Contacts of the strand formed by residues 176 - 186 (chain A) in PDB entry 1QU2
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 ILE 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A PHE* 2.9 63.9 - - + +
170A MET* 3.8 15.5 + - + -
171A ALA* 3.3 26.6 - - + +
174A GLY* 3.5 3.9 - - - -
175A LEU* 1.3 85.8 + - - +
177A TYR* 1.3 68.0 + - - +
412A TRP* 3.8 24.5 - - + -
413A PHE 3.4 9.0 - - - +
414A ALA* 5.1 1.3 - - + -
453A ILE* 4.6 8.3 - - + -
475A MET* 4.2 14.2 - - - +
529A PHE* 6.0 1.1 - - + -
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Residues in contact with TYR 177 (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 GLY 6.1 0.2 - - - -
175A LEU 4.6 5.2 - - - -
176A ILE* 1.3 78.8 - - - +
178A LYS* 1.3 73.2 + - - +
179A GLY* 4.8 2.7 - - - -
412A TRP* 3.6 10.8 - - - -
413A PHE* 2.9 77.5 + + + +
415A SER* 4.5 10.3 - - - -
418A LYS* 5.4 6.5 - - - -
450A GLU* 3.5 34.2 + - - +
475A MET* 5.6 0.2 - - - -
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Residues in contact with LYS 178 (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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177A TYR* 1.3 85.5 - - - +
179A GLY* 1.3 64.7 + - - +
410A PRO* 3.9 25.1 - - - +
411A GLN 3.6 9.9 - - - +
412A TRP* 3.8 32.1 - - + +
467A TYR* 2.8 40.0 + - + +
472A GLU* 4.4 12.6 + - - +
473A ILE* 4.1 18.8 - - + +
521A GLU* 4.3 2.9 + - - -
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Residues in contact with GLY 179 (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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177A TYR* 4.9 4.0 - - - -
178A LYS* 1.3 78.6 - - - +
180A LYS* 1.3 75.2 + - - +
410A PRO* 3.2 6.8 - - - +
411A GLN 2.8 25.1 + - - -
413A PHE* 4.0 9.2 - - - -
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Residues in contact with LYS 180 (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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179A GLY* 1.3 84.8 - - - +
181A LYS* 1.3 64.6 + - - +
335A TYR* 2.7 33.5 + - + +
345A VAL* 4.7 32.4 - - + +
408A ALA* 4.6 12.6 - - + +
409A THR 3.1 10.5 - - - +
410A PRO* 3.9 22.7 - - + -
411A GLN 4.0 1.3 - - - +
413A PHE* 3.6 9.8 - - - -
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Residues in contact with LYS 181 (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 LYS* 1.3 78.1 - - - +
182A PRO* 1.3 88.5 + - + +
183A VAL* 3.7 9.1 + - + +
332A GLU* 3.9 24.6 + - - +
335A TYR* 4.2 11.7 - - + -
336A ILE* 6.4 2.0 - - - -
407A ARG 3.5 0.2 - - - +
408A ALA* 3.8 2.2 - - - +
409A THR* 2.6 37.2 + - - +
411A GLN* 4.1 13.5 - - + -
413A PHE* 4.1 8.1 - - + -
452A VAL* 3.9 34.9 - - + +
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Residues in contact with PRO 182 (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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181A LYS* 1.3 107.9 + - + +
183A VAL* 1.3 64.0 + - - +
328A PRO 3.4 23.3 - - - +
329A GLY 4.8 0.4 - - - -
330A HIS* 4.8 0.9 - - - -
331A GLY 3.3 38.6 - - - +
332A GLU* 4.6 7.5 - - - +
335A TYR* 3.6 20.0 - - + -
406A PHE* 4.2 13.4 - - + -
407A ARG 3.2 13.7 - - - +
408A ALA* 4.6 3.8 - - + -
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Residues in contact with VAL 183 (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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181A LYS* 3.7 14.6 - - + +
182A PRO* 1.3 81.4 - - - +
184A TYR* 1.3 73.9 + - - +
185A TRP* 3.1 8.8 + - + +
192A SER* 4.0 17.9 - - - -
193A LEU 5.5 2.0 - - - +
406A PHE* 3.5 9.6 - - - -
407A ARG 2.9 30.6 + - - +
409A THR* 4.0 15.0 - - + +
411A GLN* 4.2 21.5 - - + +
456A GLN* 5.6 1.1 - - - +
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Residues in contact with TYR 184 (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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183A VAL* 1.3 73.7 - - - +
185A TRP* 1.3 58.1 + - - +
192A SER* 3.3 8.0 - - - -
193A LEU* 3.0 41.0 + - + +
194A ALA* 5.0 0.2 - - - -
195A GLU* 2.7 47.3 + - + -
198A ILE* 3.7 25.6 - - + -
200A TYR* 3.4 12.9 + - - -
395A PRO* 4.4 16.1 - - + +
404A VAL* 3.8 20.9 - - + -
405A ILE 3.7 3.6 - - - -
406A PHE* 3.7 37.7 - + - +
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Residues in contact with TRP 185 (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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183A VAL* 3.9 8.7 - - + +
184A TYR* 1.3 74.9 - - - +
186A SER* 1.3 68.3 + - - +
187A PRO* 3.2 14.9 - - + +
190A GLU 3.7 5.6 - - - -
191A SER* 3.6 26.9 - - - +
192A SER* 3.5 33.4 - - - -
349A ILE* 6.3 0.7 - - + -
350A ASP 5.0 1.3 - - - -
351A ASP* 3.5 35.3 + - - +
404A VAL* 3.6 4.2 - - - +
405A ILE* 2.6 43.8 + - + +
407A ARG* 3.1 50.3 - - + +
409A THR* 3.8 24.0 - - + -
456A GLN* 6.5 0.9 - - + -
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Residues in contact with SER 186 (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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185A TRP* 1.3 74.7 - - - +
187A PRO* 1.3 52.9 - - - +
188A SER* 3.4 7.6 + - - -
189A SER* 3.1 13.4 + - - -
190A GLU* 2.7 35.2 + - - -
191A SER 3.0 16.3 + - - -
193A LEU* 3.6 20.8 - - - +
397A ASP* 2.8 30.3 + - - +
403A PRO 4.7 1.5 + - - -
404A VAL* 4.1 8.1 - - - -
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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