Contacts of the helix formed by residues 170 - 188 (chain B) in PDB entry 1Z10
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 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ILE* 3.1 15.9 - - + +
169B ASP* 1.3 90.0 - - - +
171B THR* 1.3 64.9 + - - +
172B PHE 3.4 0.4 - - - -
173B PHE* 3.0 13.8 + - + +
174B LEU* 2.9 41.9 + - + +
311B ARG* 4.6 2.5 - - + -
487B TYR* 3.6 43.5 - - + +
489B MET* 4.1 17.9 - - + -
491B PHE* 4.5 12.1 - - + -
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Residues in contact with THR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASP* 2.7 28.9 + - - -
170B PRO* 1.3 79.8 - - - +
172B PHE* 1.3 82.5 + - + +
174B LEU* 3.5 3.3 + - - +
175B SER* 3.0 26.9 + - - +
206B LEU* 4.0 19.3 - - + -
307B SER* 4.4 2.3 + - - -
311B ARG* 3.3 38.8 + - - +
486B ASN* 6.2 0.7 - - - -
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Residues in contact with PHE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASP* 4.4 5.9 + - - -
170B PRO 3.4 0.4 - - - -
171B THR* 1.3 90.9 - - + +
173B PHE* 1.3 67.9 - - + +
174B LEU 3.2 1.1 - - - -
175B SER* 3.3 13.9 - - - -
176B ARG* 2.9 38.8 + - + +
199B LEU* 3.3 31.4 - - + -
202B LEU* 3.7 33.2 - - + -
203B ARG* 3.8 21.5 - - + -
206B LEU* 3.8 24.2 - - + -
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 4.1 14.1 - - + +
159B ALA* 4.0 18.2 - - + -
160B LEU* 4.1 18.8 - - + -
163B THR* 3.8 29.2 - - + -
168B ILE* 3.7 24.7 - - + -
169B ASP 3.4 21.3 - - - -
170B PRO* 3.0 8.1 + - + +
172B PHE* 1.3 80.9 - - + +
174B LEU* 1.3 64.8 + - + +
176B ARG* 3.5 31.3 + - - +
177B THR* 3.3 25.1 + - - -
193B TYR* 5.8 0.2 - - - -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 4.3 23.8 - - + -
160B LEU* 5.9 1.3 - - + -
170B PRO* 2.9 35.8 + - + +
171B THR 3.7 3.8 - - - +
173B PHE* 1.3 80.0 - - + +
175B SER* 1.3 58.9 + - - +
177B THR* 3.3 5.5 + - - -
178B VAL* 2.9 32.7 + - - +
307B SER* 4.4 9.9 - - - +
310B LEU* 4.0 21.5 - - + +
311B ARG* 3.7 33.4 - - + +
314B PHE* 3.9 27.6 - - + -
456B VAL* 5.7 0.2 - - + -
491B PHE* 5.7 4.0 - - + -
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B THR* 3.0 18.7 + - - +
172B PHE* 3.3 25.5 - - - -
174B LEU* 1.3 73.4 - - - +
176B ARG* 1.3 69.3 + - - +
178B VAL* 3.9 0.8 - - - +
179B SER* 2.9 27.9 + - - -
202B LEU* 3.8 15.9 - - - +
303B THR* 4.4 4.6 - - - +
304B GLU* 5.2 4.3 - - - -
307B SER* 3.5 26.7 + - - -
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Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ALA* 4.0 6.9 - - - +
172B PHE* 2.9 33.7 + - + +
173B PHE* 3.5 40.3 + - - +
175B SER* 1.3 76.7 + - - +
177B THR* 1.3 64.7 + - - +
180B ASN* 3.2 22.3 + - - -
193B TYR* 3.5 65.9 + - + +
194B LYS* 6.1 1.2 - - - +
198B PHE* 3.4 22.2 - - + -
199B LEU* 5.4 6.7 - - + -
202B LEU* 3.4 24.0 - - + -
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Residues in contact with THR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLU* 3.4 30.2 - - + +
156B LEU* 3.3 27.0 - - + +
173B PHE 3.3 15.9 + - - -
174B LEU 3.3 4.6 + - - +
175B SER 3.3 0.2 - - - -
176B ARG* 1.3 80.6 - - - +
178B VAL* 1.3 64.1 + - + +
180B ASN 3.4 5.5 + - - -
181B VAL* 3.9 4.2 + - - +
193B TYR* 2.7 24.5 + - - -
310B LEU* 6.3 0.9 - - + -
452B PHE* 3.4 34.3 - - + -
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU 2.9 19.4 + - - +
175B SER 3.9 2.9 - - - +
177B THR* 1.3 76.9 - - - +
179B SER* 1.3 64.2 + - - +
181B VAL* 3.0 21.7 + - - +
182B ILE 4.0 2.4 + - - -
302B GLY 3.7 14.2 - - - +
303B THR* 3.4 26.2 - - - +
306B VAL* 3.5 25.8 - - + -
307B SER* 3.9 10.5 - - - +
310B LEU* 3.6 19.7 - - + -
448B GLU* 3.7 17.8 - - - +
452B PHE* 4.3 7.4 - - + -
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B SER 2.9 18.9 + - - -
176B ARG 4.0 0.2 - - - -
178B VAL* 1.3 77.8 - - - +
180B ASN* 1.3 57.9 + - - +
182B ILE* 3.5 3.2 - - - +
183B SER* 2.8 35.3 + - - -
198B PHE* 3.7 12.8 - - - -
202B LEU* 3.7 13.3 - - - +
299B PHE* 3.3 18.9 - - - -
303B THR* 3.1 31.1 + - - -
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Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 5.4 0.2 - - - +
