Contacts of the helix formed by residues 198 - 215 (chain A) in PDB entry 1JZO
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 PRO 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A GLN* 4.6 2.7 - - - +
111A TYR* 3.7 0.7 - - - +
196A TYR* 3.4 30.9 - - + +
197A GLN* 1.3 85.8 - - - +
199A PRO* 1.3 68.6 - - + +
200A LYS* 3.1 1.5 + - + +
201A GLU* 2.9 35.0 + - + +
202A MET* 2.7 30.0 + - - +
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Residues in contact with PRO 199 (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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107A GLN* 3.3 29.8 - - + +
110A ASP* 3.6 32.5 - - + -
111A TYR* 3.4 35.4 - - + +
114A LEU* 3.1 25.0 - - + +
116A ILE* 4.5 1.7 - - - +
198A PRO* 1.3 83.1 - - + +
200A LYS* 1.3 58.7 + - + +
202A MET* 3.5 1.2 - - - +
203A LYS 2.9 25.3 + - - -
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Residues in contact with LYS 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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114A LEU* 4.0 12.1 - - + -
198A PRO* 3.3 1.2 - - + +
199A PRO* 1.3 80.2 - - + +
201A GLU* 1.3 79.4 + - - +
203A LYS* 3.2 2.7 + - - +
204A GLU* 2.9 33.3 + - - +
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Residues in contact with GLU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLN* 3.8 9.9 - - + +
198A PRO* 2.9 45.3 - - + +
200A LYS* 1.3 89.7 + - - +
202A MET* 1.3 57.8 + - - +
204A GLU* 3.4 6.4 + - - +
205A PHE* 2.9 28.9 + - - +
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Residues in contact with MET 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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90A ILE* 4.2 17.0 - - + -
104A LEU* 5.0 9.6 - - + -
111A TYR* 3.8 18.2 - - + +
116A ILE* 3.9 17.0 - - + -
185A VAL* 3.9 26.0 - - + -
195A GLY 5.2 1.3 - - - +
197A GLN* 3.8 47.5 - - + +
198A PRO 2.7 21.4 + - - +
199A PRO 3.5 4.3 - - - +
201A GLU* 1.3 73.9 - - - +
203A LYS* 1.3 57.8 + - - +
205A PHE* 3.0 5.5 + - - +
206A LEU* 2.8 49.6 + - + +
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Residues in contact with LYS 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 4.9 11.9 - - - +
88A HIS* 3.9 17.3 - - + -
114A LEU* 3.2 46.0 - - + +
116A ILE* 4.0 10.5 - - + +
199A PRO 2.9 17.7 + - - +
200A LYS* 3.2 5.1 + - - +
202A MET* 1.3 76.1 - - - +
204A GLU* 1.3 62.8 - - - +
206A LEU* 3.2 3.1 + - - +
207A ASP* 2.6 64.8 + - - +
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Residues in contact with GLU 204 (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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200A LYS* 2.9 18.5 + - - +
201A GLU* 3.8 9.2 - - - +
203A LYS* 1.3 86.2 - - - +
205A PHE* 1.3 58.1 + - - +
207A ASP* 3.2 10.1 + - + +
208A GLU* 2.9 39.7 + - + +
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Residues in contact with PHE 205 (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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185A VAL* 6.3 0.4 - - + -
187A LEU* 4.5 10.8 - - + -
193A VAL* 3.7 42.4 - - + -
197A GLN* 3.2 30.7 - - - +
201A GLU 2.9 9.7 + - - +
202A MET* 3.3 8.5 - - - +
204A GLU* 1.3 77.3 - - - +
206A LEU* 1.3 76.5 + - + +
208A GLU* 3.7 4.5 - - + +
209A HIS* 2.8 44.2 + + + +
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Residues in contact with LEU 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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88A HIS* 3.5 40.1 - - + +
90A ILE* 3.8 28.5 - - + -
116A ILE* 3.6 33.2 - - + -
185A VAL* 5.4 0.2 - - + -
187A LEU* 4.0 20.4 - - + -
202A MET* 2.8 28.4 + - + +
203A LYS 3.7 2.0 - - - +
205A PHE* 1.3 84.5 - - + +
207A ASP* 1.3 63.0 + - - +
209A HIS* 3.8 6.0 - - + +
210A GLN* 3.2 25.3 + - - +
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Residues in contact with ASP 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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88A HIS* 2.8 28.9 + - - -
203A LYS* 2.6 51.9 + - - +
204A GLU* 3.6 11.4 - - + +
206A LEU* 1.3 78.1 - - - +
208A GLU* 1.3 58.5 + - + +
210A GLN* 3.6 3.2 + - - +
211A LYS* 2.9 48.0 + - - +
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Residues in contact with GLU 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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204A GLU* 2.9 24.2 + - + +
205A PHE* 3.8 5.2 - - + +
207A ASP* 1.3 77.7 - - + +
209A HIS* 1.3 67.0 + - - +
211A LYS* 3.2 29.8 + - - +
212A MET* 2.9 54.8 + - + +
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Residues in contact with HIS 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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187A LEU* 3.4 37.5 - - + +
188A SER* 5.9 1.2 + - - -
189A ASN* 3.9 25.6 + - - -
191A THR* 4.4 5.8 - - + +
205A PHE* 2.8 36.9 + - + +
206A LEU* 3.8 9.2 - - + +
208A GLU* 1.3 73.8 - - - +
210A GLN* 1.3 65.7 + - + +
212A MET* 3.1 10.8 + - - +
213A THR* 2.6 44.6 + - + +
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Residues in contact with GLN 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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87A LYS 4.8 4.3 + - - +
88A HIS* 3.1 31.5 + - - -
206A LEU 3.2 11.0 + - - +
207A ASP* 3.7 5.2 - - - +
209A HIS* 1.3 88.0 - - + +
211A LYS* 1.3 64.1 + - + +
213A THR* 3.2 14.1 + - - -
214A SER* 3.4 18.7 + - - -
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Residues in contact with LYS 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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207A ASP* 2.9 39.3 + - - +
208A GLU* 3.2 30.6 + - - +
210A GLN* 1.3 78.7 - - + +
212A MET* 1.3 61.9 + - + +
213A THR 3.4 3.5 + - - -
215A GLY 3.9 23.2 + - - +
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Residues in contact with MET 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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57A THR* 5.5 9.5 - - + +
58A ALA* 4.6 14.2 - - - +
208A GLU* 2.9 51.3 + - + +
209A HIS* 3.3 3.5 - - - +
211A LYS* 1.3 78.7 - - + +
213A THR* 1.3 65.3 + - - +
215A GLY* 5.1 1.6 - - - -
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Residues in contact with THR 213 (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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58A ALA* 5.6 2.9 - - + +
60A VAL* 6.1 4.3 - - + -
189A ASN* 4.8 14.6 - - + +
209A HIS* 2.6 44.5 + - + +
210A GLN* 3.2 7.6 + - - -
211A LYS 3.3 1.0 + - - -
212A MET* 1.3 79.6 + - - +
214A SER* 1.3 64.6 + - - +
215A GLY 3.4 2.6 - - - +
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Residues in contact with SER 214 (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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210A GLN* 3.4 14.8 + - - -
211A LYS* 5.5 0.4 - - - -
213A THR* 1.3 80.2 - - - +
215A GLY* 1.3 58.0 + - - +
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Residues in contact with GLY 215 (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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211A LYS 3.9 18.0 + - - +
212A MET* 5.6 1.0 - - - -
213A THR 3.4 3.6 - - - +
214A SER* 1.3 82.5 - - - +
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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