Contacts of the helix formed by residues 196 - 212 (chain A) in PDB entry 1Z0X
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 GLN 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A TYR* 3.8 1.8 - - - -
144A MSE 3.8 1.4 - - - +
192A HIS* 3.5 23.5 - - - +
193A SER* 3.0 15.5 + - - +
195A HIS* 1.3 84.1 - - + +
197A LYS* 1.3 58.1 - - - +
198A SER* 3.0 15.9 + - - +
199A ALA* 2.7 29.8 + - - +
200A PHE 3.2 3.8 + - - -
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Residues in contact with LYS 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 3.8 34.4 + - - +
86A TYR* 3.3 41.0 + - + -
87A ASP* 2.7 40.4 + - - +
196A GLN* 1.3 72.1 - - - +
198A SER* 1.3 51.9 + - - +
200A PHE* 3.1 2.8 + - - +
201A ILE* 2.7 49.9 + - + +
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A SER 5.6 0.2 + - - -
196A GLN* 4.2 16.3 + - - +
197A LYS* 1.3 76.6 - - - +
199A ALA* 1.3 61.6 + - - +
201A ILE* 3.7 10.2 - - - +
202A GLN* 2.8 48.0 + - - +
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Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A MSE 4.2 4.9 - - + -
193A SER 3.9 6.1 - - - +
194A ILE* 3.8 27.6 - - - -
196A GLN 2.7 19.2 + - - +
198A SER* 1.3 77.8 + - - +
200A PHE* 1.3 54.7 + - - +
202A GLN* 3.2 11.7 + - - +
203A ALA* 2.9 24.3 + - - +
132B LEU* 3.5 29.8 - - + +
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Residues in contact with PHE 200 (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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82A MSE 3.5 33.7 - - + -
83A GLU 4.8 0.2 - - - -
86A TYR* 3.5 30.5 - + + -
137A LEU 4.6 4.0 - - - -
140A LEU* 3.9 15.5 - - + -
141A LEU* 3.6 43.7 - - + -
144A MSE 3.6 31.7 - - + +
196A GLN 3.2 2.2 + - - -
197A LYS 3.1 9.3 + - - +
199A ALA* 1.3 80.7 - - - +
201A ILE* 1.3 71.2 + - + +
203A ALA* 3.0 5.8 + - + +
204A VAL* 2.9 48.1 + - + +
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Residues in contact with ILE 201 (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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79A LEU* 3.8 12.1 - - + -
83A GLU* 3.2 49.8 - - + +
197A LYS* 2.7 37.3 + - + +
198A SER* 3.7 9.4 - - - +
199A ALA 3.3 0.2 - - - -
200A PHE* 1.3 81.3 - - + +
202A GLN* 1.3 64.3 + - + +
204A VAL* 3.4 3.9 + - - +
205A LYS* 3.1 52.4 + - - +
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Residues in contact with GLN 202 (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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198A SER* 2.8 43.7 + - - +
199A ALA* 3.5 5.8 - - - +
201A ILE* 1.3 78.1 - - + +
203A ALA* 1.3 60.9 + - - +
205A LYS* 3.4 10.7 + - + +
206A THR* 2.9 30.0 + - - +
128B GLU* 4.8 20.5 + - - +
129B MSE 6.1 0.9 - - - +
132B LEU* 3.3 26.4 - - + +
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Residues in contact with ALA 203 (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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140A LEU* 3.9 21.7 - - + +
144A MSE 6.5 0.2 - - + -
199A ALA 2.9 13.1 + - - +
200A PHE* 3.0 11.9 + - - +
202A GLN* 1.3 77.7 - - - +
204A VAL* 1.3 62.4 - - - +
206A THR 3.4 1.6 + - - -
207A TYR* 3.1 18.4 + - - +
132B LEU* 4.1 2.6 - - + +
136B SER* 3.3 26.9 - - - +
207B TYR* 3.5 22.2 - - + +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.2 17.3 - - + -
82A MSE 4.3 15.5 - - + -
137A LEU* 3.9 18.8 - - + -
140A LEU* 4.4 8.3 - - + -
200A PHE* 2.9 54.9 + - + +
201A ILE* 3.8 5.6 - - - +
203A ALA* 1.3 76.4 - - - +
205A LYS* 1.3 57.3 + - - +
207A TYR* 3.1 8.2 + - - +
208A LEU* 2.8 45.1 + - + +
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 3.3 25.0 + - + +
79A LEU* 3.7 27.4 - - + -
201A ILE* 3.1 41.4 + - + +
202A GLN* 3.8 10.1 - - + +
204A VAL* 1.3 72.2 - - - +
206A THR* 1.3 55.7 + - - +
