Contacts of the helix formed by residues 165 - 189 (chain A) in PDB entry 1ZIO
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 GLU 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A MET* 3.8 24.7 - - + +
125A THR* 4.0 16.3 - - + +
163A ASP 3.9 1.0 + - - -
164A ASN* 1.3 74.0 - - - +
166A ALA* 1.3 62.0 + - - +
168A VAL* 3.4 2.2 + - - +
169A ALA* 3.1 23.7 + - + +
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASN* 3.2 8.7 + - - +
165A GLU* 1.3 79.9 + - - +
167A THR* 1.3 63.7 + - - +
169A ALA* 3.5 7.5 + - - +
170A ASN* 3.4 18.4 + - - +
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Residues in contact with THR 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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54A ASP 3.8 16.4 + - - +
55A ARG 3.8 3.1 - - - -
56A GLY* 3.7 29.8 - - - +
161A ALA 4.6 0.3 + - - -
162A ASP* 3.6 27.8 - - + +
164A ASN* 3.1 26.7 + - - -
166A ALA* 1.3 73.3 - - - +
168A VAL* 1.3 62.6 + - - +
170A ASN* 3.1 7.0 + - - +
171A ARG* 2.9 31.8 + - - +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET* 3.9 26.0 - - - -
124A LEU* 3.7 33.9 - - + -
125A THR* 4.0 4.0 - - + -
162A ASP 3.8 5.8 - - - +
163A ASP* 3.4 24.0 - - - +
164A ASN 3.0 21.4 + - - +
165A GLU 3.7 5.8 - - - +
166A ALA 3.3 0.2 - - - -
167A THR* 1.3 76.9 - - - +
169A ALA* 1.3 56.4 + - - +
171A ARG* 3.2 10.9 + - - +
172A LEU* 2.8 41.7 + - + +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET* 4.3 15.4 - - + +
165A GLU* 3.1 14.0 + - + +
166A ALA* 3.7 10.5 - - - +
168A VAL* 1.3 75.5 - - - +
170A ASN* 1.3 62.5 + - - +
172A LEU* 3.5 6.5 + - - +
173A GLU* 3.2 22.7 + - - +
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Residues in contact with ASN 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG 2.8 27.0 + - - +
56A GLY 3.2 12.1 + - - -
57A ASP* 3.0 25.3 + - - +
166A ALA 3.4 9.1 + - - +
167A THR* 3.1 10.1 + - - +
169A ALA* 1.3 75.9 - - - +
171A ARG* 1.3 65.6 + - - +
173A GLU* 3.0 10.9 + - - +
174A VAL* 2.9 27.7 + - - +
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 3.9 12.7 - - + +
56A GLY* 3.5 28.7 - - - +
124A LEU* 3.8 22.6 - - - +
160A ARG* 3.3 18.0 - - - +
162A ASP* 2.8 58.3 + - - -
163A ASP* 2.9 21.0 + - - +
167A THR* 2.9 18.7 + - - +
168A VAL* 3.2 9.2 + - + +
170A ASN* 1.3 74.6 - - - +
172A LEU* 1.3 64.1 + - - +
174A VAL* 3.4 0.8 - - - +
175A ASN* 2.8 33.1 + - - +
218A AP5 3.2 45.9 + - - +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.4 6.6 - - + +
9A PRO* 4.0 24.0 - - + +
117A GLN* 4.1 38.6 - - + +
120A LEU* 3.8 32.5 - - + -
121A MET* 4.3 17.9 - - + +
124A LEU* 5.1 0.2 - - + -
168A VAL* 2.8 37.5 + - + +
169A ALA* 3.9 5.6 - - - +
170A ASN 3.2 0.2 - - - -
171A ARG* 1.3 76.6 - - - +
173A GLU* 1.3 56.8 + - - +
175A ASN* 3.9 0.5 - - - +
176A MET* 2.9 32.2 + - - +
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN* 5.7 0.7 - - - -
169A ALA 3.2 13.1 + - - +
170A ASN* 3.0 14.9 + - - +
172A LEU* 1.3 74.8 - - - +
174A VAL* 1.3 65.9 + - - +
176A MET* 3.5 16.8 + - + +
177A LYS* 3.2 54.1 + - + +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLY 3.5 20.4 - - - +
57A ASP* 4.6 7.9 - - + +
58A LEU* 4.0 30.5 - - + +
170A ASN* 2.9 24.9 + - - +
171A ARG 3.4 6.5 - - - +
