Contacts of the helix formed by residues 176 - 180 (chain D) in PDB entry 1DXO
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 LEU 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D PHE* 3.9 21.5 - - + -
116D PHE* 4.2 19.7 - - + -
120D PHE* 4.7 1.8 - - + -
142D ALA* 3.5 20.6 - - + -
144D LEU* 4.1 27.1 - - + -
171D ILE* 3.1 11.4 + - + +
172D GLN* 3.6 11.7 - - - +
175D ILE* 1.3 76.6 - - + +
177D HIS* 1.3 65.5 + - - +
179D CYS* 3.0 15.8 + - - +
181D PHE* 3.3 36.7 + - + +
183D VAL* 3.7 23.8 - - + -
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Residues in contact with HIS 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D TYR* 3.0 37.8 - + + +
133D ASP* 3.9 35.3 + - + +
172D GLN 3.0 18.4 + - - +
173D SER* 3.7 9.0 - - - +
175D ILE 3.7 0.2 - - - -
176D LEU* 1.3 72.0 - - - +
178D PHE* 1.3 55.8 + - - +
179D CYS 2.9 4.7 - - - -
180D GLY* 2.7 23.8 + - - -
181D PHE 3.0 27.7 + - - +
182D GLN* 5.1 1.3 - - - -
183D VAL* 4.1 0.8 - - + +
222D PHE* 3.4 51.7 - + + +
223D ALA 4.9 4.0 + - - -
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Residues in contact with PHE 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TRP* 3.5 27.8 - + - -
106B PHE* 4.3 8.3 - + - -
161B HIS* 3.2 28.0 - + - -
302B DQN 3.4 32.3 - + + -
126D TYR* 3.9 24.8 - - + -
130D ALA 4.7 1.2 - - - +
131D MET* 3.7 22.6 - - + -
132D TYR* 2.9 54.9 + + + -
173D SER 3.0 11.9 + - - +
174D GLY 3.2 22.7 - - - +
175D ILE 3.9 1.8 - - - +
176D LEU 3.2 0.2 - - - -
177D HIS* 1.3 76.0 - - - +
179D CYS* 1.3 59.4 + - - +
180D GLY 3.3 0.4 - - - -
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Residues in contact with CYS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TRP* 3.5 28.9 - - - -
120D PHE* 3.5 18.2 - - + -
125D ALA* 3.3 30.1 - - - +
135D GLY* 3.9 3.4 - - - -
136D PRO 3.4 6.9 - - - -
137D PHE* 3.0 39.8 + - + +
175D ILE 3.4 14.4 - - - +
176D LEU 3.0 9.7 + - - +
177D HIS 2.9 1.4 - - - -
178D PHE* 1.3 81.0 - - - +
180D GLY* 1.3 55.5 + - - +
181D PHE 3.4 1.3 - - - -
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Residues in contact with GLY 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D TYR 2.9 24.6 + - - +
133D ASP* 4.9 3.1 - - - -
135D GLY* 3.7 7.4 - - - -
138D ARG* 3.0 30.6 - - - +
177D HIS* 2.7 17.8 + - - -
178D PHE 3.3 0.8 - - - -
179D CYS* 1.3 72.5 - - - +
181D PHE* 1.3 66.7 + - - +
182D GLN* 3.6 2.3 + - - +
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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