Contacts of the helix formed by residues 183 - 189 (chain F) in PDB entry 1S9C
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 ASN 183 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E LEU* 4.3 11.8 - - + +
36E ALA 4.8 0.8 + - - -
37E SER* 3.0 31.7 + - - -
38E ILE* 2.8 37.6 + - - +
47E ILE* 4.0 4.2 - - - +
181F SER* 2.9 12.6 + - - +
182F LEU* 1.3 84.8 - - - +
184F GLN* 1.3 63.7 + - - +
185F ALA 3.2 3.1 - - - -
186F ALA* 3.0 12.9 + - + +
187F LEU* 3.0 23.2 + - + +
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Residues in contact with GLN 184 (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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32F LEU 3.9 6.9 + - - -
33F GLY* 2.9 32.3 + - - -
35F GLY* 4.2 1.6 - - - +
179F THR 4.7 1.2 - - - +
180F THR* 3.3 30.6 - - + -
181F SER* 2.9 38.7 + - - +
182F LEU 3.5 0.4 - - - -
183F ASN* 1.3 76.7 - - - +
185F ALA* 1.3 58.5 + - - +
187F LEU* 3.1 6.8 + - - +
188F TYR* 2.8 30.3 + - - +
214F LEU* 3.7 15.0 - - + -
218F CYS* 4.1 3.1 - - - -
222F PHE* 3.7 28.3 - - + -
252F PRO* 4.7 0.9 - - + -
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Residues in contact with ALA 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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38E ILE* 6.2 2.5 - - + -
183F ASN 3.2 0.6 - - - -
184F GLN* 1.3 79.4 - - - +
186F ALA* 1.3 63.3 + - - +
188F TYR* 4.5 0.4 - - - -
189F ARG* 3.0 31.6 + - - +
198F HIS* 3.3 27.1 - - + +
213F ILE 4.4 1.3 - - - +
214F LEU* 3.5 14.4 - - + +
215F HIS* 3.8 13.3 - - + +
252F PRO* 3.8 22.4 - - + +
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Residues in contact with ALA 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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28E ILE* 4.9 2.8 - - - +
32E LEU* 3.8 12.4 - - + +
38E ILE* 4.4 10.9 - - + +
47E ILE* 3.8 26.3 - - + +
183F ASN* 3.0 28.2 + - + +
185F ALA* 1.3 77.9 - - - +
187F LEU* 1.3 58.0 + - - +
189F ARG* 3.4 25.1 - - - +
190F LEU* 3.8 8.7 - - - +
198F HIS 5.0 0.2 + - - -
199F ILE* 4.5 6.5 - - + +
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Residues in contact with LEU 187 (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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29E MET* 5.6 0.2 - - + -
32E LEU* 4.0 14.5 - - + +
187E LEU* 4.0 30.3 - - + -
29F MET* 4.9 13.4 - - + +
32F LEU* 3.9 14.6 - - + +
33F GLY* 3.6 29.4 - - - +
183F ASN* 3.0 11.3 + - + +
184F GLN* 3.7 10.1 - - - +
186F ALA* 1.3 76.9 - - - +
188F TYR* 1.3 66.9 + - - +
189F ARG 3.2 1.6 - - - -
190F LEU* 3.0 38.4 + - + +
191F SER* 4.3 1.4 + - - -
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Residues in contact with TYR 188 (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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29F MET 6.0 0.2 - - - -
30F TYR* 3.4 39.7 + + - -
33F GLY* 3.8 30.0 - - - +
34F VAL* 4.2 3.6 - - + -
62F VAL* 5.6 1.4 - - - +
63F ILE* 4.5 11.0 - - + +
66F GLN* 5.0 3.7 + - - -
184F GLN 2.8 17.7 + - - +
185F ALA* 4.1 2.5 - - - +
187F LEU* 1.3 77.8 - - - +
189F ARG* 1.3 62.7 + - - +
191F SER* 3.0 24.0 + - - -
193F ASP* 5.3 5.7 + - + -
215F HIS* 3.5 44.6 - + + +
217F LEU* 3.4 26.2 + - + +
218F CYS* 3.8 26.9 - - + -
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Residues in contact with ARG 189 (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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28E ILE* 4.7 1.0 - - - +
47E ILE 4.2 7.2 + - - -
48E TYR* 4.0 8.1 - - - -
49E GLU* 2.7 44.9 + - - -
185F ALA 3.0 21.5 + - - +
186F ALA* 3.4 24.9 + - - +
188F TYR* 1.3 72.7 - - - +
190F LEU* 1.3 60.7 + - + +
191F SER 2.9 10.7 + - - -
192F GLY* 3.0 13.2 + - - -
193F ASP 3.3 25.7 + - - +
194F TRP* 3.0 52.2 + - - +
195F ASN 4.8 1.8 + - - -
198F HIS 5.3 0.9 - - - -
199F ILE* 3.7 38.0 - - - +
215F HIS* 3.7 11.8 + - - +
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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