Contacts of the helix formed by residues 179 - 194 (chain B) in PDB entry 1SZU
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 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B PRO* 4.4 2.4 - - - +
174B PRO* 4.9 7.0 - - - -
177B GLY 3.5 2.5 + - - -
178B ILE* 1.3 78.4 - - - +
180B GLU* 1.3 65.4 - - - +
181B ASP* 3.4 10.5 + - - +
182B ASP* 2.7 41.3 + - - -
183B ALA* 3.0 21.7 + - - +
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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
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172B PRO* 4.1 12.5 - - + +
174B PRO* 5.4 7.6 - - + +
179B SER* 1.3 73.2 - - - +
181B ASP* 1.3 63.2 + - - +
183B ALA* 3.2 8.3 + - - +
184B ILE* 3.0 27.2 + - - +
218B SER* 2.7 34.8 + - - -
220B ALA* 4.0 8.8 - - - +
221B PHE* 3.7 29.4 + - + +
224B ARG* 4.0 15.1 + - - +
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Residues in contact with ASP 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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179B SER* 3.1 9.1 + - - +
180B GLU* 1.3 79.2 - - - +
182B ASP* 1.3 58.9 + - - +
184B ILE* 3.8 1.0 - - - +
185B ALA* 2.8 31.3 + - - +
224B ARG* 2.7 42.4 + - - +
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Residues in contact with ASP 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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170B LEU* 4.3 10.8 - - + +
177B GLY 3.6 10.9 - - - +
178B ILE* 3.7 12.1 - - + +
179B SER* 2.7 43.6 + - - +
181B ASP* 1.3 74.6 - - - +
183B ALA* 1.3 60.6 + - - +
185B ALA* 3.3 6.8 + - - +
186B SER* 2.8 31.4 + - - -
189B ARG* 5.2 1.2 + - - -
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Residues in contact with ALA 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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134B PHE* 5.2 0.2 - - - -
169B ALA* 5.0 0.2 - - - +
170B LEU* 3.2 28.3 - - - +
171B TYR 4.6 0.2 - - - -
172B PRO* 4.0 13.0 - - + -
178B ILE* 4.5 1.0 - - - +
179B SER 3.0 12.3 + - - +
180B GLU 3.4 8.7 - - - +
182B ASP* 1.3 75.0 - - - +
184B ILE* 1.3 63.2 + - - +
186B SER* 2.5 24.0 + - - -
187B ILE* 3.4 10.0 + - - +
221B PHE* 3.4 23.1 - - + -
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Residues in contact with ILE 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 GLU 3.0 15.0 + - - +
181B ASP 4.0 0.9 - - - +
183B ALA* 1.3 72.7 - - - +
185B ALA* 1.3 67.5 + - - +
187B ILE* 3.0 27.4 + - + +
188B HIS* 3.3 21.9 + - + +
221B PHE* 3.4 29.8 - - + -
224B ARG* 3.7 45.8 - - + +
225B LEU* 4.2 11.0 - - - +
228B LEU* 4.4 7.2 - - + -
1003B SO4 3.3 27.8 - - - +
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Residues in contact with ALA 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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181B ASP 2.8 19.4 + - - +
182B ASP* 3.6 7.9 - - - +
184B ILE* 1.3 77.3 - - - +
186B SER* 1.3 58.3 + - - +
188B HIS* 3.2 11.7 + - - +
189B ARG* 3.0 43.8 + - - +
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Residues in contact with SER 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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168B ARG 4.8 2.0 - - - +
169B ALA* 3.5 6.9 - - - +
170B LEU* 3.0 41.2 + - - -
182B ASP 2.8 13.6 + - - -
183B ALA 2.5 19.5 + - - -
185B ALA* 1.3 77.7 - - - +
187B ILE* 1.3 58.7 + - - +
189B ARG* 3.5 23.3 + - - +
190B ILE* 3.3 26.5 + - - +
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Residues in contact with ILE 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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132B ILE* 4.1 15.5 - - + -
134B PHE* 4.2 14.8 - - + -
169B ALA* 3.9 17.0 - - + -
183B ALA 3.8 12.6 - - - +
184B ILE* 3.0 16.8 + - + +
186B SER* 1.3 74.4 - - - +
188B HIS* 1.3 66.2 + - - +
