LEU 3.9 0.9 - - - -
206A GLY* 4.4 0.7 - - - -
232A TRP* 3.7 35.2 + - + +
233A GLU* 1.3 82.8 - - - +
235A GLN* 1.3 66.7 + - - +
238A GLN* 4.5 6.7 - - - +
275A VAL* 4.1 22.4 - - + -
401A PBQ 4.4 15.3 - - + -
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Residues in contact with GLN 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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182A ARG* 3.7 21.0 - - - +
204A VAL* 3.4 7.1 - - - +
205A LEU* 2.7 31.2 + - + +
206A GLY* 4.8 0.9 - - - -
207A VAL* 3.7 26.6 - - + +
233A GLU* 4.3 10.8 - - + +
234A MET* 1.3 76.7 - - - +
236A THR* 1.3 66.1 + - - +
238A GLN* 3.2 23.6 + - - -
278A GLY* 4.5 0.7 - - - -
279A SER 3.0 29.0 + - - +
280A TYR* 4.6 3.0 + - - +
282A ASN* 3.0 41.2 + - - +
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Residues in contact with THR 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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84A LEU* 6.6 0.2 - - + -
157A ARG* 6.2 0.4 - - - +
177A ILE* 3.8 9.0 - - + +
178A HIS* 2.8 28.3 + - - -
179A ASP* 3.1 27.2 + - + +
182A ARG* 3.6 14.8 - - - +
205A LEU* 3.8 3.5 - - - +
235A GLN* 1.3 81.1 - - - +
237A PRO* 1.3 75.5 - - - +
238A GLN* 3.9 17.7 - - + +
282A ASN* 2.9 23.0 + - - -
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Residues in contact with PRO 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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116A PHE* 3.9 13.5 - - + -
176A CYS* 3.6 32.1 - - - -
177A ILE 3.2 9.0 - - - +
178A HIS* 3.5 15.0 - - - +
185A VAL* 3.8 10.1 - - + -
190A VAL* 4.4 4.7 - - + -
193A VAL* 4.0 18.8 - - + +
204A VAL* 3.7 1.0 - - - -
205A LEU* 3.2 46.1 + - + +
236A THR* 1.3 84.7 - - - +
238A GLN* 1.3 60.8 + - - +
239A VAL* 4.1 3.1 - - + -
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Residues in contact with GLN 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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175A VAL 3.8 0.7 - - - +
177A ILE* 2.9 46.4 + - + +
203A ALA 3.6 4.5 - - - -
204A VAL* 3.7 13.2 - - + +
234A MET* 4.5 7.7 - - - +
235A GLN 3.2 21.3 + - - +
236A THR* 3.9 14.9 - - + +
237A PRO* 1.3 76.6 - - - +
239A VAL* 1.3 60.8 + - - +
401A PBQ 3.0 44.6 + - + +
403A CD 2.4 30.6 - - - -
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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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174A LEU* 3.5 32.8 - - + -
175A VAL 3.3 6.5 - - - +
176A CYS* 4.2 5.2 - - - -
193A VAL* 3.9 35.2 - - + +
194A LEU* 3.9 20.9 - - + -
197A GLY* 3.9 15.9 - - - -
202A ALA* 3.2 4.0 - - - -
203A ALA 2.7 41.7 + - - +
237A PRO* 4.1 9.4 - - + -
238A GLN* 1.3 75.6 - - - +
240A ILE* 1.3 62.5 + - - +
401A PBQ 3.3 3.0 - - - +
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Residues in contact with ILE 240 (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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174A LEU* 4.2 4.0 - - - -
175A VAL* 2.7 44.9 + - + +
177A ILE* 4.3 12.6 - - + -
201A GLY 3.4 11.9 - - - +
202A ALA* 4.3 2.5 - - + -
239A VAL* 1.3 78.2 - - - +
241A LYS* 1.3 71.0 + - - +
244A LEU* 4.0 17.0 - - + +
245A LEU* 3.9 48.9 - - + +
265A ILE* 5.7 0.4 - - + -
266A VAL* 3.7 30.1 - - + -
269A LEU* 5.0 1.3 - - + -
401A PBQ 4.2 13.9 - - + -
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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