Contacts of the helix formed by residues 166 - 180 (chain A) in PDB entry 1D4O
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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ALA* 3.8 6.4 - - - +
141A ARG* 3.8 12.2 + - + +
165A GLY* 1.3 72.6 - - - -
167A ALA* 1.3 66.2 + - - +
168A LYS* 2.9 30.0 + - - +
169A LYS* 2.9 42.0 + - + +
170A THR* 3.0 20.3 + - - -
201A NAP 3.1 28.6 + - - -
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Residues in contact with ALA 167 (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 GLY 3.9 7.6 - - - +
33A LEU* 4.5 0.9 - - - -
36A ALA* 3.9 9.9 - - + -
38A ALA* 3.9 11.0 - - + -
104A ILE* 4.3 18.4 - - + -
105A GLY 5.4 0.2 - - - +
139A MET* 5.2 8.5 - - + +
165A GLY 4.2 1.3 - - - -
166A ASP* 1.3 74.2 - - - +
168A LYS* 1.3 59.5 + - - +
170A THR* 3.9 4.4 - - - -
171A CYS* 3.0 34.2 + - - +
201A NAP 2.9 28.2 + - + +
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Residues in contact with LYS 168 (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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36A ALA* 3.2 31.0 - - + +
37A LYS* 3.8 18.6 - - + +
38A ALA* 3.9 7.2 - - + -
40A TYR* 5.7 3.4 - - - -
41A PRO* 4.3 10.1 - - + -
166A ASP* 2.9 8.8 + - - +
167A ALA* 1.3 75.7 - - - +
169A LYS* 1.3 61.6 + - - +
171A CYS* 4.4 1.3 - - - +
172A ASP* 2.6 73.0 + - - +
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Residues in contact with LYS 169 (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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165A GLY* 3.5 11.9 - - - -
166A ASP* 2.9 52.1 + - + +
168A LYS* 1.3 77.2 - - - +
170A THR* 1.3 63.3 + - - +
172A ASP* 3.9 5.8 - - - +
173A ALA* 3.2 23.4 + - - +
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Residues in contact with THR 170 (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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12A LEU* 4.1 8.9 - - + +
139A MET* 3.8 20.6 - - + +
163A LEU* 3.5 36.9 + - + +
164A LEU 4.5 4.5 + - - -
165A GLY* 4.0 17.6 + - - -
166A ASP 3.0 16.5 + - - -
167A ALA* 3.9 6.1 - - - -
169A LYS* 1.3 80.1 - - - +
171A CYS* 1.4 57.5 + - - +
173A ALA* 3.2 6.1 + - - +
174A LEU* 2.9 29.5 + - + +
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Residues in contact with CYS 171 (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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38A ALA* 4.5 1.1 - - + -
41A PRO* 3.9 21.3 - - + +
42A ILE* 3.6 33.7 - - + +
45A LEU* 5.6 7.5 - - + +
104A ILE* 4.1 9.0 - - - -
139A MET* 4.0 24.9 - - - -
167A ALA 3.0 22.5 + - - +
170A THR* 1.4 74.4 - - - +
172A ASP* 1.4 61.7 + - - +
174A LEU* 3.8 8.7 - - - +
175A GLN* 2.8 30.0 + - - +
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Residues in contact with ASP 172 (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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41A PRO* 3.3 28.8 - - - +
168A LYS* 2.6 56.8 + - - +
169A LYS* 3.9 6.5 - - - +
171A CYS* 1.4 74.8 - - - +
173A ALA* 1.3 56.5 + - - +
175A GLN* 3.6 10.6 + - - +
176A ALA* 3.0 27.2 + - - +
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Residues in contact with ALA 173 (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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12A LEU* 3.7 29.6 - - + -
169A LYS 3.2 15.4 + - - +
170A THR 3.6 3.8 - - - +
171A CYS 3.2 0.6 - - - -
172A ASP* 1.3 77.7 - - - +
174A LEU* 1.3 64.0 + - - +
176A ALA* 3.3 7.7 + - - +
177A LYS* 3.0 29.2 + - + +
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Residues in contact with LEU 174 (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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12A LEU* 3.7 23.6 - - + +
15A ALA* 4.0 20.6 - - + -
16A ILE* 3.9 22.4 - - + -
19A ILE* 4.7 11.2 - - + -
45A LEU* 4.2 17.7 - - + -
139A MET* 3.6 31.0 - - + -
163A LEU* 4.2 3.6 - - + -
170A THR* 2.9 30.3 + - + +
171A CYS* 3.9 8.1 - - - +
173A ALA* 1.3 74.6 - - - +
175A GLN* 1.3 66.5 + - - +
177A LYS* 3.2 2.0 + - - +
178A VAL* 2.9 27.2 + - - +
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Residues in contact with GLN 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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41A PRO* 3.5 31.8 - - - +
44A ASP* 2.7 40.9 - - - +
45A LEU* 4.2 13.3 - - + +
48A MET* 3.7 7.5 - - + +
171A CYS 2.8 19.1 + - - +
172A ASP* 3.6 13.3 + - - +
174A LEU* 1.3 71.5 - - - +
176A ALA* 1.3 63.9 + - - +
178A VAL 3.3 0.5 + - - -
179A ARG* 2.9 30.6 + - - +
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Residues in contact with ALA 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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172A ASP 3.0 13.1 + - - +
173A ALA* 3.5 11.4 - - - +
174A LEU 3.2 0.2 - - - -
175A GLN* 1.3 78.3 - - - +
177A LYS* 1.3 65.9 + - + +
179A ARG* 3.4 10.8 + - - +
180A GLU* 3.2 24.5 + - - +
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Residues in contact with LYS 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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12A LEU* 3.9 29.4 - - + -
13A ASP* 2.7 38.7 + - - +
16A ILE* 3.7 37.1 - - + +
173A ALA* 3.0 20.1 + - + +
174A LEU* 3.2 0.6 + - - -
176A ALA* 1.3 79.2 - - + +
178A VAL* 1.3 63.1 + - - +
180A GLU* 3.3 33.7 + - - +
181A SER 4.1 4.9 + - - +
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Residues in contact with VAL 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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16A ILE* 3.7 19.3 - - + -
19A ILE* 5.0 6.3 - - + -
45A LEU* 3.5 20.4 - - + -
48A MET* 3.8 25.9 - - + +
49A LEU* 4.1 17.5 - - + -
52A GLN* 3.7 23.1 - - - +
174A LEU 2.9 19.8 + - - +
175A GLN 3.9 3.1 - - - +
177A LYS* 1.3 78.0 - - - +
179A ARG* 1.3 56.1 + - - +
181A SER* 2.9 25.2 + - - +
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Residues in contact with ARG 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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44A ASP* 5.2 7.0 - - - -
48A MET* 3.7 20.8 - - - -
175A GLN* 2.9 23.6 + - - +
176A ALA* 3.6 10.2 - - - +
178A VAL* 1.3 70.2 - - - +
180A GLU* 1.3 61.3 + - - +
181A SER* 3.0 14.7 + - - -
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Residues in contact with GLU 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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176A ALA 3.2 16.4 + - - +
177A LYS* 3.3 30.9 + - - +
178A VAL 3.2 0.2 - - - -
179A ARG* 1.3 74.5 - - - +
181A SER* 1.3 67.9 + - - +
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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