Contacts of the helix formed by residues 183 - 189 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32G LEU* 4.2 13.8 - - + +
36G ALA 4.8 0.8 + - - -
37G SER* 3.2 28.5 + - - -
38G ILE* 3.1 33.1 + - - +
181H SER* 2.9 12.0 + - - +
182H LEU* 1.3 87.3 - - - +
184H GLN* 1.3 65.2 + - - +
185H ALA 3.2 2.7 - - - -
186H ALA* 3.0 24.5 + - + +
187H LEU* 3.0 14.6 + - + +
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Residues in contact with GLN 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LEU 3.8 7.7 + - - -
33H GLY* 2.9 31.9 + - - -
35H GLY* 4.1 1.2 - - - +
179H THR 4.7 1.2 - - - +
180H THR* 3.3 21.4 - - + -
181H SER* 2.9 47.7 + - - +
182H LEU 3.5 0.6 - - - -
183H ASN* 1.3 77.4 - - - +
185H ALA* 1.3 57.8 + - - +
187H LEU* 3.2 7.2 + - - +
188H TYR* 2.8 30.8 + - - +
214H LEU* 3.6 14.8 - - + -
218H CYS* 4.0 9.9 - - - -
222H PHE* 3.7 22.4 - - + -
252H PRO* 4.5 1.1 - - + +
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Residues in contact with ALA 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G ILE* 6.2 2.2 - - + -
183H ASN* 3.2 0.8 - - - -
184H GLN* 1.3 79.0 - - - +
186H ALA* 1.3 64.9 + - - +
188H TYR* 4.5 0.2 - - - -
189H ARG* 3.0 30.6 + - - +
198H HIS* 3.3 26.7 - - + +
213H ILE 4.4 1.8 - - - +
214H LEU* 3.4 20.2 - - + +
215H HIS* 3.6 15.6 - - + +
252H PRO* 3.9 16.4 - - + +
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Residues in contact with ALA 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G ILE* 4.9 2.6 - - - +
32G LEU* 3.4 14.9 - - + +
38G ILE* 4.5 8.4 - - + +
47G ILE* 3.9 24.6 - - + +
183H ASN* 3.0 28.9 + - + +
185H ALA* 1.3 78.4 - - - +
187H LEU* 1.3 57.5 + - - +
189H ARG* 3.3 24.5 - - - +
190H LEU* 3.8 8.1 - - - +
198H HIS 5.0 0.4 + - - -
199H ILE* 4.5 8.0 - - + +
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Residues in contact with LEU 187 (chain H).
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* 3.9 13.0 - - + +
187G LEU* 3.8 31.6 - - + -
29H MET* 4.8 12.4 - - + +
32H LEU* 3.8 15.0 - - + +
33H GLY* 3.5 31.1 - - - +
183H ASN* 3.0 12.4 + - + +
184H GLN* 3.7 10.8 - - - +
186H ALA* 1.3 76.1 - - - +
188H TYR* 1.3 66.4 + - - +
189H ARG 3.2 1.8 - - - -
190H LEU* 3.1 36.8 + - + +
191H SER* 4.3 1.0 + - - -
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Residues in contact with TYR 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H TYR* 3.4 39.3 + + - -
33H GLY* 3.7 30.4 - - - +
34H VAL* 4.2 3.6 - - + -
62H VAL* 5.5 1.4 - - - +
63H ILE* 4.5 10.5 - - + +
66H GLN* 5.0 3.0 + - - -
184H GLN 2.8 17.3 + - - +
185H ALA* 4.1 2.2 - - - +
187H LEU* 1.3 77.2 - - - +
189H ARG* 1.3 62.9 + - - +
191H SER* 2.9 24.6 + - - -
193H ASP* 5.3 6.2 + - + -
215H HIS* 3.5 44.9 - + + +
217H LEU* 3.4 26.7 + - + +
218H CYS* 3.8 26.9 - - + -
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Residues in contact with ARG 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G ILE* 4.4 0.8 - - - +
47G ILE 3.8 15.6 + - - -
48G TYR* 4.0 8.1 - - - -
49G GLU* 2.7 43.9 + - - -
185H ALA 3.0 21.8 + - - +
186H ALA* 3.3 24.2 + - - +
188H TYR* 1.3 73.1 - - - +
190H LEU* 1.3 55.5 + - + +
191H SER 2.7 16.2 + - - -
192H GLY* 2.9 15.4 + - - -
193H ASP 3.4 24.7 + - - +
194H TRP* 3.1 49.5 + - + +
195H ASN 4.7 1.8 + - - -
198H HIS* 5.3 0.4 - - - +
199H ILE* 3.7 31.8 - - - +
215H HIS* 3.7 12.2 + - - +
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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