173A GLU* 1.3 77.3 - - - +
175A ASN* 1.3 68.6 + - - +
177A LYS* 3.4 8.0 + - + +
178A GLN* 3.0 35.2 + - + +
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Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY 5.3 1.9 - - - +
8A LEU* 3.7 7.6 - - + +
9A PRO* 3.6 33.2 - - + +
56A GLY 5.0 1.2 + - - -
58A LEU* 4.3 8.6 - - - +
88A ARG* 2.9 42.5 + - - +
171A ARG* 2.8 30.8 + - - +
172A LEU 4.1 0.2 - - - +
174A VAL* 1.3 84.9 - - - +
176A MET* 1.3 58.6 + - - +
178A GLN* 4.7 2.5 - - - -
179A MET* 2.7 42.8 + - + +
218A AP5 5.0 4.0 + - - -
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Residues in contact with MET 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.6 14.5 - - + +
117A GLN* 3.8 27.8 - - - +
172A LEU 2.9 21.6 + - - +
173A GLU* 3.8 22.9 - - + +
174A VAL 3.3 0.2 - - - -
175A ASN* 1.3 76.8 - - - +
177A LYS* 1.3 76.2 + - + +
180A LYS* 3.1 42.0 + - + +
181A PRO* 4.1 0.3 - - - +
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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
----------------------------------------------------------
173A GLU* 3.2 49.8 + - + +
174A VAL* 3.7 7.6 - - + +
176A MET* 1.3 92.5 - - - +
178A GLN* 1.3 64.7 + - + +
181A PRO* 3.2 23.0 - - - +
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Residues in contact with GLN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 3.7 20.5 - - + +
61A ASP* 5.2 3.6 + - - -
88A ARG 3.3 17.6 - - - +
89A THR* 3.4 35.2 - - + +
90A VAL* 4.4 4.7 + - - +
174A VAL* 3.0 24.9 + - + +
175A ASN* 4.4 1.3 - - - +
177A LYS* 1.3 84.3 - - + +
179A MET* 1.3 61.0 + - - +
181A PRO* 3.3 13.8 - - - +
182A LEU* 4.5 2.3 - - - +
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Residues in contact with MET 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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6A MET* 3.5 40.8 - - + -
7A GLY 3.6 31.4 - - - +
8A LEU* 3.9 10.8 - - - +
88A ARG* 3.5 29.4 - - + +
112A HIS* 3.9 21.5 - - + +
175A ASN* 2.7 28.9 + - + +
178A GLN* 1.3 72.5 - - - +
180A LYS* 1.3 70.3 + - + +
181A PRO* 3.3 0.7 - - - -
182A LEU* 2.9 31.0 + - + +
183A VAL* 4.6 1.1 - - + -
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Residues in contact with LYS 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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8A LEU* 3.7 31.8 - - + +
112A HIS* 3.7 26.6 + - - -
114A ASP* 4.0 14.5 + - - -
115A VAL 5.6 0.2 + - - -
117A GLN* 5.9 1.1 - - - +
176A MET* 3.1 36.8 + - + +
179A MET* 1.3 83.6 - - + +
181A PRO* 1.4 65.6 - - + +
182A LEU 3.0 1.3 + - - -
183A VAL* 3.1 28.2 + - + +
184A ASP* 4.4 0.5 + - - +
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Residues in contact with PRO 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 4.3 19.9 - - + +
176A MET 4.1 0.2 - - - +
177A LYS 3.2 25.8 - - - +
178A GLN 3.3 11.2 - - - +
180A LYS* 1.4 92.5 - - + +
182A LEU* 1.3 60.4 + - - +
183A VAL 3.2 0.6 + - - -
184A ASP* 3.4 9.4 + - + +
185A PHE* 3.3 18.8 + - - +
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Residues in contact with LEU 182 (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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6A MET* 3.7 22.9 - - - -
