Contacts of the helix formed by residues 146 - 158 (chain C) in PDB entry 3IZ0
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 LYS 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C THR* 1.3 85.9 - - - +
147C PHE* 1.3 65.8 - - - +
148C GLU* 3.2 20.6 + - - +
149C GLU* 3.4 41.0 + - + +
150C GLU* 3.1 24.6 + - + +
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Residues in contact with PHE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C VAL* 3.6 24.5 - - + -
125C PHE* 5.4 2.0 - + - -
126C LEU* 3.6 39.0 - - + -
142C LEU* 4.5 13.7 - - + -
143C PRO 5.5 3.8 - - - +
145C THR 3.6 2.3 - - - -
146C LYS* 1.3 74.0 - - - +
148C GLU* 1.3 78.2 + - + +
149C GLU 3.0 5.4 - - - -
150C GLU* 4.2 7.2 - - - -
151C VAL* 2.9 33.8 + - + +
169C MET* 3.2 43.7 - - + -
170C TYR* 4.4 12.6 - + - -
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Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LYS* 3.4 25.1 + - - +
147C PHE* 1.3 95.6 + - + +
149C GLU* 1.3 73.1 + - - +
152C PRO* 3.2 21.5 - - - +
166C LYS* 3.9 29.7 + - + +
169C MET* 3.7 24.6 - - + +
170C TYR* 3.2 46.9 + - + +
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Residues in contact with GLU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LYS* 3.4 50.4 + - + +
147C PHE 3.0 0.2 - - - -
148C GLU* 1.3 84.3 + - - +
150C GLU* 1.3 63.3 + - - +
152C PRO* 3.3 5.1 - - - +
153C ARG* 3.1 46.1 + - - +
166C LYS* 3.1 30.6 + - + +
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C TYR* 4.3 2.3 + - - +
142C LEU* 5.7 4.0 - - + -
143C PRO* 4.5 28.0 - - + +
145C THR 5.6 0.4 - - - +
146C LYS* 3.1 18.0 + - + +
147C PHE* 3.1 6.7 + - - +
149C GLU* 1.3 73.6 - - - +
151C VAL* 1.3 69.0 + - + +
153C ARG* 2.4 37.9 + - - +
154C ILE* 2.9 56.1 + - + +
111D CYS* 5.3 7.8 - - - -
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C PHE* 4.0 13.5 - - + -
126C LEU* 4.1 22.0 - - + -
129C PHE* 3.9 33.4 - - + -
142C LEU* 4.8 4.0 - - + -
147C PHE* 2.9 23.3 + - + +
150C GLU* 1.3 72.9 - - + +
152C PRO* 1.4 68.3 - - + +
154C ILE* 3.2 2.3 + - - +
155C PHE* 3.1 45.1 + - + -
169C MET* 3.6 23.1 - - + -
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Residues in contact with PRO 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C GLU 3.2 30.3 - - - +
149C GLU 3.3 7.9 - - - +
151C VAL* 1.4 93.0 - - + +
153C ARG* 1.3 61.7 + - - +
155C PHE* 3.2 3.5 + - - +
156C LYS* 3.0 22.6 + - - +
164C LEU* 3.5 38.4 - - + +
165C SER 4.5 2.2 - - - +
166C LYS 5.0 0.4 - - - +
169C MET* 3.6 19.1 - - + -
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Residues in contact with ARG 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C GLU* 3.1 37.9 + - - +
150C GLU* 2.4 64.8 + - - +
152C PRO* 1.3 78.5 - - - +
154C ILE* 1.3 59.1 + - + +
156C LYS* 3.1 10.7 + - + +
157C ASP* 2.8 50.5 + - - +
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Residues in contact with ILE 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C PHE* 3.9 20.6 - - + -
133C TYR* 3.4 50.9 - - + +
140C TYR* 3.4 23.8 - - + +
150C GLU* 2.9 38.4 + - + +
151C VAL 3.2 6.3 + - - +
153C ARG* 1.3 74.4 - - + +
155C PHE* 1.3 66.4 + - - +
157C ASP* 3.2 8.2 + - + +
158C LEU* 3.0 30.0 + - + +
110D LEU* 6.1 0.2 - - + -
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Residues in contact with PHE 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C PHE* 5.3 2.9 - + - -
129C PHE* 3.6 25.8 - + - -
151C VAL* 3.1 32.4 + - + -
152C PRO 3.8 4.5 - - - +
154C ILE* 1.3 77.6 - - + +
156C LYS* 1.3 63.2 + - - +
158C LEU* 3.4 8.0 + - + +
159C GLY 3.4 3.6 + - - -
160C TYR* 3.0 51.6 + + + +
164C LEU* 3.6 28.0 - - + -
184C ALA* 3.3 40.2 - - + -
185C LEU* 4.4 9.9 - - + -
187C TRP* 4.1 9.6 - + - -
188C LEU* 4.1 25.8 - - + -
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Residues in contact with LYS 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C PRO 3.0 13.6 + - - +
153C ARG* 3.4 13.5 - - + +
155C PHE* 1.3 76.7 - - - +
157C ASP* 1.3 65.5 + - - +
159C GLY* 2.8 23.0 + - - -
160C TYR 4.0 7.6 + - - +
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Residues in contact with ASP 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ARG* 2.8 44.1 + - - +
154C ILE* 3.2 8.7 + - - +
156C LYS* 1.3 79.3 - - - +
158C LEU* 1.3 59.2 + - - +
159C GLY 3.3 0.6 + - - -
42D PRO* 4.5 20.2 - - + +
43D GLU* 6.0 1.4 - - - +
85D PHE* 5.2 5.4 - - - +
110D LEU* 3.9 39.0 - - + +
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C PHE* 6.2 0.7 - - + -
133C TYR* 4.2 2.9 - - + -
136C LEU* 3.8 22.7 - - + -
154C ILE* 3.0 35.4 + - + +
155C PHE* 3.8 9.0 - - + +
156C LYS 3.1 0.4 - - - -
157C ASP* 1.3 77.4 - - - +
159C GLY* 1.3 59.9 + - - +
160C TYR 3.6 0.2 - - - -
187C TRP* 3.5 16.7 - - + -
188C LEU* 3.6 31.9 - - + -
191C CYS* 5.3 0.9 - - - -
81D GLY 4.3 2.5 - - - -
82D PHE* 3.3 44.6 - - + +
85D PHE* 4.6 4.3 - - + -
110D LEU* 3.7 29.6 - - + -
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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