Contacts of the helix formed by residues 175 - 191 (chain B) in PDB entry 1ZJA
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 THR 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ASP* 2.6 43.5 + - + +
126B TYR* 4.5 6.1 - - + -
172B ASN* 3.5 13.6 + - - +
173B TRP 3.0 1.2 - - - -
174B ASP* 1.3 79.8 - - - +
176B PRO* 1.4 71.7 - - + +
177B LYS* 4.1 10.5 - - + +
178B LEU* 3.0 20.5 + - + +
179B ARG* 3.0 22.2 + - - +
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Residues in contact with PRO 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ASP 3.3 9.6 - - - +
175B THR* 1.4 85.8 - - + +
177B LYS* 1.3 64.5 + - - +
179B ARG* 3.1 31.9 + - - +
180B GLU* 2.9 31.2 + - + +
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Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 4.2 19.1 - - + +
175B THR* 3.3 7.7 + - + +
176B PRO* 1.3 79.4 - - - +
178B LEU* 1.3 62.1 + - - +
180B GLU* 3.4 8.0 + - - +
181B GLU* 3.1 28.5 + - - +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B TRP* 3.9 24.2 - - + -
126B TYR* 3.6 48.9 - - + +
171B LEU* 4.1 12.8 - - + -
172B ASN 3.5 30.7 - - - +
173B TRP* 4.3 5.8 - - + -
175B THR* 3.0 17.7 + - - +
177B LYS* 1.3 76.2 - - - +
179B ARG* 1.3 69.4 + - - +
181B GLU* 3.0 5.6 + - + +
182B LEU* 3.0 46.8 + - + +
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Residues in contact with ARG 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B TRP* 2.8 70.1 + - + +
174B ASP 3.7 16.8 + - - -
175B THR 3.0 9.6 + - - +
176B PRO* 3.1 32.2 + - - +
178B LEU* 1.3 80.1 - - - +
180B GLU* 1.3 57.6 + - + +
182B LEU* 3.1 8.5 + - - +
183B TYR* 3.0 47.3 + - + +
234B ARG* 5.9 2.4 - - - +
235B TYR* 3.7 24.5 + - - -
238B GLU* 2.7 36.7 + - - +
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Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PRO* 2.9 23.9 + - + +
177B LYS* 3.7 8.1 - - - +
179B ARG* 1.3 76.7 - - + +
181B GLU* 1.3 62.8 + - + +
183B TYR* 3.4 20.4 + - - +
184B ALA* 3.1 23.4 + - - +
187B ARG* 4.8 8.1 + - - -
238B GLU* 5.2 1.9 - - - +
242B LYS* 3.5 29.0 - - - +
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Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG* 4.6 5.2 + - - -
111B TRP* 3.6 38.6 + - + -
123B TYR* 4.1 6.9 + - - -
126B TYR* 2.6 30.4 + - + +
177B LYS 3.1 15.8 + - - +
178B LEU* 3.0 9.9 + - + +
180B GLU* 1.3 77.3 - - + +
182B LEU* 1.3 63.2 + - - +
184B ALA* 3.3 7.2 + - - +
185B MET* 3.0 22.4 + - - +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 5.0 2.0 - - + -
102B ILE* 4.0 35.0 - - + +
111B TRP* 4.0 28.0 - - + -
171B LEU* 4.1 10.8 - - + -
173B TRP* 3.5 37.0 - - + +
178B LEU* 3.0 36.4 + - + +
179B ARG* 3.6 7.4 - - - +
181B GLU* 1.3 77.9 - - - +
183B TYR* 1.3 67.9 + - + +
185B MET* 3.1 12.3 + - + +
186B LEU* 2.9 26.2 + - - +
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Residues in contact with TYR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B TRP* 3.8 19.2 - + - -
179B ARG* 3.0 38.8 + - + +
180B GLU* 3.8 22.0 - - - +
181B GLU 3.3 0.4 - - - -
182B LEU* 1.3 78.4 - - + +
184B ALA* 1.3 63.6 + - - +
186B LEU* 3.2 6.3 + - + +
187B ARG* 3.0 38.3 + - - +
235B TYR 4.0 0.5 + - - -
238B GLU* 2.6 37.2 + - + +