87A PRO* 3.6 30.3 - - + +
88A ARG* 3.7 5.6 - - - -
89A THR 3.7 23.8 - - - +
90A VAL* 3.9 19.3 - - + +
93A ALA* 3.5 27.6 - - + -
178A GLN 4.5 1.8 - - - +
179A MET* 2.9 18.0 + - + +
181A PRO* 1.3 76.8 - - - +
183A VAL* 1.3 63.8 + - - +
185A PHE* 4.0 9.0 - - + -
186A TYR* 3.0 35.8 + - + +
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Residues in contact with VAL 183 (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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6A MET* 4.0 13.0 - - + -
112A HIS* 4.0 29.6 - - + +
179A MET* 4.6 0.9 - - + -
180A LYS* 3.1 26.6 + - + +
182A LEU* 1.3 76.4 - - - +
184A ASP* 1.3 58.8 + - + +
186A TYR 3.9 0.2 - - - -
187A GLU* 2.9 31.5 + - + +
192A LEU* 3.7 27.6 - - + +
194A ASN* 5.0 1.8 - - - +
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Residues in contact with ASP 184 (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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180A LYS 4.4 0.4 + - - -
181A PRO* 3.4 10.1 + - + +
182A LEU 3.3 0.2 - - - -
183A VAL* 1.3 78.1 - - - +
185A PHE* 1.3 65.7 + - - +
187A GLU* 3.7 9.3 - - - +
188A GLN* 3.0 46.0 + - - +
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Residues in contact with PHE 185 (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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90A VAL* 4.4 17.7 - - + -
93A ALA* 3.8 22.9 - - + -
94A GLU* 4.1 34.8 - - + -
97A GLU* 4.8 3.1 - - + -
181A PRO 3.3 11.0 + - - +
182A LEU* 3.3 16.6 + - + +
183A VAL 3.3 0.2 - - - -
184A ASP* 1.3 82.3 - - - +
186A TYR* 1.3 88.8 + + - +
188A GLN* 3.5 15.0 - - - +
189A LYS* 3.5 40.2 - - - +
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Residues in contact with TYR 186 (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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6A MET* 4.4 8.1 - - - -
87A PRO* 3.2 34.7 - - + +
93A ALA* 3.5 16.0 + - + +
96A LEU* 4.1 2.4 - - - +
97A GLU* 4.7 2.8 + - - -
107A LEU* 4.1 13.1 - - + +
110A VAL* 3.8 35.4 - - + -
182A LEU* 3.0 36.8 + - + +
183A VAL 4.2 0.2 - - - +
185A PHE* 1.3 92.3 - + - +
187A GLU* 1.3 66.6 + - - +
188A GLN 3.1 1.6 - - - -
189A LYS* 3.2 6.2 + - + +
190A GLY 3.1 3.6 + - - -
191A TYR* 3.1 53.4 + + - -
192A LEU* 3.3 22.4 + - + +
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A VAL* 2.9 21.1 + - + +
184A ASP* 3.7 13.5 - - - +
186A TYR* 1.3 77.1 - - - +
188A GLN* 1.3 63.3 + - + +
190A GLY* 3.1 14.6 + - - +
192A LEU* 3.3 34.9 - - + +
194A ASN* 5.2 2.1 + - - -
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Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASP* 3.0 41.3 + - - +
185A PHE* 3.5 9.6 - - - +
186A TYR 3.1 0.4 - - - -
187A GLU* 1.3 79.2 - - + +
189A LYS* 1.3 60.3 + - + +
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 4.0 19.6 + - - +
185A PHE* 3.5 49.3 - - + +
186A TYR* 3.2 9.1 + - + +
187A GLU 3.2 0.4 - - - -
188A GLN* 1.3 79.4 - - + +
190A GLY* 1.3 59.7 + - - +
191A TYR* 3.5 48.7 + - + +
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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
------------------------------------------------------------
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