Contacts of the helix formed by residues 170 - 187 (chain B) in PDB entry 2YZ2
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 ASP 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ASN* 3.4 31.5 - - - +
42A THR* 3.5 23.3 + - - +
196A HIS* 3.8 32.1 + - + +
168B GLY 4.0 1.0 + - - -
169B LEU* 1.3 78.6 - - - +
171B ARG* 1.3 67.6 + - - +
172B GLU* 3.0 15.0 + - - +
173B GLY* 3.2 16.7 + - - -
174B LYS* 3.0 22.5 + - - +
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Residues in contact with ARG 171 (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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196A HIS* 5.1 2.6 - - - +
233A PHE* 4.7 34.5 - - + +
235A THR* 6.2 4.6 - - - +
170B ASP* 1.3 74.8 - - - +
172B GLU* 1.3 60.9 + - + +
174B LYS* 3.6 27.2 + - - +
175B THR* 2.8 47.0 + - - +
178B LEU* 5.3 1.0 - - - +
200B THR* 2.8 42.8 + - - +
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Residues in contact with GLU 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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41A ASN* 3.2 37.6 + - - +
233A PHE* 3.4 34.0 - - + -
170B ASP* 3.0 11.0 - - - +
171B ARG* 1.3 78.0 - - + +
173B GLY* 1.3 61.1 + - - +
175B THR* 3.5 6.7 + - - -
176B ASP* 3.0 30.1 + - - +
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Residues in contact with GLY 173 (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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142B GLY* 6.0 6.7 - - - -
145B ARG* 5.9 1.7 - - - +
169B LEU* 3.9 19.9 - - - +
170B ASP* 3.2 16.9 + - - -
172B GLU* 1.3 77.2 - - - +
174B LYS* 1.3 58.7 + - - +
176B ASP* 3.2 5.4 + - - +
177B LEU* 2.8 32.4 + - - +
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Residues in contact with LYS 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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196A HIS* 5.0 6.5 + - - -
197A ASP* 6.0 2.8 - - - +
166B LEU* 4.1 44.2 - - + -
169B LEU* 3.3 29.3 + - + +
170B ASP 3.0 19.7 + - - +
171B ARG* 3.7 34.0 - - - +
173B GLY* 1.3 75.0 - - - +
175B THR* 1.3 56.7 + - - +
177B LEU* 3.7 0.5 - - - +
178B LEU* 2.8 39.8 + - + +
197B ASP* 3.2 23.0 + - - +
200B THR* 4.6 3.2 + - + +
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Residues in contact with THR 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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171B ARG* 2.8 40.5 + - - +
172B GLU* 3.7 6.0 - - - -
173B GLY 3.3 0.2 - - - -
174B LYS* 1.3 76.9 - - - +
176B ASP* 1.3 57.8 + - - +
178B LEU* 3.5 4.8 + - - +
179B ARG* 3.0 28.8 + - + +
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Residues in contact with ASP 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLY* 4.8 3.8 - - - +
146B ARG* 2.7 44.9 + - - +
172B GLU 3.0 17.4 + - - +
173B GLY* 3.8 4.9 - - - +
175B THR* 1.3 76.1 - - - +
177B LEU* 1.3 67.9 + - - +
179B ARG* 2.8 40.0 + - - +
180B ILE* 3.2 22.3 + - - +
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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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145B ARG* 3.4 42.4 - - + +
149B ILE* 3.4 33.0 - - + -
162B LEU* 4.4 2.9 - - + -
165B PRO* 3.8 30.1 - - + +
166B LEU* 4.2 10.3 - - + -
169B LEU* 4.1 6.7 - - + -
173B GLY 2.8 19.7 + - - +
174B LYS 3.8 2.7 - - - +
176B ASP* 1.3 73.2 + - - +
178B LEU* 1.3 65.2 + - + +
180B ILE* 3.1 16.0 + - - +
181B VAL* 3.2 25.0 + - + +
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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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165B PRO* 5.9 1.6 - - + -
166B LEU* 4.2 16.6 - - + -
171B ARG* 5.3 0.9 - - - +
174B LYS* 2.8 26.6 + - + +
175B THR* 3.8 4.5 - - - +
177B LEU* 1.3 76.2 - - + +
179B ARG* 1.3 59.5 + - - +
181B VAL* 3.5 14.2 + - + +
182B GLU* 3.0 32.0 + - - +
193B LEU* 5.5 5.4 - - + -
200B THR* 3.3 36.3 - - + +
201B VAL* 3.7 23.1 - - + -
204B HIS* 3.8 41.2 - - + +
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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
