Contacts of the strand formed by residues 174 - 181 (chain B) in PDB entry 3QNF
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 LEU 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B THR* 4.8 17.0 - - + -
167B TYR 3.7 5.4 - - - +
168B ARG* 4.6 4.3 - - + +
172B GLY 3.7 2.1 + - - +
173B GLU* 1.3 84.7 - - - +
175B ARG* 1.3 66.7 + - - +
176B ILE* 4.2 22.9 - - + -
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Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B THR* 3.3 5.4 - - - -
167B TYR* 2.9 78.3 + - + +
169B THR* 5.0 12.3 + - + -
173B GLU* 3.5 33.5 + - + +
174B LEU* 1.3 80.8 - - - +
176B ILE* 1.3 64.8 + - - +
212B ARG* 6.0 3.8 - - - +
253B ASP* 4.4 18.4 + - - +
273B PRO* 4.7 11.9 - - - +
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Residues in contact with ILE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 3.7 38.0 - - + +
72B THR 5.6 0.7 - - - +
74B LEU* 3.8 23.3 - - + -
155B LEU* 5.8 0.9 - - + -
164B LYS* 4.6 8.7 - - + -
165B SER 3.5 9.9 - - - +
166B THR* 4.0 15.9 - - + -
167B TYR* 5.4 0.4 - - - -
174B LEU* 4.2 14.4 - - + -
175B ARG* 1.3 76.7 - - - +
177B LEU* 1.3 73.6 + - - +
212B ARG* 5.4 8.7 + - - +
213B HIS* 4.5 10.7 + - - -
251B ILE 5.0 0.3 - - - +
252B SER* 5.3 0.2 - - - -
253B ASP* 3.7 15.8 - - - +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 4.8 2.5 - - - -
164B LYS* 3.6 4.0 - - - -
165B SER* 2.7 61.3 + - - +
167B TYR* 4.0 14.8 - - + -
176B ILE* 1.3 79.6 - - - +
178B ALA* 1.3 63.2 + - - +
179B SER* 4.1 11.2 - - - -
250B ILE* 5.2 0.7 - - + -
251B ILE 3.6 11.2 - - - +
252B SER* 4.3 11.0 - - - -
253B ASP* 5.3 2.0 - - - +
254B PHE* 3.7 20.9 - - + -
311B ILE* 4.0 18.4 - - + -
312B PRO* 3.4 34.3 - - + -
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 3.8 27.5 - - + +
155B LEU* 4.4 7.4 - - + -
162B PHE* 3.7 24.5 - - + -
163B TYR 3.5 7.0 - - - +
177B LEU* 1.3 72.9 - - - +
179B SER* 1.3 62.9 + - - +
250B ILE* 3.4 5.7 - - - +
251B ILE* 2.7 44.2 + - + +
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B PHE* 3.4 5.7 - - - -
163B TYR* 2.8 64.6 + - - -
177B LEU* 4.1 16.6 - - - -
178B ALA* 1.3 77.1 - - - +
180B THR* 1.3 68.9 + - - +
249B PHE 3.7 6.5 - - - -
250B ILE* 4.5 5.6 - - - +
311B ILE* 4.0 19.7 - - - +
314B PHE* 5.1 0.5 - - - -
326B THR* 5.3 1.9 - - - +
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Residues in contact with THR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B GLY 3.1 3.8 - - - -
162B PHE* 4.0 3.6 - - + -
163B TYR* 3.7 4.4 + - - -
179B SER* 1.3 86.1 + - - +
181B GLN* 1.3 68.0 + - - +
182B PHE* 3.4 33.0 - - + -
247B VAL 4.1 1.0 + - - -
248B ALA* 3.2 15.8 - - - +
249B PHE* 3.2 56.0 + - + +
250B ILE* 5.2 1.5 - - - +
314B PHE* 4.9 3.3 - - - -
321B ASN* 4.7 7.7 + - - +
326B THR* 5.0 4.5 + - - +
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Residues in contact with GLN 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B PHE 4.2 13.2 - - - +
160B HIS* 3.5 10.8 + - + +
161B GLY 2.8 28.4 + - - +
163B TYR* 3.7 17.7 - - + +
180B THR* 1.3 76.7 - - - +
182B PHE* 1.3 59.0 + - - +
183B GLU* 3.4 42.1 + - - +
186B ALA* 3.3 5.4 - - - +
314B PHE* 3.5 15.1 - - + -
316B SER* 4.6 15.5 - - - -
319B MET* 3.3 35.6 - - - +
321B ASN* 4.9 3.1 - - - +
326B THR* 4.5 0.2 + - - -
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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