152B GLU* 3.0 40.4 + - - +
176B ARG 3.2 11.8 + - - +
177B THR 3.8 0.7 - - - +
178B VAL 3.2 1.0 + - - -
179B SER* 1.3 77.8 - - - +
181B VAL* 1.3 56.8 + - - +
183B SER* 3.8 3.1 - - - -
184B SER* 2.9 32.7 + - - -
190B ARG* 3.4 9.2 - - + +
191B PHE* 2.7 49.8 + - - -
193B TYR* 3.3 16.6 - - - -
198B PHE* 3.4 14.4 - - - -
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 4.4 11.2 - - + -
148B ARG* 5.2 4.7 - - + +
149B ILE* 3.8 28.0 - - + +
152B GLU* 4.5 11.2 - - + -
177B THR 3.9 9.9 - - - +
178B VAL 3.0 13.7 + - - +
180B ASN* 1.3 75.4 - - - +
182B ILE* 1.3 67.4 + - - +
184B SER* 3.1 20.3 + - - -
185B ILE* 3.3 11.1 + - + +
444B LEU* 3.9 14.4 - - + -
448B GLU* 3.4 21.8 - - - +
452B PHE* 3.9 20.6 - - + -
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Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.6 6.3 - - + -
178B VAL 4.0 1.0 + - - -
179B SER* 3.5 10.5 - - - +
181B VAL* 1.3 80.3 - - - +
183B SER* 1.3 66.5 + - - +
185B ILE* 3.2 24.7 + - + +
186B VAL* 2.9 38.8 + - + +
298B LEU* 3.6 24.9 - - + +
299B PHE* 4.1 13.7 - - + +
302B GLY* 4.0 18.6 - - - +
303B THR* 3.8 19.5 - - - +
444B LEU* 4.2 7.0 - - + -
448B GLU* 4.8 0.6 + - - +
500B HEM 4.0 23.6 - - + -
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B SER* 2.8 24.4 + - - -
180B ASN* 3.7 9.6 - - - -
182B ILE* 1.3 78.8 - - - +
184B SER* 1.3 55.9 + - - +
186B VAL* 4.0 2.0 - - - -
187B PHE* 2.8 46.0 + - - +
188B GLY 3.6 0.2 + - - -
189B ASP 3.6 6.2 - - - +
191B PHE* 3.1 35.3 - - - -
299B PHE* 3.3 16.0 - - - -
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Residues in contact with SER 184 (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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148B ARG* 3.1 46.7 + - - +
152B GLU* 5.6 0.2 + - - -
180B ASN 2.9 18.9 + - - -
181B VAL 3.1 7.8 + - - -
183B SER* 1.3 74.5 - - - +
185B ILE* 1.3 57.2 + - - +
188B GLY* 3.0 30.5 + - - +
189B ASP* 3.9 13.5 + - - +
190B ARG* 3.8 16.3 + - - +
265B ARG 5.2 0.5 - - - +
266B ASP* 4.6 0.2 - - - +
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Residues in contact with ILE 185 (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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135B LEU* 3.8 25.4 - - + -
138B PHE* 4.2 28.1 - - + +
140B VAL* 4.1 16.6 - - + -
145B ILE* 3.6 38.8 - - + -
148B ARG* 4.2 5.4 - - - +
181B VAL 3.7 11.9 - - - +
182B ILE* 3.2 20.8 + - + +
184B SER* 1.3 80.5 - - - +
186B VAL* 1.3 63.1 + - + +
266B ASP* 3.2 8.1 - - - +
267B PHE* 3.0 25.6 + - + -
444B LEU* 4.2 9.4 - - + -
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Residues in contact with VAL 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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182B ILE* 2.9 45.6 + - + +
183B SER* 4.0 1.6 - - - -
185B ILE* 1.3 76.7 - - + +
187B PHE* 1.3 93.1 + - + +
188B GLY 3.5 0.4 - - - -
266B ASP* 3.3 15.8 - - - +
267B PHE* 3.7 23.8 - - + -
268B ILE* 3.4 19.8 + - - +
295B THR* 4.3 15.7 - - + +
298B LEU* 4.3 17.9 - - + -
299B PHE* 5.0 7.0 - - + -
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Residues in contact with PHE 187 (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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183B SER* 2.8 32.1 + - - +
186B VAL* 1.3 90.6 - - + +
188B GLY* 1.3 57.8 + - - +
189B ASP* 3.2 13.1 + - - +
191B PHE* 4.0 13.5 - + + -
247B PHE* 3.8 17.0 - + - -
248B ILE* 3.6 32.1 - - + -
251B LYS* 4.1 39.4 + - + +
255B ASN* 5.0 4.3 - - - +
266B ASP* 2.8 14.3 - - - +
268B ILE* 4.0 16.4 - - + -
295B THR* 4.3 1.6 - - + -
299B PHE* 3.8 29.2 - + - -
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Residues in contact with GLY 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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148B ARG* 4.9 4.2 + - - -
184B SER* 3.0 19.9 + - - +
187B PHE* 1.3 77.7 - - - +
189B ASP* 1.3 62.8 + - - +
265B ARG* 4.1 11.9 - - - +
266B ASP* 3.1 19.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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