Contacts of the strand formed by residues 181 - 189 (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 TYR 181 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92G GLU* 4.8 4.1 + - - -
104H GLY* 5.0 4.9 - - - -
105H GLU* 3.5 27.1 + - + +
176N TYR* 3.4 28.3 - + + -
177N THR* 3.5 7.6 - - - -
178N PHE 3.5 7.6 + - - +
179N THR 3.3 0.8 - - - -
180N SER* 1.3 92.9 - - - +
182N THR* 1.3 64.4 + - - +
183N ILE* 3.8 3.5 + - - +
201N TYR* 4.2 3.6 - - - -
202N PRO* 3.2 18.4 - - - +
247N ARG* 3.6 58.4 + - + -
248N LYS 3.9 2.0 - - - +
249N SER* 3.5 38.4 - - - +
257N ASP* 5.0 0.4 - - - -
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Residues in contact with THR 182 (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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181N TYR* 1.3 75.1 - - - +
183N ILE* 1.3 60.0 + - - +
184N GLN* 2.8 27.3 + - - +
199N TYR* 4.1 13.2 - - + -
200N ILE 3.4 11.9 - - - -
201N TYR* 3.4 30.5 - - + -
247N ARG* 3.6 4.0 - - - -
248N LYS* 2.6 50.8 + - - +
249N SER 4.9 0.2 - - - +
250N SER* 4.5 13.5 - - - -
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Residues in contact with ILE 183 (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* 4.2 14.1 - - + -
171N CYS* 4.3 9.0 - - - -
173N ALA* 5.0 0.2 - - + -
176N TYR* 3.2 27.6 - - - +
178N PHE* 4.4 8.5 - - + -
181N TYR 4.3 5.6 - - - +
182N THR* 1.3 77.6 - - - +
184N GLN* 1.3 62.4 + - - +
185N TRP* 3.9 23.8 + - + +
199N TYR* 3.2 21.6 - - - -
200N ILE* 3.1 20.8 + - + -
202N PRO* 4.4 3.4 - - + -
228N VAL* 3.8 22.4 - - + -
245N CYS* 4.1 19.3 - - + -
246N ALA 3.6 3.8 - - - +
247N ARG* 4.4 7.4 - - + -
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Residues in contact with GLN 184 (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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115N TYR* 3.6 8.9 + - - -
182N THR* 2.8 23.4 + - - +
183N ILE* 1.3 73.0 - - - +
185N TRP* 1.3 60.8 + - - +
186N VAL* 4.7 0.2 - - - -
196N TRP* 2.5 37.7 + - + +
198N GLY 3.8 2.0 - - - -
199N TYR* 3.2 27.0 - - - +
244N TYR 3.6 0.2 - - - +
245N CYS* 3.2 1.9 - - - -
246N ALA* 2.5 53.2 + - - +
248N LYS* 3.6 33.1 - - + +
256N LEU* 3.8 23.6 - - + -
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Residues in contact with TRP 185 (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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155N GLN* 3.5 28.9 - - - -
169N MET* 3.7 36.6 - - + -
170N PRO 4.6 4.7 - - - -
171N CYS* 3.9 19.3 - - + -
183N ILE* 3.9 16.0 - - + +
184N GLN* 1.3 76.0 - - - +
186N VAL* 1.3 62.3 + - - +
196N TRP* 3.9 2.6 - - - -
197N ILE* 2.9 31.5 + - + +
198N GLY 2.9 17.0 + - - +
219N LEU* 3.4 25.4 - - + +
228N VAL* 3.6 18.3 - - + +
230N MET* 3.5 41.1 - - + -
243N TYR* 4.2 14.4 - - + -
244N TYR 3.4 12.1 - - - -
245N CYS* 4.1 11.9 - - + -
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Residues in contact with VAL 186 (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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117N PHE* 3.9 22.4 - - + -
184N GLN 4.6 2.2 - - - +
185N TRP* 1.3 81.1 - - - +
187N LYS* 1.3 60.0 + - - +
194N LEU* 3.6 28.7 - - + -
195N GLU 3.3 17.0 - - - +
196N TRP* 4.7 4.3 - - + -
197N ILE* 3.9 3.1 - - - -
242N VAL 3.8 0.5 - - - +
243N TYR* 3.3 3.5 - - - +
244N TYR* 2.7 46.1 + - + +
246N ALA* 4.7 0.4 - - + -
256N LEU* 3.8 28.5 - - + -
259N TRP* 3.9 17.7 - - + -
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Residues in contact with LYS 187 (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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186N VAL* 1.3 72.6 - - - +
188N GLN* 1.3 61.2 + - - +
189N THR* 3.6 24.1 - - + +
192N GLN* 4.7 6.9 + - - +
193N GLY 3.6 1.7 - - - +
194N LEU* 3.4 1.6 - - - -
195N GLU* 2.7 60.1 + - + +
197N ILE* 3.4 20.7 - - + +
213N PHE* 3.8 23.0 - - + -
238N GLU* 3.8 20.5 + - - +
239N ASP* 4.1 10.8 + - - +
241N ALA* 3.6 18.8 - - + -
242N VAL 3.6 3.6 - - - -
243N TYR* 3.7 24.9 - - + +
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Residues in contact with GLN 188 (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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57N GLN* 2.8 45.7 + - - +
106N TYR* 3.8 5.7 + - - -
187N LYS* 1.3 73.3 - - - +
189N THR* 1.3 70.7 + - - +
190N PRO* 4.5 1.6 - - + +
193N GLY* 3.6 5.7 - - - +
194N LEU* 3.6 27.1 - - + +
241N ALA* 3.2 4.5 - - - +
242N VAL* 2.7 45.9 + - + +
244N TYR* 3.1 27.6 + - + -
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Residues in contact with THR 189 (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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187N LYS* 3.6 21.7 - - + +
188N GLN* 1.3 81.2 - - - +
190N PRO* 1.3 68.0 - - - +
191N ARG* 3.1 30.0 + - - +
192N GLN* 2.7 42.3 + - + +
193N GLY* 3.2 21.6 + - - +
195N GLU* 5.1 1.8 - - - +
240N SER 4.2 0.9 - - - +
241N ALA* 3.5 20.4 - - + -
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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