208A LEU* 3.1 1.9 + - - -
209A ASP* 2.6 44.6 + - - +
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Residues in contact with THR 206 (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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202A GLN 2.9 16.3 + - - -
203A ALA 3.6 8.5 - - - -
205A LYS* 1.3 75.8 - - - +
207A TYR* 1.3 61.5 + - - +
209A ASP* 3.4 9.1 + - - +
210A GLY* 3.2 3.8 + - - -
129B MSE 5.8 1.1 - - + +
132B LEU* 5.2 2.9 - - - +
207B TYR* 3.7 25.5 + - + +
210B GLY* 3.1 29.5 - - - +
211B LEU* 3.6 44.6 - - + +
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Residues in contact with TYR 207 (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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129A MSE 3.5 23.0 - - - +
132A LEU* 3.8 2.8 + - - +
133A ALA* 3.5 20.5 - - + -
136A SER* 3.7 26.4 + - - -
137A LEU* 3.9 22.9 - - + -
140A LEU* 5.3 5.8 - - + -
203A ALA 3.1 12.2 + - - +
204A VAL* 3.1 9.5 + - - +
205A LYS 3.0 0.4 - - - -
206A THR* 1.3 76.4 - - - +
208A LEU* 1.3 66.4 + - + +
210A GLY* 3.0 4.3 + - - -
211A LEU* 3.0 41.4 + - + -
140B LEU* 5.2 4.7 - - + -
203B ALA* 3.6 25.7 - - + -
206B THR* 3.6 19.4 - - + +
207B TYR* 4.3 21.3 - + + +
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Residues in contact with LEU 208 (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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74A TRP* 3.4 7.7 - - + -
75A TYR* 3.3 55.4 - - + +
78A LEU* 3.5 29.2 - - + -
79A LEU* 4.3 12.1 - - + +
137A LEU* 4.4 8.7 - - + -
204A VAL* 2.8 36.6 + - + +
205A LYS 3.7 1.3 - - - +
207A TYR* 1.3 77.7 - - + +
209A ASP* 1.3 61.9 + - - +
211A LEU* 3.2 28.7 + - + +
212A GLN* 3.2 19.9 + - - +
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Residues in contact with ASP 209 (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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75A TYR* 2.7 23.5 + - - -
205A LYS* 2.6 29.2 + - - +
206A THR* 3.4 11.5 - - - +
207A TYR 3.1 0.2 - - - -
208A LEU* 1.3 73.9 - - - +
210A GLY* 1.3 60.9 + - - +
212A GLN* 3.2 35.7 + - - +
213A ALA* 4.0 4.5 + - - +
210B GLY* 3.9 17.1 - - - +
213B ALA* 4.7 11.3 - - + +
214B ASP* 3.9 21.9 - - - +
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Residues in contact with GLY 210 (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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206A THR 3.2 4.2 + - - -
207A TYR 3.0 5.5 + - - -
209A ASP* 1.3 79.0 - - - +
211A LEU* 1.3 56.5 + - - +
213A ALA* 3.0 19.1 + - - +
214A ASP* 2.5 25.9 + - - +
206B THR* 3.4 24.5 - - - -
209B ASP* 4.0 3.6 - - - -
210B GLY* 3.5 11.2 - - - -
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Residues in contact with LEU 211 (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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74A TRP* 3.8 15.0 - - + -
78A LEU* 5.0 0.4 - - + -
120A LEU* 4.6 8.5 - - + -
125A PHE* 3.3 39.6 - - + -
129A MSE 3.8 26.9 - - + -
133A ALA* 3.9 16.2 - - + -
207A TYR* 3.0 30.4 + - + +
208A LEU* 3.2 36.8 + - + +
210A GLY* 1.3 73.1 - - - +
212A GLN* 1.3 57.2 + - - +
213A ALA 2.9 10.6 + - - -
214A ASP* 3.2 22.3 + - + +
216A THR* 3.6 2.4 - - - -
206B THR* 4.0 2.9 - - + +
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Residues in contact with GLN 212 (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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74A TRP* 3.4 22.7 - - + -
75A TYR* 3.3 19.8 - - - -
125A PHE* 5.1 0.4 - - - -
208A LEU 3.2 9.9 - - - +
209A ASP* 3.2 37.0 + - - +
210A GLY 3.2 1.2 - - - -
211A LEU* 1.3 76.1 - - - +
213A ALA* 1.3 58.1 + - - +
216A THR* 4.3 8.9 - - - -
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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