Contacts of the helix formed by residues 174 - 182 (chain X) in PDB entry 2AT8
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58X TYR* 5.6 3.2 - - - -
69X TYR* 3.7 20.0 + - - +
91X LYS* 2.7 26.6 + - - +
172X ALA 4.4 0.4 + - - -
173X TYR* 1.3 71.9 - - - +
175X ASN* 1.3 60.9 + - - +
176X ASP* 3.2 14.6 + - - +
177X SER* 2.6 34.8 + - - -
178X LEU* 3.2 24.7 + - - +
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Residues in contact with ASN 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ASP* 5.0 4.0 + - - -
22X VAL* 3.7 28.2 - - + +
24X TYR* 2.5 40.0 + - - -
173X TYR* 3.4 11.3 + - - +
174X ASP* 1.3 74.5 + - - +
176X ASP* 1.3 67.3 + - - +
178X LEU* 3.2 4.9 + - - +
179X LYS* 3.0 37.9 + - + +
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Residues in contact with ASP 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174X ASP* 3.2 10.4 + - - +
175X ASN* 1.3 81.6 + - - +
177X SER* 1.3 58.4 + - - +
179X LYS* 3.4 7.2 + - - +
180X SER* 3.0 30.1 + - - -
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Residues in contact with SER 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X TYR* 4.4 7.2 - - - -
91X LYS* 3.4 37.5 + - - +
92X ASN* 4.8 3.1 + - - -
174X ASP* 2.6 35.9 + - - -
176X ASP* 1.3 77.5 - - - +
178X LEU* 1.3 56.6 + - - +
180X SER* 3.2 7.0 + - - -
181X LEU* 2.9 37.5 + - - +
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Residues in contact with LEU 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X VAL* 4.1 19.1 - - + -
43X ALA* 3.9 28.5 - - + +
44X LEU 4.2 4.9 - - - +
45X ALA* 3.5 15.3 - - + +
56X ALA* 3.5 45.7 - - + +
57X LEU 3.8 21.8 - - - +
58X TYR* 3.9 13.2 - - + +
69X TYR* 4.2 9.4 - - + -
173X TYR* 5.4 4.0 - - + -
174X ASP 3.2 16.0 + - - +
175X ASN* 3.2 10.3 + - - +
177X SER* 1.3 79.0 - - - +
179X LYS* 1.3 62.9 + - - +
181X LEU* 3.4 6.0 + - + -
182X LEU 3.5 2.1 + - - -
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Residues in contact with LYS 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X GLY 3.6 21.8 - - - +
21X ASP* 3.6 28.4 + - - +
22X VAL* 4.2 12.3 - - + -
45X ALA* 4.5 4.5 - - + -
175X ASN* 3.0 28.7 + - + +
176X ASP* 3.9 7.4 - - - +
178X LEU* 1.3 75.9 - - - +
180X SER* 1.3 63.4 + - - +
182X LEU* 3.3 22.6 + - - +
183X THR* 4.5 3.6 + - - +
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Residues in contact with SER 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91X LYS 4.6 4.5 + - - -
92X ASN* 5.8 0.9 - - - -
176X ASP 3.0 18.5 + - - -
177X SER* 3.2 13.2 + - - -
179X LYS* 1.3 77.3 - - - +
181X LEU* 1.3 61.4 + - - +
183X THR* 2.9 34.0 + - - -
184X LYS* 3.8 11.7 - - - +
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Residues in contact with LEU 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X ALA* 3.6 24.0 - - + -
69X TYR* 3.5 42.0 - - + -
70X ASP 4.6 3.6 - - - +
71X VAL* 3.6 18.5 - - + +
89X VAL* 3.9 9.6 - - + -
90X ASP 3.8 3.1 - - - +
91X LYS 3.6 11.7 - - - +
92X ASN 4.1 1.3 - - - -
93X GLY* 3.4 39.5 - - - +
177X SER 2.9 25.7 + - - +
178X LEU* 4.6 0.7 - - - -
179X LYS 3.2 0.4 - - - -
180X SER* 1.3 76.4 + - - +
182X LEU* 1.4 63.4 + - - +
184X LYS* 3.0 20.5 + - + +
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Residues in contact with LEU 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X GLY* 3.7 36.8 - - - +
45X ALA* 3.5 33.4 - - + +
47X GLY* 3.9 11.2 - - - +
48X THR 6.1 0.2 - - - -
49X ALA* 3.4 17.0 - - + +
54X LYS* 2.8 51.7 + - + +
55X GLU 5.7 0.4 - - - -
56X ALA* 3.8 12.3 - - - +
71X VAL* 5.7 0.4 - - - -
178X LEU 3.5 6.7 + - - +
179X LYS* 3.3 16.4 + - + +
180X SER 3.0 1.0 + - - -
181X LEU* 1.4 78.4 - - - +
183X THR* 1.3 58.2 + - + +
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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