Contacts of the helix formed by residues 171 - 183 (chain B) in PDB entry 1SZ1
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 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B GLY* 4.2 0.8 + - - -
163B ALA* 3.7 29.6 - - - +
169B GLY 3.9 2.6 + - - -
170B PHE* 1.3 72.6 - - - +
172B GLY* 1.3 66.5 + - - +
173B TYR* 4.4 5.3 - - - +
174B LEU* 3.0 36.1 + - - +
175B CYS* 3.1 14.0 + - - -
226B VAL* 3.8 17.7 + - - +
229B ASN* 6.4 0.2 - - - -
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Residues in contact with GLY 172 (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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152B LYS* 4.2 10.3 - - - -
161B TYR* 3.8 29.9 + - - -
162B GLY* 5.8 0.2 - - - -
171B SER* 1.3 70.4 - - - +
173B TYR* 1.3 61.4 + - - +
175B CYS* 3.1 8.5 + - - +
176B GLU* 3.0 27.8 + - - +
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Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG* 6.0 1.6 - - - -
133B HIS* 3.1 53.5 - + + +
136B TRP* 5.7 1.4 - + + +
137B LEU* 3.5 28.0 - - + -
171B SER* 3.3 5.3 - - - +
172B GLY* 1.3 74.5 - - - +
174B LEU* 1.3 56.3 + - - +
176B GLU* 3.3 7.8 + - - +
177B LEU* 2.9 50.5 + - + +
218B ASP* 2.6 32.9 + - - -
219B PRO* 3.8 12.0 - - - +
220B VAL* 4.4 1.4 - - - +
226B VAL* 3.6 22.2 - - + -
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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
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169B GLY 5.1 1.8 - - - +
170B PHE* 3.7 28.9 - - + -
171B SER* 3.0 32.2 + - - +
173B TYR* 1.3 75.7 - - - +
175B CYS* 1.3 66.6 + - - +
177B LEU* 3.0 7.4 + - + +
178B LEU* 2.9 39.4 + - + +
214B PHE* 5.9 0.7 - - + -
216B VAL* 3.8 41.7 - - + -
226B VAL* 3.7 15.7 - - + +
227B ALA* 4.0 22.9 - - + -
230B LEU* 5.2 2.5 - - + -
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Residues in contact with CYS 175 (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 VAL* 4.5 11.0 - - + -
151B LEU* 3.5 21.2 - - + +
152B LYS* 4.5 5.8 - - + -
155B LEU* 3.8 28.5 - - - -
161B TYR* 4.2 8.7 - - - -
170B PHE* 4.0 9.0 - - - -
171B SER 3.1 21.8 - - - -
172B GLY* 3.1 11.0 + - - +
174B LEU* 1.3 75.3 - - - +
176B GLU* 1.3 64.1 + - - +
178B LEU* 3.1 8.5 + - - +
179B ILE* 3.0 27.9 + - - +
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Residues in contact with GLU 176 (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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47B SER* 5.7 0.3 + - - -
50B ARG* 3.5 26.6 + - - -
52B THR* 3.2 29.3 + - - -
137B LEU* 3.3 26.2 - - + +
141B ILE* 3.2 25.6 - - + +
148B VAL* 3.7 20.6 - - + -
152B LYS* 5.0 5.2 + - - -
172B GLY 3.0 17.5 + - - +
173B TYR* 3.6 9.6 - - - +
175B CYS* 1.3 76.7 - - - +
177B LEU* 1.3 62.1 + - - +
178B LEU 3.1 0.3 + - - -
179B ILE* 3.3 3.5 + - - +
180B VAL* 3.1 28.9 + - - +
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Residues in contact with LEU 177 (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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136B TRP* 3.9 27.1 - - + -
137B LEU* 4.2 5.4 - - + -
173B TYR* 2.9 52.2 + - + +
174B LEU 3.3 7.9 - - - +
176B GLU* 1.3 76.1 - - - +
178B LEU* 1.3 56.5 + - + +
180B VAL* 3.5 6.7 - - - +
181B PHE* 3.1 27.0 + - - +
