Contacts of the helix formed by residues 183 - 189 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181G SER* 2.9 12.4 + - - +
182G LEU* 1.3 88.7 - - - +
184G GLN* 1.3 64.2 + - - +
185G ALA 3.2 3.1 - - - -
186G ALA* 2.9 25.3 + - + +
187G LEU* 3.0 13.6 + - + +
32H LEU* 4.5 9.9 - - + +
36H ALA 4.9 0.6 + - - -
37H SER* 3.1 27.8 + - - -
38H ILE* 2.9 35.1 + - - +
47H ILE* 4.4 2.1 - - - +
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Residues in contact with GLN 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G LEU 3.8 7.5 + - - -
33G GLY* 2.9 32.3 + - - -
35G GLY* 4.0 1.2 - - - +
179G THR 4.7 1.0 - - - +
180G THR* 3.3 30.5 - - + -
181G SER* 2.9 39.2 + - - +
182G LEU 3.5 0.8 - - - -
183G ASN* 1.3 76.4 - - - +
185G ALA* 1.3 57.7 + - - +
187G LEU* 3.3 6.7 + - - +
188G TYR* 2.9 31.0 + - - +
214G LEU* 3.5 15.3 - - + -
218G CYS* 4.0 10.5 - - - -
222G PHE* 3.7 21.4 - - + -
252G PRO* 4.6 0.7 - - + -
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Residues in contact with ALA 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G ASN 3.2 0.4 - - - -
184G GLN* 1.3 79.4 - - - +
186G ALA* 1.3 63.3 + - - +
188G TYR* 4.5 0.4 - - - +
189G ARG* 2.9 31.8 + - - +
198G HIS* 3.3 27.8 - - + +
213G ILE 4.3 2.0 - - - +
214G LEU* 3.4 19.3 - - + +
215G HIS* 3.6 14.9 - - + +
252G PRO* 3.9 16.6 - - + +
38H ILE* 6.0 2.9 - - + -
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Residues in contact with ALA 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G ASN* 2.9 30.0 + - + +
185G ALA* 1.3 77.7 - - - +
187G LEU* 1.3 57.8 + - - +
189G ARG* 3.3 24.5 - - - +
190G LEU* 3.8 7.1 - - - +
198G HIS 5.0 0.6 + - - -
199G ILE* 4.5 4.5 - - + +
28H ILE* 5.0 0.5 - - - +
32H LEU* 3.5 16.4 - - + +
38H ILE* 4.3 13.3 - - + +
47H ILE* 3.9 25.9 - - + +
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Residues in contact with LEU 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G MET* 4.8 12.2 - - + +
32G LEU* 3.8 14.8 - - + +
33G GLY* 3.5 29.6 - - - +
183G ASN* 3.0 15.1 + - + +
184G GLN* 3.8 7.0 - - - +
186G ALA* 1.3 76.1 - - - +
188G TYR* 1.3 66.8 + - - +
189G ARG 3.2 1.6 - - - -
190G LEU* 3.0 38.3 + - + +
191G SER* 4.3 1.4 + - - -
32H LEU* 3.9 12.8 - - + +
187H LEU* 3.8 32.3 - - + -
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Residues in contact with TYR 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G MET 5.9 0.2 - - - -
30G TYR* 3.4 39.4 + + - -
33G GLY* 3.7 30.4 - - - +
34G VAL* 4.2 2.9 - - + -
62G VAL* 5.5 1.9 - - - +
63G ILE* 4.4 10.6 - - + +
66G GLN* 4.9 4.1 + - - -
184G GLN 2.9 19.1 + - - +
185G ALA 4.1 1.6 - - - +
187G LEU* 1.3 77.0 - - - +
189G ARG* 1.3 63.4 + - - +
191G SER* 3.0 22.1 + - - -
193G ASP* 5.3 6.4 + - + -
215G HIS* 3.4 44.0 - + + +
217G LEU* 3.3 27.3 + - + +
218G CYS* 3.7 26.9 - - + -
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Residues in contact with ARG 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G ALA 2.9 22.7 + - - +
186G ALA* 3.3 24.0 - - - +
188G TYR* 1.3 71.3 - - - +
190G LEU* 1.3 60.0 + - + +
191G SER 2.8 11.6 + - - -
192G GLY* 2.9 15.2 + - - -
193G ASP 3.3 25.7 + - - +
194G TRP* 3.1 47.8 + - + +
195G ASN 4.7 2.4 + - - -
198G HIS 5.3 0.6 - - - -
199G ILE* 3.7 27.6 - - - +
215G HIS* 3.5 13.1 - - - +
28H ILE* 4.5 0.4 - - - +
47H ILE 3.7 17.2 + - - -
48H TYR* 3.7 13.3 - - - -
49H GLU* 2.7 42.8 + - - -
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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