Contacts of the helix formed by residues 178 - 194 (chain B) in PDB entry 1Z83
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 SER 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B GLY* 1.3 74.7 - - - +
179B VAL* 1.3 64.8 + - - +
180B ASP* 3.5 8.7 + - - +
181B SER* 2.7 48.3 + - - -
182B VAL* 3.1 8.7 + - - +
632B AP5 3.7 2.7 - - - -
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Residues in contact with VAL 179 (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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23B THR* 4.0 16.4 - - + -
24B GLN* 3.3 16.9 + - - +
27B LYS* 3.6 29.8 - - + +
178B SER* 1.3 73.4 - - - +
180B ASP* 1.3 60.1 + - - +
183B PHE* 3.0 25.3 + - - +
632B AP5 3.5 39.0 + - + +
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Residues in contact with ASP 180 (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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27B LYS* 4.2 18.4 + - - -
178B SER* 3.1 7.7 + - - +
179B VAL* 1.3 82.2 - - - +
181B SER* 1.3 62.4 + - - +
183B PHE* 3.9 5.3 - - - +
184B SER* 3.1 24.3 + - - -
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Residues in contact with SER 181 (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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176B GLU 4.3 2.3 + - - -
177B GLY* 3.6 6.8 - - - -
178B SER* 2.7 43.5 + - - -
180B ASP* 1.3 73.0 - - - +
182B VAL* 1.3 65.6 + - - +
184B SER* 2.8 23.5 + - - -
185B GLN* 3.3 17.9 + - - +
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Residues in contact with VAL 182 (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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24B GLN* 3.6 32.8 - - + +
118B VAL* 5.2 1.1 - - + -
173B VAL* 4.0 22.9 - - + -
174B ASN 3.6 17.7 - - - +
175B ALA* 3.7 24.9 - - + +
176B GLU 4.2 2.9 - - - +
177B GLY 4.4 1.8 - - - +
178B SER 3.1 15.8 + - - +
181B SER* 1.3 80.2 + - - +
183B PHE* 1.3 61.9 + - - +
185B GLN* 3.1 22.9 + - - +
186B VAL* 3.1 12.1 + - + +
632B AP5 4.5 4.9 - - - +
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Residues in contact with PHE 183 (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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24B GLN* 3.2 21.1 + - - +
27B LYS* 3.4 59.5 - - + -
28B ILE* 3.7 23.8 - - + -
31B LYS* 4.0 20.2 - - + -
32B TYR* 4.5 1.8 - + - -
179B VAL 3.0 18.0 + - - +
180B ASP* 4.0 4.9 - - - +
182B VAL* 1.3 76.4 - - - +
184B SER* 1.3 57.9 + - - +
186B VAL* 3.1 9.2 + - + +
187B CYS* 2.8 54.4 + - - -
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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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180B ASP 3.1 15.3 + - - -
181B SER* 2.8 22.2 + - - -
183B PHE* 1.3 77.0 - - - +
185B GLN* 1.3 61.3 + - - +
187B CYS* 3.5 7.3 + - - +
188B THR* 3.1 25.3 + - - -
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Residues in contact with GLN 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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172B LYS 4.8 0.9 - - - +
173B VAL* 3.5 18.1 - - + -
174B ASN* 2.8 54.3 + - - +
176B GLU 5.3 1.2 + - - -
181B SER* 3.3 22.7 + - - +
182B VAL* 3.1 11.2 + - - +
184B SER* 1.3 75.8 + - - +
186B VAL* 1.3 67.0 + - - +
188B THR* 3.2 17.4 + - - -
189B HIS* 3.3 19.2 + - + +
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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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24B GLN* 3.6 20.4 - - + +
28B ILE* 3.8 35.7 - - + -
116B LEU* 4.1 17.3 - - + -
118B VAL* 6.2 0.7 - - + -
173B VAL* 4.0 23.6 - - + -
182B VAL* 3.1 15.8 + - + +
183B PHE* 3.1 15.5 + - + +