203B VAL* 4.0 21.6 - - + +
216B VAL* 4.6 7.4 - - + -
217B VAL 4.8 0.2 - - - +
219B PRO* 3.9 19.5 - - + -
226B VAL* 3.7 28.7 - - + -
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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
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151B LEU* 4.1 11.2 - - + -
170B PHE* 4.3 20.2 - - + -
174B LEU* 2.9 38.8 + - + +
175B CYS* 3.3 16.4 - - - +
176B GLU 3.1 0.2 - - - -
177B LEU* 1.3 72.8 - - + +
179B ILE* 1.3 62.1 + - - +
180B VAL 3.1 1.6 - - - -
181B PHE* 2.8 22.1 + - - +
182B TYR* 3.0 24.6 + - + -
188B THR* 4.2 13.9 - - + -
195B TRP* 3.9 31.2 - - + -
201B ILE* 4.2 17.9 - - + -
214B PHE* 6.2 0.2 - - + -
216B VAL* 5.3 4.7 - - + -
238B PHE* 5.9 0.2 - - + -
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Residues in contact with ILE 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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141B ILE* 5.5 1.8 - - + -
144B LYS* 3.8 34.2 - - + +
147B GLU* 3.4 28.7 - - + +
148B VAL* 3.5 27.8 - - + -
151B LEU* 4.0 13.7 - - + -
175B CYS 3.0 14.3 + - - +
176B GLU 3.8 2.7 - - - +
178B LEU* 1.3 73.7 - - - +
180B VAL* 1.3 57.9 + - + +
183B GLY* 2.9 30.9 + - - +
184B SER* 3.9 6.5 - - - +
185B PHE* 3.5 25.1 - - + +
188B THR* 3.9 9.0 - - - +
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Residues in contact with VAL 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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136B TRP* 4.4 24.0 - - + -
137B LEU* 3.8 22.0 - - + -
140B ARG* 4.3 28.9 - - + +
141B ILE* 4.3 14.1 - - + -
144B LYS* 5.4 9.0 - - + +
176B GLU 3.1 13.4 + - - +
177B LEU* 3.5 11.7 - - - +
178B LEU 3.1 0.4 - - - -
179B ILE* 1.3 80.5 - - + +
181B PHE* 1.3 63.4 + - - +
183B GLY* 4.0 4.9 + - - -
203B VAL* 4.6 3.6 - - + -
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Residues in contact with PHE 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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177B LEU 3.1 14.2 + - - +
178B LEU* 2.8 18.0 + - - +
180B VAL* 1.3 75.9 - - - +
182B TYR* 1.3 88.3 + + + +
201B ILE* 3.9 18.4 - - + -
202B ASP 3.5 21.1 - - - -
203B VAL* 3.7 24.5 - - + -
206B GLY* 3.5 22.0 - - - -
207B GLU 3.7 22.7 - - - -
208B VAL* 3.8 22.4 - - + -
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Residues in contact with TYR 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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178B LEU* 3.0 19.4 + - + -
181B PHE* 1.3 105.9 - + - +
183B GLY* 1.3 59.8 + - - +
184B SER 3.6 0.9 - - - -
187B GLU* 3.3 42.9 - - + +
188B THR* 3.6 35.2 - - + +
191B ASN* 3.4 31.6 - - + +
195B TRP* 3.1 41.7 + + - -
201B ILE* 3.9 11.5 - - + +
208B VAL* 4.8 7.8 - - + +
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Residues in contact with GLY 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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144B LYS* 4.1 28.0 - - - +
147B GLU* 4.7 1.6 - - - +
179B ILE* 2.9 18.4 + - - +
180B VAL 4.0 4.0 + - - -
181B PHE 3.7 0.8 - - - -
182B TYR* 1.3 79.0 - - - +
184B SER* 1.3 63.6 + - - +
187B GLU* 5.1 0.4 - - - -
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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