Contacts of the helix formed by residues 183 - 189 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A SER* 2.9 12.1 + - - +
182A LEU* 1.3 85.1 - - - +
184A GLN* 1.3 64.9 + - - +
185A ALA 3.1 3.1 - - - -
186A ALA* 2.9 23.3 + - + +
187A LEU* 2.9 13.9 + - + +
32B LEU* 4.3 12.2 - - + +
36B ALA 4.6 0.6 + - - -
37B SER* 2.9 33.0 + - - -
38B ILE* 2.7 35.5 + - - +
47B ILE* 4.0 4.2 - - - +
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Residues in contact with GLN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU 3.8 8.5 + - - -
33A GLY* 3.0 31.3 + - - -
35A GLY* 4.1 1.0 - - - +
179A THR 4.7 1.0 - - - +
180A THR* 3.3 30.3 - - + -
181A SER* 2.9 39.0 + - - +
182A LEU 3.5 0.2 - - - -
183A ASN* 1.3 76.1 - - - +
185A ALA* 1.3 58.1 + - - +
187A LEU* 3.2 7.3 + - - +
188A TYR* 2.9 29.8 + - - +
214A LEU* 3.7 14.6 - - + -
218A CYS* 4.1 3.6 - - - -
222A PHE* 3.7 29.2 - - + -
252A PRO* 4.6 1.1 - - + +
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Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ASN* 3.1 0.8 - - - -
184A GLN* 1.3 78.2 - - - +
186A ALA* 1.3 63.8 + - - +
188A TYR* 4.5 0.7 - - - +
189A ARG* 3.0 30.9 + - - +
198A HIS* 3.3 26.7 - - + +
214A LEU* 3.5 15.5 - - + +
215A HIS* 3.8 14.0 - - + +
252A PRO* 3.8 23.5 - - + +
38B ILE* 5.9 2.7 - - + -
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ASN* 2.9 27.8 + - + +
185A ALA* 1.3 79.0 - - - +
187A LEU* 1.3 57.3 + - - +
189A ARG* 3.3 25.4 + - - +
190A LEU* 3.8 8.3 - - - +
198A HIS 5.0 0.4 + - - -
199A ILE* 4.5 5.8 - - + +
28B ILE* 4.9 0.9 - - - +
32B LEU* 3.7 13.1 - - + +
38B ILE* 4.2 11.7 - - + +
47B ILE* 3.7 28.8 - - + +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A MET* 4.8 13.8 - - + +
32A LEU* 3.9 15.7 - - + +
33A GLY* 3.6 30.0 - - - +
183A ASN* 2.9 11.1 + - + +
184A GLN* 3.7 11.0 - - - +
186A ALA* 1.3 76.5 - - - +
188A TYR* 1.3 66.5 + - - +
189A ARG 3.2 1.8 - - - -
190A LEU* 3.0 38.6 + - + +
191A SER* 4.3 1.4 + - - -
32B LEU* 3.9 13.5 - - + -
187B LEU* 4.0 30.7 - - + -
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Residues in contact with TYR 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A MET 5.9 0.2 - - - -
30A TYR* 3.4 41.0 + + - -
33A GLY* 3.6 31.8 - - - +
34A VAL* 4.3 3.8 - - + -
62A VAL* 5.6 1.2 - - - +
63A ILE* 4.5 11.0 - - + +
66A GLN* 5.0 4.5 + - - -
184A GLN 2.9 18.1 + - - +
185A ALA* 4.1 2.0 - - - +
187A LEU* 1.3 77.0 - - - +
189A ARG* 1.3 64.3 + - - +
191A SER* 2.9 24.0 + - - -
193A ASP* 5.3 5.3 + - + -
215A HIS* 3.4 44.9 - + + +
217A LEU* 3.4 25.4 + - + +
218A CYS* 3.7 27.6 - - + -
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ALA 3.0 22.4 + - - +
186A ALA* 3.3 23.5 + - - +
188A TYR* 1.3 72.5 - - - +
190A LEU* 1.3 60.1 + - + +
191A SER 2.8 11.3 + - - -
192A GLY* 2.9 14.9 + - - -
193A ASP 3.3 25.6 + - - +
194A TRP* 3.0 51.8 + - - +
195A ASN 4.8 2.0 + - - -
198A HIS 5.3 0.9 - - - -
199A ILE* 3.7 27.7 - - - +
215A HIS* 3.6 12.4 - - - +
28B ILE* 4.6 0.8 - - - +
47B ILE 4.0 13.7 + - - -
48B TYR* 3.8 12.3 - - - -
49B GLU* 2.7 44.3 + - - -
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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