Contacts of the strand formed by residues 241 - 249 (chain N) in PDB entry 7K63
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 ALA 241 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187N LYS* 3.6 24.5 - - + -
188N GLN 3.2 15.3 - - - +
189N THR* 3.5 20.4 - - + +
190N PRO* 5.3 1.8 - - - -
239N ASP 3.1 5.9 + - - +
240N SER* 1.3 76.8 - - - +
242N VAL* 1.3 63.4 + - - +
243N TYR* 3.2 11.2 - - + -
264N SER* 4.6 2.0 - - - -
265N VAL 3.0 27.1 + - - -
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Residues in contact with VAL 242 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60N TRP* 6.0 7.2 - - + -
186N VAL 3.8 0.5 - - - +
187N LYS* 3.6 0.9 - - - -
188N GLN* 2.7 47.2 + - + +
241N ALA* 1.3 74.5 - - - +
243N TYR* 1.3 61.8 + - - +
244N TYR* 3.4 39.1 - - + +
261N GLN 5.1 0.4 - - - +
262N GLY* 4.0 16.8 - - - -
263N THR 3.6 5.4 - - - +
264N SER* 4.0 20.2 - - - +
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Residues in contact with TYR 243 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155N GLN* 2.4 28.8 + - - -
169N MET* 3.9 22.4 - - + -
185N TRP* 4.2 9.0 - - + -
186N VAL 3.3 4.3 - - - +
187N LYS* 3.7 25.1 - - + +
197N ILE* 3.5 31.6 - - + -
213N PHE* 5.5 1.0 - + - -
230N MET* 4.2 7.0 - - + -
232N LEU* 3.4 27.9 - - + +
239N ASP* 3.1 29.3 + - - +
241N ALA* 3.2 24.7 - - + -
242N VAL* 1.3 73.2 - - - +
244N TYR* 1.3 55.8 + - - +
262N GLY* 3.3 0.9 - - - -
263N THR 2.9 28.4 + - - +
265N VAL* 3.9 18.4 - - + -
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Residues in contact with TYR 244 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57N GLN* 4.3 2.2 - - - -
60N TRP* 5.3 4.5 - - - -
61N LYS 3.8 11.3 + - - -
62N SER* 3.9 18.8 - - - -
63N PRO* 4.1 7.2 - - + -
155N GLN* 3.8 2.2 - - - -
184N GLN 3.6 0.2 - - - +
185N TRP* 3.4 5.6 - - - -
186N VAL* 2.7 45.1 + - - +
188N GLN* 3.1 41.9 + - + -
194N LEU* 4.7 3.4 - - + -
242N VAL* 3.4 28.2 - - + +
243N TYR* 1.3 74.1 - - - +
245N CYS* 1.3 61.6 - - - +
259N TRP* 3.5 31.2 - + + -
260N GLY 3.3 19.1 - - - +
261N GLN 3.5 19.4 + - - -
262N GLY* 3.5 8.3 - - - -
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Residues in contact with CYS 245 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N LEU* 4.0 8.3 - - + -
155N GLN* 3.4 29.0 + - - +
171N CYS* 3.3 35.4 - - - -
183N ILE* 4.1 10.3 - - + -
184N GLN 3.3 4.0 - - - -
185N TRP* 4.1 17.2 - - + -
244N TYR* 1.3 74.7 - - - +
246N ALA* 1.3 60.8 + - - +
259N TRP* 3.3 5.2 - - - +
260N GLY* 2.8 39.6 + - - -
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Residues in contact with ALA 246 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N LEU* 4.4 0.9 - - - -
183N ILE* 4.4 2.7 - - - +
184N GLN* 2.5 50.1 + - - +
186N VAL* 4.7 1.1 - - + -
245N CYS* 1.3 78.1 - - - +
247N ARG* 1.3 63.0 + - - +
256N LEU* 3.6 36.1 - - + -
258N TYR 3.3 5.8 - - - +
259N TRP* 4.0 19.1 - - + -
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Residues in contact with ARG 247 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H GLU* 4.5 6.7 + - - -
151N VAL* 3.6 21.3 - - - +
153N LEU* 3.7 14.6 - - + +
176N TYR* 3.6 44.6 - - - +
181N TYR* 3.6 52.1 + - + -
182N THR 3.6 5.8 - - - +
183N ILE* 4.4 4.9 - - + -
246N ALA* 1.3 73.4 - - - +
248N LYS* 1.3 59.9 + - - +
256N LEU* 3.3 3.6 - - - -
257N ASP* 2.6 64.3 + - - +
258N TYR* 2.8 36.0 + - + +
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Residues in contact with LYS 248 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N HIS* 4.0 15.2 - - - -
115N TYR* 4.2 20.4 + - + -
181N TYR* 4.2 3.1 - - - -
182N THR* 2.6 41.7 + - - +
184N GLN* 3.6 34.5 - - + +
246N ALA 3.6 0.2 + - - -
247N ARG* 1.3 76.2 - - - +
249N SER* 1.3 70.6 + - - +
250N SER 4.9 1.6 + - - -
251N ARG 3.2 25.7 + - - -
252N LEU* 4.2 7.1 + - - +
254N SER 3.2 14.9 + - - +
255N THR 3.5 21.5 - - - +
256N LEU* 3.7 15.9 - - + -
257N ASP* 4.7 0.9 - - - -
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Residues in contact with SER 249 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G GLU* 3.8 8.3 + - - -
105H GLU* 3.3 24.4 - - - +
180N SER 4.4 1.4 + - - -
181N TYR* 3.5 27.0 - - - +
182N THR* 4.5 0.9 + - - +
248N LYS* 1.3 98.5 + - - +
250N SER* 1.3 65.8 + - - +
251N ARG* 3.0 14.3 + - - +
254N SER* 3.5 25.8 - - - -
255N THR 4.5 1.0 + - - -
257N ASP* 5.3 2.9 + - - -
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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