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123B PHE 5.1 1.2 + - - -
124B VAL 3.6 10.7 + - - -
125B GLY* 5.0 3.0 - - - -
146B ARG* 3.5 15.4 - - - +
175B THR* 3.0 16.8 + - + +
176B ASP* 2.8 33.3 + - - +
178B LEU* 1.3 75.8 - - - +
180B ILE* 1.3 89.7 + - - +
182B GLU* 3.2 9.6 + - + +
183B LYS* 3.2 44.2 + - + +
204B HIS* 5.9 0.2 - - - -
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Residues in contact with ILE 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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123B PHE* 4.1 20.6 - - + +
124B VAL* 3.9 30.1 - - + +
146B ARG* 5.4 3.1 - - + -
149B ILE* 3.7 35.9 - - + -
160B LEU* 6.2 2.2 - - + -
176B ASP* 3.2 16.1 + - - +
177B LEU* 3.1 10.2 + - - +
179B ARG* 1.3 110.5 - - - +
181B VAL* 1.3 62.5 + - + +
183B LYS* 3.1 8.0 + - + +
184B TRP* 3.0 26.5 + - + +
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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
----------------------------------------------------------
35B CYS* 4.7 5.8 - - - -
149B ILE* 5.8 1.6 - - + -
160B LEU* 5.0 7.2 - - + -
162B LEU* 4.0 26.5 - - + -
177B LEU* 3.2 20.8 + - + +
178B LEU* 3.6 20.0 - - + +
179B ARG 3.2 0.4 - - - -
180B ILE* 1.3 76.5 - - + +
182B GLU* 1.3 66.3 + - - +
184B TRP* 3.2 7.6 + - - +
185B LYS* 3.0 31.3 + - + +
191B VAL* 4.2 26.7 - - + -
193B LEU* 4.8 6.3 - - + -
204B HIS* 5.3 6.7 - - + +
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Residues in contact with GLU 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 12.6 + - - +
179B ARG* 3.2 11.1 + - + +
181B VAL* 1.3 76.9 - - - +
183B LYS* 1.3 56.0 + - + +
185B LYS* 2.7 44.0 + - - +
186B THR* 2.9 32.3 + - - +
203B ASN 4.4 1.4 - - - +
204B HIS* 2.6 46.3 - - + +
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Residues in contact with LYS 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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122B GLU 4.7 2.4 + - - -
123B PHE* 3.1 60.2 + - + +
179B ARG* 3.2 33.8 + - + +
180B ILE* 3.1 9.2 + - - +
182B GLU* 1.3 76.4 - - + +
184B TRP* 1.3 61.2 + - - +
186B THR* 3.3 10.2 + - - -
187B LEU* 3.2 25.5 + - - +
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Residues in contact with TRP 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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123B PHE* 3.5 22.1 - + + -
153B ILE* 3.5 42.0 - - + -
156B GLU* 4.8 1.6 - - - -
157B PRO* 3.3 39.5 - - + -
159B ILE 4.6 0.2 - - - -
160B LEU* 3.2 35.6 - - + +
180B ILE 3.0 12.8 + - - +
181B VAL* 3.4 12.8 - - - +
183B LYS* 1.3 73.0 - - - +
185B LYS* 1.3 66.4 + - - +
187B LEU* 3.1 30.9 + - + +
189B LYS* 3.5 39.5 + - + +
190B THR 3.0 27.6 + - - -
191B VAL* 4.0 14.6 - - + -
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Residues in contact with LYS 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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33B GLY 4.8 11.7 - - - +
35B CYS* 3.8 21.5 - - + +
181B VAL* 3.0 23.7 + - + +
182B GLU* 2.7 38.4 + - - +
184B TRP* 1.3 75.8 - - - +
186B THR* 1.3 54.6 + - - +
188B GLY* 2.7 26.7 + - - -
189B LYS 4.1 10.5 - - - +
191B VAL* 3.8 17.3 - - + -
204B HIS* 2.9 27.8 + - - +
205B VAL* 4.8 0.6 - - - +
206B ASP* 4.5 14.3 + - - -
222B ARG* 5.6 1.2 - - - +
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Residues in contact with THR 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 GLU* 2.9 17.8 + - - +
183B LYS* 3.6 12.1 - - - -
184B TRP 3.1 0.6 - - - -
185B LYS* 1.3 76.4 - - - +
187B LEU* 1.3 64.0 + - - +
188B GLY* 3.2 1.4 + - - -
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Residues in contact with LEU 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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123B PHE* 3.9 30.7 - - + -
183B LYS 3.2 13.7 + - - +
184B TRP* 3.1 18.6 + - + +
186B THR* 1.3 78.6 - - - +
188B GLY* 1.4 57.3 + - - +
189B LYS* 3.9 34.2 - - + +
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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