239B MET* 3.7 35.1 + - + -
242B LYS* 3.8 25.8 - - + -
243B VAL* 3.5 25.5 - - + +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG* 3.7 19.3 + - - +
180B GLU 3.1 16.8 + - - +
181B GLU* 3.7 7.0 - - - +
183B TYR* 1.3 76.4 - - - +
185B MET* 1.3 63.0 + - - +
187B ARG* 3.3 21.8 + - - +
188B PHE* 3.1 18.5 + - - +
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Residues in contact with MET 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 5.6 2.2 - - - -
69B TYR* 3.3 48.7 - - + +
70B ARG* 3.7 18.6 - - + +
100B VAL* 4.4 4.5 - - + -
102B ILE* 3.5 32.1 - - + -
111B TRP* 5.9 2.9 - - + -
181B GLU 3.0 13.3 + - - +
182B LEU* 3.3 17.3 - - + +
184B ALA* 1.3 76.0 - - - +
186B LEU* 1.3 84.9 + - + +
188B PHE* 3.1 17.5 + - - +
189B TRP* 3.4 22.8 + - + +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 3.6 31.2 - - + -
102B ILE* 4.7 4.5 - - + -
182B LEU 2.9 18.6 + - - +
183B TYR* 3.2 8.5 + - + +
185B MET* 1.3 88.5 - - + +
187B ARG* 1.3 58.4 + - - +
189B TRP 3.2 2.6 + - - -
190B LEU* 2.9 31.8 + - + +
197B MET* 3.7 25.9 - - + +
199B PHE* 4.3 0.9 - - + -
239B MET* 3.7 37.2 - - + -
243B VAL* 4.0 17.0 - - + -
244B PHE* 4.0 13.7 - - + -
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B GLU* 4.8 7.9 + - - -
183B TYR* 3.0 27.1 + - - +
184B ALA* 3.5 35.4 - - - +
185B MET 3.2 0.4 - - - -
186B LEU* 1.3 74.1 - - - +
188B PHE* 1.3 57.3 + - - +
190B LEU* 4.3 4.3 - - - -
191B ASP* 2.7 45.0 + - - +
242B LYS* 2.9 39.8 + - - +
243B VAL* 4.6 5.8 - - + +
246B HIS* 5.7 1.2 - - - -
247B TYR* 3.6 30.2 - - + +
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG* 3.8 57.0 - - + +
79B MET* 4.1 11.7 - - + -
184B ALA 3.1 12.2 + - - +
185B MET 3.1 9.8 + - - +
187B ARG* 1.3 77.8 - - - +
189B TRP* 1.3 104.8 + + - +
191B ASP* 3.7 7.2 + - - +
192B LYS* 3.5 32.2 + - + +
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Residues in contact with TRP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B HIS* 3.4 27.6 - + - -
55B TYR* 3.6 27.8 - + - -
69B TYR 2.8 28.8 + - - -
70B ARG* 4.2 7.0 - - - -
71B GLU 4.6 1.3 - - - -
72B VAL* 4.5 4.7 - - + -
79B MET* 3.9 20.2 - - + -
82B PHE* 3.5 29.6 - + - -
98B VAL* 5.2 2.7 - - + -
185B MET* 3.4 27.6 + - - -
186B LEU* 3.2 6.9 + - - +
187B ARG 3.2 0.4 - - - -
188B PHE* 1.3 93.5 - + - +
190B LEU* 1.3 66.1 + - - +
191B ASP 3.2 0.2 - - - -
192B LYS* 3.1 40.8 + - + +
194B VAL* 3.3 22.8 - - + +
197B MET* 3.9 15.3 - - + -
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU 2.9 20.8 + - - +
187B ARG 4.0 0.4 - - - +
189B TRP* 1.3 77.4 - - - +
191B ASP* 1.3 59.0 + - - +
193B GLY* 2.9 20.3 + - - -
194B VAL* 4.0 15.5 + - + +
197B MET* 3.7 22.4 - - + -
243B VAL* 3.4 33.0 - - + -
244B PHE* 3.8 10.5 - - + -
247B TYR* 3.6 41.2 - - + -
249B ALA* 3.5 31.2 - - + -
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Residues in contact with ASP 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ARG* 2.7 29.6 + - - +
188B PHE* 4.0 7.4 - - - +
190B LEU* 1.3 77.5 - - - +
192B LYS* 1.3 60.7 + - + +
193B GLY 3.1 1.3 + - - -
247B TYR* 2.6 31.2 + - - -
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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