Contacts of the strand formed by residues 161 - 168 (chain C) 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 GLY 161 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C HIS* 1.3 71.8 - - - +
162C PHE* 1.3 58.5 + - - -
163C TYR* 3.4 5.0 - - - -
180C THR* 3.2 4.3 - - - -
181C GLN 2.9 37.0 + - - -
182C PHE* 3.8 6.3 - - - -
186C ALA* 3.4 31.5 - - - +
189C MET* 3.9 8.1 - - - -
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Residues in contact with PHE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ILE* 3.6 24.0 - - + -
69C ALA* 3.7 15.3 - - + -
76C PHE* 4.0 20.5 - + + -
154C ASN 4.9 0.3 - - - +
155C LEU* 3.6 19.3 - - + -
156C SER* 2.9 23.1 + - - -
160C HIS 3.7 0.8 + - - -
161C GLY* 1.3 70.8 - - - -
163C TYR* 1.3 59.7 + - - +
178C ALA* 3.8 22.0 - - + -
179C SER 3.4 17.5 - - - -
180C THR* 3.8 4.0 - - + -
182C PHE* 4.2 0.6 - - - -
189C MET* 4.7 9.1 + - - +
190C ALA* 4.0 20.6 - - + +
249C PHE* 3.5 35.0 - + - -
251C ILE* 3.8 25.1 - - + -
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Residues in contact with TYR 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C LEU* 4.7 3.6 - - - -
156C SER* 3.2 24.0 - - - +
159C PHE* 3.6 50.3 - + + +
160C HIS 3.7 1.3 - - - +
161C GLY 3.4 12.3 - - - -
162C PHE* 1.3 75.6 - - - +
164C LYS* 1.3 72.1 + - - +
165C SER* 3.8 14.4 + - - -
178C ALA* 3.5 5.1 - - - -
179C SER* 2.9 49.0 + - - -
180C THR 3.7 22.7 + - - -
181C GLN* 3.8 10.9 - - + +
311C ILE* 4.0 4.1 - - + +
313C ASP 5.5 1.6 - - - -
314C PHE* 3.4 34.9 - - - -
315C GLN 5.5 0.2 + - - -
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Residues in contact with LYS 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU* 4.4 31.6 - - + -
155C LEU* 4.4 12.3 - - + +
156C SER 3.1 14.3 + - - +
157C GLU* 5.3 6.1 - - - +
159C PHE* 4.3 10.0 - - - -
163C TYR* 1.3 80.9 - - - +
165C SER* 1.3 59.8 + - - +
166C THR* 5.4 3.6 - - + -
176C ILE* 4.6 7.2 - - + -
177C LEU 3.6 7.0 - - - +
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Residues in contact with SER 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C PHE* 4.5 4.9 - - - -
163C TYR* 3.8 15.7 + - - -
164C LYS* 1.3 73.9 - - - +
166C THR* 1.3 68.2 + - - +
176C ILE* 3.6 1.7 - - - +
177C LEU* 2.8 56.9 + - - -
179C SER* 5.4 0.2 - - - -
311C ILE* 4.2 6.3 - - - +
312C PRO* 4.2 2.5 - - - +
313C ASP* 3.5 31.5 + - - +
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Residues in contact with THR 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C LYS* 5.4 3.8 - - + -
165C SER* 1.3 83.4 + - - +
167C TYR* 1.3 67.3 + - - +
174C LEU* 4.7 17.3 - - + -
175C ARG 3.5 5.6 - - - +
176C ILE* 3.8 29.4 - - + -
312C PRO* 3.7 14.3 - - - +
313C ASP* 5.1 5.9 + - - +
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Residues in contact with TYR 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C THR* 1.3 77.5 - - - +
168C ARG* 1.3 68.3 + - - +
169C THR* 4.0 8.6 + - - -
174C LEU* 4.6 2.4 - - - +
175C ARG* 2.9 66.4 + - + +
176C ILE 5.4 0.2 - - - -
177C LEU* 4.0 17.9 - - + -
253C ASP* 2.4 34.6 + - - -
272C VAL* 3.5 40.6 - - + -
273C PRO* 3.2 19.2 - - + +
274C ASP* 4.5 9.6 - - - -
312C PRO* 4.0 13.9 - - + -
329C GLU* 5.6 0.9 - - - +
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Residues in contact with ARG 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C TYR* 1.3 79.9 - - - +
169C THR* 1.3 67.6 + - - +
172C GLY* 2.7 37.2 + - - -
173C GLU* 3.4 5.6 - - - +
174C LEU* 3.2 43.9 - - + +
274C ASP* 3.8 5.9 - - - +
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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