185B GLN* 1.3 75.9 - - - +
187B CYS* 1.3 62.2 + - - +
189B HIS* 3.2 7.4 + - - +
190B LEU* 3.0 30.2 + - + +
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Residues in contact with CYS 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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31B LYS* 3.0 32.8 - - - +
32B TYR* 3.6 12.8 - - - +
183B PHE* 2.8 52.9 + - - +
184B SER* 3.9 7.0 - - - +
185B GLN 3.2 0.4 - - - -
186B VAL* 1.3 77.2 - - - +
188B THR* 1.3 54.6 + - - +
190B LEU* 4.5 0.7 - - - -
191B ASP* 2.7 44.3 + - - +
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Residues in contact with THR 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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184B SER 3.1 13.1 + - - -
185B GLN* 3.2 13.3 + - - -
187B CYS* 1.3 77.7 - - - +
189B HIS* 1.3 67.5 + - + +
191B ASP* 4.1 5.3 - - - +
192B ALA* 3.2 22.9 + - - +
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Residues in contact with HIS 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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114B LEU* 4.6 5.2 - - + +
116B LEU* 4.2 10.3 - - + -
171B ARG* 3.6 49.6 + - + +
172B LYS 3.1 22.6 + - - -
173B VAL* 3.7 18.5 - - + +
185B GLN* 3.3 17.2 + - - +
186B VAL 3.2 7.4 + - - +
188B THR* 1.3 80.9 - - + +
190B LEU* 1.3 66.0 + - + +
192B ALA* 3.6 7.0 + - - +
193B LEU* 3.4 22.7 + - - +
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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
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11B ILE* 4.0 27.1 - - + -
28B ILE* 3.8 23.1 - - + -
32B TYR* 3.7 38.1 - - + +
91B LEU* 5.9 0.4 - - + -
114B LEU* 4.1 15.9 - - + -
116B LEU* 5.3 8.1 - - + -
186B VAL* 3.0 38.4 + - + +
189B HIS* 1.3 74.2 - - + +
191B ASP* 1.3 60.9 + - - +
193B LEU* 3.2 5.7 + - + +
194B LEU* 2.8 43.6 + - + +
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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
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31B LYS* 4.6 6.8 + - - -
32B TYR* 2.6 32.5 + - - -
187B CYS* 2.7 32.6 + - - +
188B THR* 4.1 5.6 - - - +
190B LEU* 1.3 71.8 - - - +
192B ALA* 1.3 61.3 + - - +
193B LEU 3.2 0.5 + - - -
194B LEU* 3.4 21.0 + - - +
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Residues in contact with ALA 192 (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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171B ARG* 6.2 2.0 - - - +
188B THR 3.2 17.5 + - - +
189B HIS* 3.8 7.0 - - - +
190B LEU 3.3 0.4 - - - -
191B ASP* 1.3 78.0 - - - +
193B LEU* 1.3 62.5 + - + +
194B LEU 5.1 0.2 - - - -
3C GLU* 3.5 46.3 - - + +
7C LYS* 4.0 14.7 - - - +
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Residues in contact with LEU 193 (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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113B THR* 5.3 10.1 - - + -
114B LEU* 4.0 32.5 - - + -
171B ARG* 5.0 7.6 - - - +
189B HIS 3.4 9.5 + - - +
190B LEU* 3.2 11.1 + - + +
191B ASP 3.1 0.6 - - - -
192B ALA* 1.3 82.5 - - + +
194B LEU* 1.3 74.1 + - + +
6C LYS* 6.3 2.7 - - + -
7C LYS* 3.9 18.4 - - - +
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Residues in contact with LEU 194 (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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9B ASN* 4.2 11.2 - - - +
11B ILE* 6.2 2.2 - - + -
32B TYR* 3.6 34.5 - - + -
34B TYR* 3.5 36.3 - - + +
190B LEU* 2.8 28.7 + - + +
191B ASP* 3.5 15.9 - - - +
192B ALA 5.1 0.4 - - - +
193B LEU* 1.3 86.2 - - + +
7C LYS* 5.0 5.5 - - - +
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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