Contacts of the helix formed by residues 218 - 231 (chain A) in PDB entry 1ZK2
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A ILE* 3.4 11.1 - - - +
191A LYS* 4.3 3.4 - - + +
217A GLY* 1.3 75.6 - - - +
219A PRO* 1.3 79.1 - - + +
220A ASN* 3.8 27.0 + - - +
221A ASP* 2.9 43.0 + - - +
224A TYR* 5.8 0.7 - - - -
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Residues in contact with PRO 219 (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 GLY* 3.6 29.4 - - - +
18A ILE* 4.1 6.8 - - + +
21A ALA* 3.5 25.1 - - + +
190A ILE* 3.4 11.2 - - + -
191A LYS 3.3 21.8 - - - +
192A THR* 4.4 2.5 - - + -
193A PRO* 6.2 0.9 - - + -
218A GLU* 1.3 89.3 - - + +
220A ASN* 1.3 62.6 + - - +
222A ILE* 3.0 16.1 + - - +
223A ALA 3.0 8.8 + - - -
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Residues in contact with ASN 220 (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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21A ALA* 3.5 16.9 - - - +
24A THR* 5.6 1.6 - - - +
25A LYS* 3.5 33.0 - - - +
218A GLU* 3.0 23.8 + - - +
219A PRO* 1.3 74.7 - - - +
221A ASP* 1.3 65.8 + - - +
223A ALA* 3.6 4.4 - - - +
224A TYR* 3.0 46.9 + - + -
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Residues in contact with ASP 221 (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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190A ILE* 4.6 3.4 - - + -
217A GLY* 3.3 10.0 - - - -
218A GLU* 2.9 45.3 + - - +
220A ASN* 1.3 78.7 - - - +
222A ILE* 1.3 66.7 + - + +
224A TYR* 3.9 6.7 + - - +
225A ILE* 3.9 17.2 + - - +
244A VAL* 4.1 22.6 - - + +
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Residues in contact with ILE 222 (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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18A ILE* 3.5 30.5 - - + -
22A ILE* 4.5 0.2 - - - -
140A MET* 4.0 20.6 - - - -
185A VAL* 4.1 10.5 - - + -
187A PRO* 3.6 28.9 - - + -
190A ILE* 3.8 28.0 - - + -
219A PRO 3.0 8.1 + - - +
221A ASP* 1.3 80.0 - - - +
223A ALA* 1.3 64.9 + - - +
225A ILE* 3.2 7.6 - - - +
226A CYS* 3.2 26.3 + - - -
244A VAL* 3.9 25.8 - - + +
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Residues in contact with ALA 223 (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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21A ALA 3.4 33.0 - - - +
22A ILE* 3.7 14.8 - - - +
25A LYS* 3.6 17.0 - - + -
26A PHE* 4.6 0.7 - - - -
219A PRO 3.0 6.4 + - - +
220A ASN* 3.2 16.1 + - - +
222A ILE* 1.3 76.4 - - - +
224A TYR* 1.3 57.5 + - - +
226A CYS* 3.1 4.3 + - - +
227A VAL* 2.9 31.5 + - - +
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Residues in contact with TYR 224 (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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3A ARG* 5.0 14.7 + - - +
25A LYS* 3.2 41.9 + - + -
29A GLU* 6.1 1.1 - - - -
218A GLU* 5.8 0.4 - - - -
220A ASN* 3.0 40.8 + - + +
221A ASP* 4.4 7.2 - - - +
222A ILE 3.3 0.2 - - - -
223A ALA* 1.3 76.2 - - - +
225A ILE* 1.3 62.8 + - - +
227A VAL* 3.3 11.8 + - + +
228A TYR* 3.3 19.1 + - - +
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A VAL* 3.8 24.9 - - + -
221A ASP 3.9 11.3 + - - +
222A ILE* 3.2 16.8 + - - +
224A TYR* 1.3 78.2 - - - +
