Contacts of the helix formed by residues 166 - 185 (chain B) in PDB entry 2YZ5
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 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ARG 4.7 0.7 - - - +
165B LEU* 1.3 95.0 - - + +
167B GLU* 1.3 57.2 + - - +
168B GLU* 3.1 11.4 - - + +
169B ALA* 2.8 37.6 + - + +
170B LEU 2.9 10.7 + - - -
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Residues in contact with GLU 167 (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 LEU 3.3 5.2 + - - -
166B PRO* 1.3 70.1 - - - +
168B GLU* 1.3 74.9 + - - +
170B LEU* 3.7 9.7 - - - +
171B LEU* 3.0 40.1 + - + +
207B ALA* 3.6 30.9 - - + +
210B ARG* 4.8 9.2 + - - -
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Residues in contact with GLU 168 (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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166B PRO* 4.3 9.4 - - + +
167B GLU* 1.3 95.7 + - - +
169B ALA* 1.3 65.9 + - - +
171B LEU* 3.9 9.7 - - + +
172B GLU* 3.0 25.3 + - - +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LYS* 4.3 23.8 - - + +
165B LEU* 4.4 11.9 - - + -
166B PRO* 2.8 29.7 + - + +
168B GLU* 1.3 78.0 - - - +
170B LEU* 1.3 64.1 + - - +
172B GLU* 3.4 6.2 + - - +
173B LEU* 3.0 32.7 + - - +
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Residues in contact with LEU 170 (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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133B PHE* 4.3 18.6 - - + -
137B PHE* 3.7 27.4 - - + -
156B ASP* 4.5 4.7 - - + +
159B LYS* 6.3 0.7 - - + -
165B LEU* 4.6 21.5 - - + +
166B PRO 2.9 11.1 + - - +
167B GLU* 3.7 12.6 - - - +
169B ALA* 1.3 78.2 - - - +
171B LEU* 1.3 63.1 + - + +
173B LEU* 4.0 2.9 - - - +
174B ALA* 3.0 27.7 + - - +
205B ALA* 4.0 27.8 - - + -
207B ALA* 5.4 5.6 - - + -
208B LEU* 4.0 20.2 - - + -
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Residues in contact with LEU 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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167B GLU* 3.0 42.1 + - + +
168B GLU* 3.9 8.5 - - + +
170B LEU* 1.3 76.0 - - + +
172B GLU* 1.3 63.1 + - - +
174B ALA* 3.9 0.5 - - - +
175B GLU* 3.1 28.1 + - - +
178B LEU* 5.6 0.9 - - + +
207B ALA* 3.5 32.5 - - + +
208B LEU* 4.1 13.2 - - + -
211B ARG* 4.2 19.5 - - + +
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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
----------------------------------------------------------
130B LYS* 4.2 17.3 + - - -
168B GLU 3.0 19.4 + - - +
169B ALA* 3.8 4.3 - - - +
171B LEU* 1.3 79.7 - - - +
173B LEU* 1.3 69.5 + - + +
174B ALA 3.5 0.2 + - - -
175B GLU* 3.6 15.6 + - - +
176B PRO* 3.6 5.9 - - - +
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Residues in contact with LEU 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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130B LYS* 3.8 41.5 - - + +
133B PHE* 4.2 6.3 - - + -
134B ARG* 3.7 41.3 - - + +
137B PHE* 3.5 31.4 - - + +
165B LEU* 3.9 18.6 - - + -
169B ALA 3.0 18.8 + - - +
170B LEU* 5.1 0.2 - - - -
172B GLU* 1.3 85.3 - - + +
174B ALA* 1.3 60.3 + - - +
175B GLU 3.4 0.2 - - - -
176B PRO* 3.6 11.7 - - - +
177B ALA 5.0 0.2 + - - -
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Residues in contact with ALA 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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137B PHE* 3.8 29.8 - - + -
155B LEU* 5.1 2.2 - - + -
170B LEU 3.0 18.5 + - - +
171B LEU 4.2 0.9 - - - +
173B LEU* 1.3 76.1 - - - +
175B GLU* 1.3 67.1 + - - +
176B PRO 3.4 1.3 - - - -
177B ALA* 3.0 7.2 + - + +
178B LEU* 2.9 28.2 + - + +
208B LEU* 3.6 23.8 - - + -
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Residues in contact with GLU 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 LEU* 3.1 18.5 + - - +
172B GLU* 3.6 7.9 - - - +
174B ALA* 1.3 75.5 - - - +
176B PRO* 1.3 68.7 - - + +
178B LEU* 3.0 7.7 + - - +
179B ARG* 2.7 82.2 + - - +
211B ARG* 3.2 43.9 + - - +
215B LEU* 5.2 1.6 - - - -
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Residues in contact with PRO 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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137B PHE* 6.5 0.2 - - + -
