Contacts of the helix formed by residues 183 - 189 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181E SER* 2.9 12.8 + - - +
182E LEU* 1.3 84.8 - - - +
184E GLN* 1.3 64.0 + - - +
185E ALA 3.1 3.1 - - - -
186E ALA* 2.9 23.0 + - + +
187E LEU* 2.9 15.2 + - + +
32F LEU* 4.5 7.5 - - + +
36F ALA 4.4 3.1 + - - +
37F SER* 2.9 30.0 + - - -
38F ILE* 2.7 36.1 + - - +
47F ILE* 4.2 2.3 - - - +
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Residues in contact with GLN 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU 4.0 7.7 + - - -
33E GLY* 3.0 30.7 + - - -
35E GLY* 4.1 1.0 - - - +
179E THR 4.7 1.0 - - - +
180E THR* 3.3 29.6 - - + -
181E SER* 2.9 34.9 + - - +
182E LEU 3.5 0.6 - - - -
183E ASN* 1.3 76.6 - - - +
185E ALA* 1.3 58.8 + - - +
187E LEU* 3.3 7.4 + - - +
188E TYR* 2.9 30.1 + - - +
214E LEU* 3.6 15.9 - - + -
218E CYS* 4.0 9.6 - - - -
222E PHE* 3.7 23.7 - - + -
252E PRO* 4.6 0.4 - - + -
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Residues in contact with ALA 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E ASN 3.1 0.6 - - - -
184E GLN* 1.3 75.5 - - - +
186E ALA* 1.3 66.5 + - - +
188E TYR* 4.5 0.4 - - - +
189E ARG* 3.0 31.2 + - - +
198E HIS* 3.3 26.9 - - + +
213E ILE 4.4 1.8 - - - +
214E LEU* 3.4 13.1 - - + +
215E HIS* 3.6 15.2 - - + +
252E PRO* 3.8 22.6 - - + +
38F ILE* 5.8 3.4 - - + -
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Residues in contact with ALA 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E ASN* 2.9 28.6 + - + +
185E ALA* 1.3 78.6 - - - +
187E LEU* 1.3 57.4 + - - +
189E ARG* 3.3 25.3 - - - +
190E LEU* 3.8 6.8 - - - +
198E HIS 5.0 0.4 + - - -
199E ILE* 4.5 4.9 - - + +
28F ILE* 5.0 0.5 - - - +
32F LEU* 3.6 14.7 - - + +
38F ILE* 4.2 12.6 - - + +
47F ILE* 3.8 27.3 - - + +
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Residues in contact with LEU 187 (chain E).
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* 4.9 12.1 - - + +
32E LEU* 3.8 15.0 - - + +
33E GLY* 3.5 32.4 - - - +
183E ASN* 2.9 14.9 + - + +
184E GLN* 3.8 7.2 - - - +
186E ALA* 1.3 76.5 - - - +
188E TYR* 1.3 66.2 + - - +
189E ARG 3.2 1.8 - - - -
190E LEU* 3.1 37.5 + - + +
191E SER* 4.3 1.0 + - - -
32F LEU* 3.9 13.0 - - + -
187F LEU* 4.0 31.0 - - + -
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Residues in contact with TYR 188 (chain E).
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 5.9 0.2 - - - -
30E TYR* 3.5 37.2 + + - -
33E GLY* 3.7 30.0 - - - +
34E VAL* 4.2 3.8 - - + -
62E VAL* 5.5 1.6 - - - +
63E ILE* 4.6 10.1 - - + +
66E GLN* 5.1 3.1 + - - -
184E GLN 2.9 17.3 + - - +
185E ALA 4.1 1.8 - - - +
187E LEU* 1.3 78.5 - - - +
189E ARG* 1.3 63.0 + - - +
191E SER* 3.0 23.1 + - - -
193E ASP* 5.3 6.2 + - + -
215E HIS* 3.3 45.3 - + + +
217E LEU* 3.3 28.6 + - + +
218E CYS* 3.8 28.7 - - + -
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Residues in contact with ARG 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ALA 3.0 22.3 + - - +
186E ALA* 3.3 24.2 + - - +
188E TYR* 1.3 72.2 - - - +
190E LEU* 1.3 61.4 + - + +
191E SER 2.8 10.9 + - - -
192E GLY* 2.9 14.0 + - - -
193E ASP 3.4 25.6 + - - +
194E TRP* 3.1 49.9 + - - +
195E ASN 4.8 2.2 + - - -
198E HIS 5.5 0.2 - - - -
199E ILE* 3.7 29.1 - - - +
215E HIS* 3.6 12.9 - - - +
28F ILE* 4.5 0.4 - - - +
47F ILE 3.7 16.0 + - - -
48F TYR* 3.8 12.7 - - - -
49F GLU* 2.6 43.4 + - - -
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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