226A CYS* 1.3 61.4 + - - +
228A TYR* 3.3 26.1 + - + +
229A LEU* 3.0 26.5 + - + +
242A PHE* 4.0 35.0 - - + -
244A VAL* 4.0 20.2 - - + -
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Residues in contact with CYS 226 (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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22A ILE* 3.7 28.7 - - + -
26A PHE* 3.7 16.3 - - + -
87A VAL* 4.7 1.8 - - + -
138A ILE* 3.5 22.7 - - + +
140A MET* 4.0 18.4 - - - -
185A VAL* 4.3 7.6 - - - -
222A ILE* 3.2 17.8 + - - +
223A ALA 3.1 9.7 + - - +
225A ILE* 1.3 74.8 - - - +
227A VAL* 1.3 59.7 + - - +
229A LEU* 3.3 2.0 + - - -
230A ALA* 2.9 31.2 + - - +
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Residues in contact with VAL 227 (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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3A ARG* 3.5 35.4 - - + +
4A LEU* 3.7 13.2 - - + +
25A LYS* 3.9 23.6 - - + +
26A PHE* 3.8 23.8 - - + -
29A GLU* 4.1 17.5 - - + -
223A ALA 2.9 20.4 + - - +
224A TYR* 3.3 13.4 + - + +
226A CYS* 1.3 74.9 - - - +
228A TYR* 1.3 63.1 + - - +
230A ALA 3.3 0.2 + - - -
231A SER* 2.9 26.5 + - - -
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Residues in contact with TYR 228 (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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3A ARG* 3.8 14.1 - - - +
224A TYR 3.3 9.3 + - - +
225A ILE* 3.5 23.8 - - + +
226A CYS 3.3 0.2 - - - -
227A VAL* 1.3 80.6 - - - +
229A LEU* 1.3 77.7 + - + +
231A SER* 3.3 11.1 + - - +
233A GLU* 3.9 31.1 + - + -
234A SER* 2.8 45.9 + - - -
237A ALA* 4.3 8.8 - - - +
242A PHE* 4.0 16.5 - + - -
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Residues in contact with LEU 229 (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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136A SER* 2.7 23.4 + - - +
138A ILE* 3.7 22.4 - - + -
181A ARG* 3.0 18.2 + - - +
183A ASN* 4.2 21.8 - - + +
185A VAL* 3.4 33.4 - - + -
225A ILE* 3.0 21.9 + - + +
226A CYS 3.3 0.2 + - - -
227A VAL 3.3 0.2 - - - -
228A TYR* 1.3 96.9 - - + +
230A ALA* 1.3 51.5 + - - +
234A SER* 3.0 7.5 + - - -
237A ALA* 4.8 0.7 - - + -
242A PHE* 3.7 41.3 - - + -
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Residues in contact with ALA 230 (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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4A LEU* 3.7 15.5 - - + -
7A LYS* 3.6 21.6 + - + +
26A PHE* 3.7 14.8 - - + -
85A THR* 3.6 26.9 + - + +
134A GLY 4.4 0.5 - - - +
136A SER* 4.0 14.2 - - - -
138A ILE* 3.7 2.2 - - + +
181A ARG* 4.2 4.3 + - - -
226A CYS 2.9 17.5 + - - +
229A LEU* 1.3 75.0 - - - +
231A SER* 1.3 64.5 + - - +
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Residues in contact with SER 231 (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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3A ARG* 3.1 24.4 + - - -
4A LEU* 3.5 8.7 - - - -
7A LYS* 4.8 1.6 - - - +
181A ARG* 3.3 5.6 + - - -
227A VAL* 2.9 18.6 + - - -
228A TYR 3.3 6.0 + - - -
230A ALA* 1.3 79.1 - - - +
232A ASN* 1.3 61.7 + - - +
233A GLU* 3.0 37.0 + - - +
234A SER* 3.0 23.0 + - - -
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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