141B GLU* 3.8 29.6 - - - +
145B ARG* 4.8 0.7 + - - -
172B GLU 3.6 7.4 - - - +
173B LEU* 3.6 15.5 - - - +
174B ALA 3.6 0.4 - - - -
175B GLU* 1.3 94.9 - - + +
177B ALA* 1.3 60.4 + - - +
179B ARG* 3.3 16.9 + - + +
180B ALA* 3.1 23.2 + - - +
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Residues in contact with ALA 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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137B PHE* 3.9 29.1 + - + +
140B VAL* 4.1 19.1 - - + -
141B GLU* 4.2 12.7 - - - +
144B ALA* 4.6 0.9 - - - +
155B LEU* 4.5 9.9 - - + -
173B LEU 5.0 0.2 + - - -
174B ALA 3.0 11.5 + - - +
176B PRO* 1.3 79.3 - - - +
178B LEU* 1.3 57.7 + - - +
180B ALA* 3.3 4.2 + - - +
181B VAL* 3.0 33.0 + - - +
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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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155B LEU* 3.8 27.1 - - + -
171B LEU* 5.6 1.3 - - + +
174B ALA 2.9 18.8 + - - +
175B GLU* 3.6 9.2 - - - +
177B ALA* 1.3 73.8 - - - +
179B ARG* 1.3 66.9 + - - +
181B VAL* 3.3 3.9 + - + -
182B ALA* 2.9 24.4 + - - +
188B LEU* 4.1 15.0 - - + -
208B LEU* 4.2 21.3 - - + +
211B ARG* 3.5 35.9 - - + -
212B ALA* 4.5 5.6 - - + +
215B LEU* 3.7 13.5 - - + -
217B ILE* 3.5 21.5 - - + +
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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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145B ARG* 4.9 2.5 - - - +
175B GLU* 2.7 79.0 + - - +
176B PRO* 3.6 14.1 - - + +
178B LEU* 1.3 74.9 - - - +
180B ALA* 1.3 53.1 + - - +
182B ALA* 3.1 7.0 + - - +
183B GLU* 2.6 51.8 + - - +
211B ARG* 4.9 2.8 - - - +
215B LEU* 4.7 11.7 - - - -
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Residues in contact with ALA 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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141B GLU* 4.0 11.7 - - + +
144B ALA* 3.7 17.3 - - + -
145B ARG* 3.3 37.4 + - - +
176B PRO 3.1 10.6 + - - +
177B ALA 3.5 9.0 - - - +
179B ARG* 1.3 79.5 - - - +
181B VAL* 1.3 53.1 + - - +
183B GLU* 3.8 0.4 - - - +
184B ALA* 2.7 38.6 + - - +
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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
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140B VAL* 5.0 4.9 - - + -
144B ALA* 4.0 11.0 - - + -
152B ILE* 3.8 24.7 - - + -
155B LEU* 5.6 1.6 - - + -
177B ALA* 3.0 22.5 + - + +
178B LEU* 3.6 9.6 - - + +
180B ALA* 1.3 75.6 - - - +
182B ALA* 1.3 58.0 + - - +
185B GLY* 3.0 6.8 + - - -
186B LEU* 2.8 61.6 + - + +
187B PHE 4.4 0.9 - - - +
188B LEU* 4.3 17.3 - - + -
217B ILE* 3.9 20.2 - - + -
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Residues in contact with ALA 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 2.9 13.7 + - - +
179B ARG* 3.4 10.3 - - - +
181B VAL* 1.3 75.6 - - - +
183B GLU* 1.3 66.9 + - + +
185B GLY* 3.1 14.0 + - - -
186B LEU 5.3 0.4 - - - -
215B LEU* 4.1 22.0 - - + +
217B ILE* 3.9 21.3 - - + +
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Residues in contact with GLU 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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145B ARG* 2.5 48.2 + - - +
179B ARG* 2.6 33.5 + - + +
180B ALA 3.8 2.7 - - - +
182B ALA* 1.3 75.2 - - + +
184B ALA* 1.3 59.0 + - - +
185B GLY* 3.4 0.7 + - - -
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Residues in contact with ALA 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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144B ALA 3.1 28.5 - - - +
145B ARG* 5.0 4.9 - - - +
147B GLY* 6.5 0.7 - - - -
180B ALA 2.7 18.2 + - - +
183B GLU* 1.3 73.8 - - - +
185B GLY* 1.3 60.8 + - - +
186B LEU* 3.4 18.1 - - + +
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Residues in contact with GLY 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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150B HIS 4.8 0.2 - - - +
181B VAL 3.0 5.6 + - - -
182B ALA* 3.1 12.4 + - - -
183B GLU 3.2 1.2 + - - -
184B ALA* 1.3 80.0 - - - +
186B LEU* 1.3 65.0 + - - +
187B PHE* 3.8 16.8 - - - -
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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