190B ILE* 3.0 11.9 + - - +
191B PHE* 3.0 47.7 + - + -
203B ILE* 4.2 4.5 - - + -
221B PHE* 5.2 0.2 - - + -
225B LEU* 3.7 29.8 - - + -
228B LEU* 4.0 19.1 - - + -
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Residues in contact with HIS 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 ILE* 3.3 27.5 + - + +
185B ALA* 3.2 10.0 + - - +
187B ILE* 1.3 74.2 - - - +
189B ARG* 1.3 60.4 + - - +
191B PHE* 3.1 23.9 + + + +
192B LYS* 2.8 31.1 + - - +
228B LEU* 3.9 18.1 - - + +
232B HIS* 5.4 5.0 + - - -
1003B SO4 3.3 29.2 + - - -
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Residues in contact with ARG 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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170B LEU* 4.9 7.9 - - - +
182B ASP 5.2 0.8 + - - -
185B ALA* 3.0 27.7 + - - +
186B SER* 3.6 34.9 - - - +
188B HIS* 1.3 76.9 - - - +
190B ILE* 1.3 57.6 + - + +
192B LYS* 4.4 2.2 - - - -
193B ASN* 2.8 54.6 + - + +
135D SER* 4.8 6.3 - - - -
168D ARG* 5.3 7.6 - - + -
170D LEU* 3.2 41.2 - - - +
178D ILE* 4.6 15.6 - - - +
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Residues in contact with ILE 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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132B ILE* 4.0 28.9 - - + -
167B TYR* 3.7 40.6 - - + -
168B ARG 3.3 33.9 - - - +
169B ALA* 4.1 4.5 - - + +
186B SER 3.3 14.3 + - - +
187B ILE* 3.0 8.6 + - - +
189B ARG* 1.3 75.8 - - + +
191B PHE* 1.3 65.2 + - - +
194B ASP* 2.9 29.7 + - + +
195B ALA* 3.1 21.3 + - + +
200B ILE* 5.1 0.2 - - + -
1032D EDO 5.7 1.8 - - - +
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Residues in contact with PHE 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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132B ILE* 4.0 20.4 - - + -
187B ILE* 3.0 36.3 + - + -
188B HIS* 3.1 26.0 + + + +
190B ILE* 1.3 76.2 - - - +
192B LYS* 1.3 59.5 + - - +
195B ALA 3.3 21.1 - - - +
196B ALA* 3.8 11.6 + - - +
197B PRO* 3.6 28.1 - - + +
200B ILE* 4.1 7.6 - - + -
203B ILE* 4.9 0.2 - - + -
228B LEU* 3.9 16.2 - - + -
232B HIS* 4.0 15.7 - + - -
234B ILE* 3.6 32.3 - - + -
152D VAL* 4.2 6.6 - - - +
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Residues in contact with LYS 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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188B HIS 2.8 16.8 + - - +
189B ARG* 3.8 4.7 - - - +
191B PHE* 1.3 80.0 - - - +
193B ASN* 1.3 68.7 + - - +
1009B SO4 3.2 33.3 + - - +
150D GLY 5.4 2.7 - - - +
151D LYS* 3.3 21.2 - - + +
152D VAL* 3.1 21.7 + - - +
153D ASN 5.0 0.5 + - - -
392D PRO* 3.1 41.7 + - + -
393D TYR* 3.6 28.6 - - + +
394D TYR* 4.4 1.8 + - - -
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Residues in contact with ASN 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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189B ARG* 2.8 45.7 + - - +
192B LYS* 1.3 86.6 - - - +
194B ASP* 1.3 73.5 + - - +
135D SER* 3.2 15.8 - - - -
136D GLY 3.0 18.9 + - - +
146D LEU 5.4 0.2 - - - +
147D ALA 5.1 0.3 - - - +
149D THR 3.6 10.4 - - - +
150D GLY* 2.8 25.0 - - - +
151D LYS 3.6 11.1 + - - -
152D VAL* 3.5 10.8 - - - +
168D ARG* 3.9 10.9 + - + +
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Residues in contact with ASP 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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167B TYR* 3.7 29.9 + - + -
190B ILE* 2.9 17.1 + - + +
193B ASN* 1.3 78.7 - - - +
195B ALA* 1.3 62.8 + - - +
147D ALA 4.0 3.8 - - - +
152D VAL* 3.4 11.0 - - - +
161D LEU* 4.3 4.7 - - - +
162D MET* 5.5 5.4 + - - +
166D VAL* 4.7 8.5 - - - +
168D ARG* 2.6 56.6 + - - +
1032D EDO 4.3 9.0 + - - -
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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