Contacts of the helix formed by residues 163 - 174 (chain A) in PDB entry 1DWQ
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 THR 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ARG* 4.4 0.2 - - - -
161A LYS 3.9 0.6 + - - -
162A CYS* 1.3 78.2 - - - +
164A ASP* 1.3 59.5 + - - +
165A GLY* 3.3 18.4 - - - +
166A GLU* 3.0 28.4 + - + +
167A TYR* 2.8 26.2 + - - +
21B LYS* 6.3 1.3 - - + -
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Residues in contact with ASP 164 (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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155A ARG* 3.1 24.9 + - - +
162A CYS 3.7 0.5 + - - +
163A THR* 1.3 72.6 - - - +
165A GLY* 1.3 53.1 + - - +
167A TYR* 3.7 4.3 - - + +
168A GLU* 2.8 35.9 + - - +
24B PRO* 3.9 21.2 - - + +
28B ARG* 3.7 27.5 + - - +
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Residues in contact with GLY 165 (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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163A THR* 3.2 11.4 - - - +
164A ASP* 1.3 76.0 - - - +
166A GLU* 1.3 60.2 + - - +
169A LEU* 3.1 15.8 + - - +
20B HIS* 2.9 48.7 - - - +
21B LYS* 4.8 8.3 - - - -
24B PRO* 4.3 3.1 - - - +
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Residues in contact with GLU 166 (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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17A TRP* 5.4 2.1 - - - -
20A HIS* 2.9 41.0 + - - -
21A LYS* 4.2 11.2 + - + +
159A PHE* 4.5 4.3 - - - -
162A CYS* 4.0 14.8 - - + -
163A THR* 3.0 28.2 + - + +
165A GLY* 1.3 78.4 - - - +
167A TYR* 1.3 65.2 + - - +
169A LEU* 3.2 12.5 + - - +
170A ALA* 3.0 21.8 + - - +
240A LEU* 3.6 30.1 - - + +
20B HIS* 4.9 5.1 + - - -
166B GLU* 5.4 1.4 - - - +
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Residues in contact with TYR 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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151A PHE* 3.1 24.9 + - - +
154A LEU* 3.9 13.0 - - + -
155A ARG* 3.5 73.0 - - + +
159A PHE* 4.4 14.4 - + + -
162A CYS* 4.7 1.2 - - + +
163A THR 2.8 15.4 + - - +
164A ASP* 3.8 4.9 - - + +
166A GLU* 1.3 77.8 - - - +
168A GLU* 1.3 64.7 + - - +
170A ALA* 3.1 16.3 + - + +
171A LYS* 3.2 52.1 + - + +
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Residues in contact with GLU 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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164A ASP 2.8 22.8 + - - +
165A GLY 4.0 0.2 - - - +
167A TYR* 1.3 73.9 - - + +
169A LEU* 1.3 64.0 + - - +
171A LYS* 3.1 35.4 + - - +
172A MET* 3.1 44.4 + - + +
20B HIS 3.8 14.1 - - - +
23B LYS* 3.1 36.6 + - + +
24B PRO* 3.6 21.5 - - + +
27B GLU* 4.0 6.8 - - - +
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Residues in contact with LEU 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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17A TRP* 4.3 16.2 - - + -
20A HIS* 3.6 31.9 - - + +
165A GLY 3.1 19.6 + - - +
166A GLU* 3.2 11.6 + - - +
168A GLU* 1.3 76.5 - - - +
170A ALA* 1.3 62.8 + - - +
172A MET* 2.9 15.6 + - - +
173A VAL* 3.2 24.9 + - + +
17B TRP* 3.9 23.6 - - + -
20B HIS* 3.9 17.4 - - + +
169B LEU* 3.9 38.6 - - + -
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Residues in contact with ALA 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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17A TRP* 3.8 13.9 - - + -
154A LEU* 4.9 6.1 - - + -
159A PHE* 3.6 35.7 - - + -
166A GLU 3.0 10.9 + - - +
167A TYR* 3.1 12.3 + - + +
169A LEU* 1.3 75.2 - - - +
171A LYS* 1.3 58.8 + - + +
174A MET* 2.9 46.6 + - + +
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Residues in contact with LYS 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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151A PHE* 3.4 59.1 - - + -
154A LEU* 4.5 2.7 - - + -
167A TYR* 3.5 51.1 + - + +
168A GLU* 3.1 41.5 + - - +
170A ALA* 1.3 75.5 - - - +
172A MET* 1.3 61.5 + - - +
173A VAL 3.6 0.3 + - - -
174A MET* 4.3 6.5 + - - +
23B LYS* 4.1 7.9 - - - +
27B GLU* 5.5 0.8 + - - -
43B ILE* 5.4 1.4 - - - +
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Residues in contact with MET 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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168A GLU* 3.1 21.3 + - + +
169A LEU* 2.9 8.9 + - - +
171A LYS* 1.3 76.9 - - - +
173A VAL* 1.3 59.8 + - - +
16B ALA* 3.5 27.0 - - + +
17B TRP* 3.7 26.3 + - + +
19B TRP 3.7 19.3 - - - +
20B HIS* 3.7 24.5 - - - -
23B LYS* 4.0 17.3 - - + -
35B ALA* 3.9 22.0 - - + +
37B ASP* 4.4 8.0 - - - +
43B ILE* 3.7 17.3 + - - +
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Residues in contact with VAL 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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13A CYS 4.5 0.7 - - - +
17A TRP* 3.4 51.0 + - + +
42A GLY* 5.1 2.3 + - - +
169A LEU* 3.2 21.3 - - + +
172A MET* 1.3 80.2 - - - +
174A MET* 1.3 67.1 + - - +
175A ARG* 3.7 6.1 + - - +
17B TRP* 4.2 29.6 - - + -
42B GLY* 5.6 0.9 - - - -
43B ILE* 3.5 30.0 - - + +
173B VAL* 4.5 14.8 - - + -
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Residues in contact with MET 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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13A CYS* 3.2 31.9 - - + +
14A HIS* 3.3 41.5 - - + +
17A TRP* 3.8 15.5 - - + -
148A LYS* 3.1 40.7 - - - +
149A LEU* 4.4 3.8 - - + -
151A PHE* 5.3 0.7 - - + -
154A LEU* 4.1 17.0 - - + -
159A PHE* 4.2 0.7 - - + -
170A ALA* 2.9 36.9 + - + +
171A LYS* 4.3 7.4 + - - +
172A MET 3.9 1.0 - - - -
173A VAL* 1.3 75.3 - - - +
175A ARG* 1.3 56.7 + - - +
43B ILE* 3.3 14.6 - - - +
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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