Contacts of the helix formed by residues 163 - 171 (chain O) in PDB entry 3HOU
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 ILE 163 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O ALA 3.7 5.2 - - - +
40O GLU* 3.1 36.3 - - + +
41O ILE 3.8 8.3 - - - +
42O PRO* 3.9 3.8 - - + -
82O TYR* 4.2 15.7 - - + +
84O ARG* 5.7 1.1 - - - +
162O GLY* 1.3 79.1 - - - +
164O ALA* 1.3 69.2 + - - +
165O LYS* 4.1 13.5 - - + -
166O GLU* 3.1 21.6 + - + +
167O HIS 3.1 8.7 + - - +
170O TRP* 3.4 12.9 - - - +
10W PHE* 3.8 44.2 - - + -
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Residues in contact with ALA 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995N ARG* 4.7 4.5 - - - -
997N GLU* 5.4 3.6 - - - +
38O ILE* 3.4 13.0 - - + +
39O ALA* 2.8 39.5 + - + +
41O ILE 4.9 1.0 + - - -
163O ILE* 1.3 70.9 - - - +
165O LYS* 1.3 62.2 + - - +
167O HIS* 2.5 31.3 + - - +
168O ALA* 3.7 5.2 + - - -
170O TRP* 3.9 4.8 + - - +
171O GLY* 4.3 12.1 - - - +
6W ARG* 3.5 2.4 + - - -
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Residues in contact with LYS 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995N ARG* 3.5 32.4 - - - +
997N GLU* 5.3 0.4 - - - -
39O ALA* 3.4 12.4 + - + +
40O GLU* 3.2 42.9 + - + +
163O ILE* 3.3 7.3 + - + +
164O ALA* 1.3 77.8 - - - +
166O GLU* 1.3 51.5 - - - +
254O LYS* 4.1 3.6 - - - +
6W ARG* 2.2 26.4 + - - +
9W LEU* 3.4 30.8 + - + +
10W PHE* 4.0 34.5 - - + +
37W LYS 5.8 0.6 + - - -
38W GLU* 5.2 5.5 + - - +
39W ASP* 4.0 27.2 + - - +
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Residues in contact with GLU 166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O ARG* 4.4 11.8 + - - +
162O GLY* 5.7 0.4 - - - -
163O ILE* 3.1 14.1 + - + +
164O ALA 2.8 2.6 + - - -
165O LYS* 1.3 71.4 - - - +
167O HIS* 1.3 61.7 + - - +
170O TRP* 3.9 14.6 - - + -
6W ARG* 2.8 42.8 + - - +
7W PHE* 4.2 22.6 + - - +
10W PHE* 3.1 33.8 - - + -
70X ARG* 2.8 45.2 + - - -
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Residues in contact with HIS 167 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847N ASP* 3.0 58.1 + - + +
852N ARG* 4.3 1.0 + - - -
65O HIS* 4.9 4.0 - + - -
69O LEU* 5.9 1.8 - - + -
163O ILE 3.1 3.9 + - - +
164O ALA* 2.5 32.0 + - - +
166O GLU* 1.3 76.7 - - - +
168O ALA* 1.3 68.6 + - - +
169O LYS* 3.3 27.6 + - + +
170O TRP* 3.5 23.7 + - + -
6W ARG* 3.4 6.1 - - - +
69X ALA 4.3 0.4 - - - -
70X ARG* 3.1 54.1 - - + +
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Residues in contact with ALA 168 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844N SER* 3.8 9.9 - - - +
847N ASP* 3.1 26.2 + - + +
848N ARG* 3.8 37.6 + - + +
164O ALA* 3.7 7.8 + - - +
167O HIS* 1.3 73.5 - - - +
169O LYS* 1.3 53.3 + - - +
170O TRP 2.6 6.2 + - - -
171O GLY* 2.6 32.6 + - - +
6V ARG* 5.3 3.0 + - - -
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Residues in contact with LYS 169 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848N ARG* 5.7 1.9 - - - +
43O THR* 4.8 2.9 - - - +
45O ALA* 4.1 13.4 - - + +
46O ILE 3.0 23.2 + - - +
47O ASP* 2.8 28.7 + - - +
68O GLY* 3.2 29.3 - - - +
69O LEU* 4.3 8.7 - - + +
167O HIS* 3.3 25.5 - - + +
168O ALA* 1.3 76.0 - - - +
170O TRP* 1.3 93.8 + - + +
171O GLY 3.5 2.1 + - - +
6V ARG* 3.8 22.0 + - - +
69X ALA 3.0 24.0 + - - +
70X ARG* 3.7 4.0 - - - +
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Residues in contact with TRP 170 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O ILE 4.0 5.5 - - - +
43O THR* 3.1 39.2 + - - -
45O ALA* 3.7 16.3 - - + +
47O ASP* 3.7 20.4 - - + -
160O LYS* 3.1 23.6 + - + -
161O LYS 4.2 9.0 - - - -
162O GLY* 3.3 25.8 - - - +
163O ILE 3.4 30.3 - - - +
164O ALA 4.2 2.8 + - - -
166O GLU* 3.9 16.2 - - + -
167O HIS* 3.5 28.6 + - + -
168O ALA 2.6 5.5 + - - -
169O LYS* 1.3 105.4 - - + +
171O GLY* 1.3 58.0 + - - -
172O PRO* 3.7 3.3 - - - +
70X ARG* 3.5 27.4 - - - -
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Residues in contact with GLY 171 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O ILE 4.2 11.7 - - - -
43O THR* 4.7 1.4 + - - +
164O ALA* 4.3 9.9 - - - +
168O ALA 2.6 20.7 + - - -
169O LYS 4.2 3.3 - - - +
170O TRP* 1.3 72.8 - - - +
172O PRO* 1.3 67.2 - - - +
173O ALA 3.6 1.1 - - - -
174O ALA 5.4 1.8 - - - -
235O VAL* 4.1 0.7 - - - +
237O SER* 4.6 2.6 + - - -
6V ARG* 3.7 20.8 + - - -
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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
------------------------------------------------------------
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