Contacts of the helix formed by residues 163 - 174 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS* 6.0 3.4 - - - +
155B ARG* 4.1 0.2 - - - -
161B LYS 3.8 1.4 + - - -
162B CYS* 1.3 78.5 - - - +
164B ASP* 1.3 59.9 + - - +
165B GLY* 3.4 10.5 - - - +
166B GLU* 3.1 37.7 + - + +
167B TYR* 2.8 27.5 + - - +
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Residues in contact with ASP 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PRO* 4.3 20.4 - - + +
28A ARG* 4.4 19.4 + - - +
155B ARG* 2.8 26.1 + - - +
162B CYS 4.6 0.2 - - - +
163B THR* 1.3 73.2 + - - +
165B GLY* 1.3 56.4 + - - +
167B TYR* 3.8 5.1 - - - +
168B GLU* 2.9 31.4 + - - +
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Residues in contact with GLY 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A HIS* 2.8 49.5 - - - +
21A LYS* 4.9 8.5 - - - -
24A PRO* 4.5 2.8 - - - +
163B THR* 3.3 10.8 - - - +
164B ASP* 1.3 78.7 - - - +
166B GLU* 1.3 57.7 + - - +
168B GLU 3.9 0.2 - - - -
169B LEU* 3.0 14.6 + - - +
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A HIS* 5.1 4.6 + - - -
166A GLU* 5.4 1.2 - - - +
17B TRP* 6.0 0.2 - - - -
20B HIS* 2.8 40.5 + - - -
21B LYS* 3.8 16.6 + - - +
159B PHE* 4.4 4.7 - - - -
162B CYS* 4.1 8.1 - - + -
163B THR* 3.1 28.8 + - + +
165B GLY* 1.3 77.0 - - - +
167B TYR* 1.3 65.5 + - - +
169B LEU* 3.1 12.2 + - - +
170B ALA* 3.0 23.4 + - - +
240B LEU* 3.6 35.7 - - + +
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Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B PHE* 3.0 24.6 + - - +
154B LEU* 3.9 11.9 - - + -
155B ARG* 3.6 69.5 - - + +
159B PHE* 4.4 14.1 - + + -
162B CYS* 4.7 0.2 - - - +
163B THR 2.8 16.8 + - - +
164B ASP* 3.8 5.6 - - - +
166B GLU* 1.3 75.4 - - - +
168B GLU* 1.3 66.3 + - - +
170B ALA* 3.2 9.6 + - + +
171B LYS* 3.1 62.4 + - + +
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Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A HIS* 3.7 21.8 - - - +
23A LYS* 3.1 39.7 + - + +
24A PRO* 3.8 13.1 - - + +
27A GLU* 4.0 9.2 - - - +
164B ASP 2.9 19.3 + - - +
167B TYR* 1.3 80.8 - - + +
169B LEU* 1.3 63.2 + - - +
171B LYS* 3.3 29.0 + - - +
172B MET* 3.1 46.8 + - + +
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Residues in contact with LEU 169 (chain B).
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* 4.2 17.5 - - + -
20A HIS* 3.8 16.9 - - + +
169A LEU* 3.9 39.5 - - + -
17B TRP* 4.0 16.8 - - + -
20B HIS* 3.7 31.9 - - + +
165B GLY 3.0 16.6 + - - +
166B GLU* 3.3 13.5 - - - +
168B GLU* 1.3 73.3 - - - +
170B ALA* 1.3 58.2 + - - +
172B MET* 2.9 20.6 + - - +
173B VAL* 3.1 32.7 + - + +
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TRP* 3.8 14.7 - - + -
154B LEU* 4.8 4.7 - - + -
159B PHE* 3.6 38.6 - - + -
166B GLU 3.0 9.9 + - - +
167B TYR* 3.3 12.1 - - + +
169B LEU* 1.3 76.4 - - - +
171B LYS* 1.3 62.4 + - - +
172B MET 3.3 0.2 + - - -
173B VAL 3.3 0.2 + - - -
174B MET* 3.0 38.2 + - + +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LYS* 4.0 8.7 - - - +
27A GLU* 5.5 0.8 + - - -
43A ILE* 5.3 1.2 - - - +
151B PHE* 3.8 52.2 - - + -
154B LEU* 4.4 2.9 - - + -
167B TYR* 3.1 54.7 + - + +
168B GLU* 3.3 42.0 + - - +
170B ALA* 1.3 76.5 - - - +
172B MET* 1.3 60.4 + - - +
173B VAL 3.4 0.3 + - - -
174B MET* 4.1 6.5 + - - +
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Residues in contact with MET 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 3.2 35.2 - - + +
17A TRP* 3.8 17.2 + - - +
19A TRP 3.8 18.2 - - - +
20A HIS* 3.6 24.0 - - - -
23A LYS* 4.0 14.8 - - + -
35A ALA* 3.7 24.7 - - + +
37A ASP* 4.4 7.4 - - - +
43A ILE* 3.8 16.0 + - - +
168B GLU* 3.1 22.8 + - + +
169B LEU* 2.9 9.0 + - - +
171B LYS* 1.3 76.7 - - + +
173B VAL* 1.3 64.0 + - + +
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Residues in contact with VAL 173 (chain B).
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* 4.1 33.0 - - + -
42A GLY* 5.6 0.9 - - - -
43A ILE* 3.5 32.3 - - + +
173A VAL* 4.5 12.3 - - + -
13B CYS 4.6 0.9 - - - +
17B TRP* 3.5 47.1 + - + +
42B GLY* 5.0 3.0 + - - +
169B LEU* 3.1 22.4 + - + +
170B ALA 4.3 0.2 - - - +
172B MET* 1.3 82.1 - - - +
174B MET* 1.3 67.1 + - - +
175B ARG* 3.6 6.6 + - - +
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Residues in contact with MET 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 3.3 16.1 - - - +
13B CYS* 3.2 26.5 - - + +
14B HIS* 3.5 46.9 - - + +
17B TRP* 3.8 10.8 - - + -
149B LEU* 4.6 12.8 - - + +
151B PHE* 5.5 4.7 - - + -
154B LEU* 4.1 24.9 - - + -
159B PHE* 4.2 1.1 - - + -
170B ALA* 3.0 37.5 + - + +
171B LYS* 4.1 6.3 + - - +
172B MET 3.8 0.6 - - - -
173B VAL* 1.3 77.8 - - - +
175B ARG* 1.3 65.5 + - - +
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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