Contacts of the helix formed by residues 174 - 182 (chain A) in PDB entry 1SY2
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 ASP 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A TYR* 5.5 4.2 - - - -
69A TYR* 3.6 19.9 + - - +
91A LYS* 4.3 13.5 + - - +
172A ALA 4.4 0.2 + - - -
173A TYR* 1.3 71.7 - - - +
175A ASN* 1.3 62.3 + - - +
176A ASP* 3.3 14.2 + - - +
177A SER* 2.7 40.5 + - - -
178A LEU* 3.2 16.6 + - - +
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Residues in contact with ASN 175 (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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22A VAL* 4.0 18.9 - - + +
24A TYR* 2.6 40.9 + - - -
173A TYR* 3.5 14.8 + - - +
174A ASP* 1.3 73.3 + - - +
176A ASP* 1.3 67.7 + - - +
178A LEU* 3.3 4.7 + - - +
179A LYS* 3.1 33.8 + - + +
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Residues in contact with ASP 176 (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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174A ASP* 3.2 10.4 - - - +
175A ASN* 1.3 81.9 + - - +
177A SER* 1.3 63.6 + - - +
179A LYS* 3.4 7.2 + - - +
180A SER* 3.0 25.4 + - - -
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Residues in contact with SER 177 (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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69A TYR* 4.1 14.8 - - - -
91A LYS* 3.6 31.9 + - - +
92A ASN* 5.0 2.6 + - - -
174A ASP* 2.7 35.8 + - - -
176A ASP* 1.3 77.0 - - - +
178A LEU* 1.3 56.5 + - - +
180A SER* 3.2 7.7 + - - -
181A LEU* 2.9 35.8 + - - +
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Residues in contact with LEU 178 (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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22A VAL* 4.1 17.5 - - + -
43A ALA* 3.9 28.0 - - + +
44A LEU 4.1 7.9 - - - +
45A ALA* 3.5 21.3 - - + +
56A ALA* 3.6 39.5 - - + +
57A LEU 3.8 22.4 - - - +
58A TYR* 3.9 13.9 - - + +
69A TYR* 4.3 8.3 - - + -
173A TYR* 5.6 2.9 - - + -
174A ASP 3.2 13.3 + - - +
175A ASN* 3.3 10.1 + - - +
177A SER* 1.3 78.4 - - - +
179A LYS* 1.3 63.1 + - - +
181A LEU* 3.4 7.8 + - + -
182A LEU 3.6 2.1 + - - -
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Residues in contact with LYS 179 (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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20A GLY 3.6 22.2 - - - +
21A ASP* 3.6 28.4 + - - +
22A VAL* 4.2 12.3 - - + -
45A ALA* 4.5 4.3 - - + -
175A ASN* 3.1 25.3 + - + +
176A ASP* 4.0 7.2 - - - +
178A LEU* 1.3 75.4 - - - +
180A SER* 1.3 63.3 + - - +
182A LEU* 3.3 23.9 + - + +
183A THR* 4.5 3.8 + - - +
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Residues in contact with SER 180 (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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91A LYS 4.6 5.0 + - - -
92A ASN* 5.8 1.4 + - - -
176A ASP 3.0 18.1 + - - -
177A SER* 3.2 12.3 + - - -
179A LYS* 1.3 78.4 - - - +
181A LEU* 1.3 61.6 + - - +
183A THR* 3.0 28.7 + - - -
184A LYS* 3.1 19.4 + - - +
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Residues in contact with LEU 181 (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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56A ALA* 3.6 25.1 - - + -
69A TYR* 3.5 42.0 - - + -
70A ASP 4.7 2.9 - - - +
71A VAL* 3.7 15.1 - - + +
89A VAL* 3.9 10.3 - - + -
90A ASP 3.8 3.6 - - - +
91A LYS 3.7 11.7 - - - +
92A ASN 4.1 1.3 - - - -
93A GLY* 3.4 39.0 - - - +
177A SER 2.9 24.2 + - - +
178A LEU* 3.7 0.9 - - - +
179A LYS 3.3 0.4 - - - -
180A SER* 1.3 75.2 - - - +
182A LEU* 1.3 65.1 + - - +
184A LYS* 3.0 22.3 + - + +
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Residues in contact with LEU 182 (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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20A GLY* 3.8 35.7 - - - +
45A ALA* 3.5 33.2 - - + +
47A GLY* 3.9 11.9 - - - +
48A THR 6.1 0.4 - - - +
49A ALA* 3.3 17.5 - - + +
54A LYS* 2.8 50.8 + - + +
56A ALA* 3.8 12.1 - - + +
71A VAL* 5.2 0.9 - - - -
178A LEU 3.6 6.7 + - - +
179A LYS* 3.3 16.4 + - - +
180A SER 3.1 0.8 - - - -
181A LEU* 1.3 77.2 - - - +
183A THR* 1.3 58.8 + - + +
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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