Contacts of the strand formed by residues 182 - 186 (chain F) in PDB entry 3NO1
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 182 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ILE* 3.3 15.4 - - - +
156F ALA* 3.1 18.7 + - - +
175F TYR* 4.9 0.9 - - - +
180F LEU* 3.3 8.8 + - - +
181F ALA* 1.3 81.2 - - - +
183F VAL* 1.3 61.9 + - - +
210F PHE* 3.4 19.5 - - - -
211F ILE 3.0 13.7 - - - -
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Residues in contact with VAL 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ILE* 3.7 7.2 - - - +
156F ALA 3.0 15.7 - - - +
158F GLY* 3.8 13.0 - - - +
172F MSE 3.6 24.5 - - + -
175F TYR* 4.0 18.4 - - + -
182F GLY* 1.3 74.1 - - - +
184F LYS* 1.3 72.2 + - - +
185F PHE* 3.9 12.3 - - + +
210F PHE* 3.7 4.9 - - + -
211F ILE 2.8 10.9 + - - +
212F ILE* 3.3 28.9 - - + -
213F CYS* 2.9 27.1 + - - +
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Residues in contact with LYS 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F ILE* 3.9 13.4 - - + +
156F ALA 2.8 7.7 + - - -
157F ILE* 3.6 30.1 - - + +
158F GLY 3.0 22.3 + - - +
183F VAL* 1.3 71.9 - - - +
185F PHE* 1.3 60.2 + - - +
186F LYS* 3.7 1.5 + - - +
213F CYS* 3.5 19.7 - - + +
214F ILE 4.7 0.4 - - - -
215F ASP* 3.7 32.5 - - + +
239F TRP* 5.1 2.9 - - - -
241F GLU* 3.2 30.0 + - - +
318F HIS* 4.2 8.5 - - - +
338F GLU* 2.7 44.6 + - - -
397F MG 4.0 3.0 - - - -
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Residues in contact with PHE 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F GLY 3.6 2.2 - - - -
159F GLY* 3.3 23.1 - - - -
168F ILE* 3.9 39.0 - - + -
171F GLU* 4.3 1.3 - - - -
172F MSE 4.1 19.1 - - + -
183F VAL* 3.6 10.0 - - + -
184F LYS* 1.3 71.3 - - - +
186F LYS* 1.3 67.1 + - - +
187F VAL* 3.6 0.3 + - - +
198F ARG* 3.4 47.3 - - + -
199F ILE* 3.3 31.4 - - + -
202F ALA* 4.2 9.4 - - + -
212F ILE* 4.8 4.5 - - + -
213F CYS 2.8 16.2 + - - +
214F ILE* 3.2 7.7 - - + +
215F ASP* 3.0 22.2 + - - -
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Residues in contact with LYS 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ILE* 3.5 30.4 - - + +
158F GLY 3.0 21.3 + - - +
159F GLY 3.6 11.4 + - - +
160F TYR* 4.1 28.3 - - + +
161F TYR* 4.5 8.7 - - + -
184F LYS* 4.7 1.3 - - - +
185F PHE* 1.3 73.3 - - - +
187F VAL* 1.3 62.8 + - - +
198F ARG* 3.1 29.7 + - - -
215F ASP* 3.4 18.6 + - + +
217F ASN* 3.1 37.0 + - - +
318F HIS* 6.0 2.2 + - - -
340F PHE* 6.2 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