Contacts of the helix formed by residues 166 - 185 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ARG 4.7 0.9 - - - +
165A LEU* 1.3 96.1 - - + +
167A GLU* 1.3 66.5 + - - +
168A GLU* 3.2 29.4 - - + +
169A ALA* 3.0 12.0 + - + +
170A LEU* 3.0 19.5 + - - +
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Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU 3.6 2.2 + - - -
166A PRO* 1.3 69.6 - - - +
168A GLU* 1.3 64.7 + - - +
170A LEU* 3.2 8.6 + - - +
171A LEU* 2.9 36.5 + - + +
207A ALA* 4.2 24.0 - - + +
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Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PRO* 3.2 26.1 - - + +
167A GLU* 1.3 79.1 + - - +
169A ALA* 1.3 77.1 + - + +
171A LEU* 3.7 8.2 - - - +
172A GLU* 3.1 23.0 + - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LYS* 4.0 30.3 - - + +
165A LEU* 4.5 9.0 - - + -
166A PRO* 3.0 20.5 + - + +
168A GLU* 1.3 84.4 - - + +
170A LEU* 1.3 68.2 + - - +
172A GLU* 3.2 6.3 + - - +
173A LEU* 2.9 30.8 + - - +
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 4.3 19.3 - - + -
137A PHE* 3.8 26.7 - - + -
156A ASP* 4.3 5.4 - - + +
159A LYS* 6.2 0.9 - - + -
165A LEU* 4.6 17.8 - - + +
166A PRO 3.0 12.7 + - - +
167A GLU* 3.6 11.0 - - - +
169A ALA* 1.3 75.4 - - - +
171A LEU* 1.3 62.3 + - + +
173A LEU* 4.1 3.1 - - - +
174A ALA* 3.1 27.7 + - - +
205A ALA* 3.9 20.6 - - + -
207A ALA* 5.1 7.6 - - + -
208A LEU* 3.7 28.7 - - + -
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 2.9 28.5 + - + +
168A GLU* 3.7 7.0 - - - +
170A LEU* 1.3 77.2 - - - +
172A GLU* 1.3 62.7 + - - +
174A ALA* 3.4 1.4 + - - +
175A GLU* 3.1 26.2 + - - +
178A LEU* 5.3 1.3 - - + +
207A ALA* 3.6 37.2 - - + +
208A LEU* 4.0 13.9 - - + -
211A ARG* 4.0 22.7 - - + -
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LYS* 4.9 9.7 + - - +
168A GLU 3.1 16.8 + - - +
169A ALA* 3.2 6.6 + - - +
171A LEU* 1.3 77.9 - - - +
173A LEU* 1.3 71.1 + - + +
174A ALA 3.4 0.3 + - - -
175A GLU* 3.4 17.9 + - + +
176A PRO* 3.7 5.4 - - - +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LYS* 3.6 41.5 - - + +
133A PHE* 3.8 18.4 - - + -
134A ARG* 3.5 46.1 - - + +
137A PHE* 3.5 31.1 - - + +
165A LEU* 3.9 11.2 - - + -
169A ALA* 2.9 19.5 + - - +
170A LEU* 5.3 0.4 - - - -
172A GLU* 1.3 84.0 - - + +
174A ALA* 1.3 59.8 + - - +
175A GLU 3.4 0.2 - - - -
176A PRO* 3.7 10.8 - - - +
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PHE* 3.8 28.9 - - + -
155A LEU* 5.1 1.3 - - + -
170A LEU 3.1 19.2 + - - +
171A LEU 3.8 1.6 - - - +
173A LEU* 1.3 76.7 - - - +
175A GLU* 1.3 65.4 + - - +
176A PRO* 3.5 0.9 - - - -
177A ALA* 3.2 4.7 + - - +
178A LEU* 2.9 31.4 + - + +
208A LEU* 3.7 23.3 - - + -
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU 3.1 13.6 + - - +
172A GLU* 3.4 12.3 + - + +
174A ALA* 1.3 76.3 - - - +
176A PRO* 1.3 72.5 - - + +
178A LEU* 3.1 5.6 + - - +
179A ARG* 2.6 68.3 + - - +
211A ARG* 2.7 47.2 + - - +
215A LEU* 4.7 0.8 - - - +
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Residues in contact with PRO 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU* 3.8 28.5 - - - +
172A GLU 3.7 6.3 - - - +
173A LEU* 3.7 12.1 - - - +
174A ALA 3.7 3.1 - - - -
175A GLU* 1.3 95.5 - - + +
177A ALA* 1.3 61.0 + - - +
179A ARG* 3.3 10.7 + - + +
180A ALA* 3.0 22.7 + - - +
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A PHE* 3.5 35.6 + - + +
140A VAL* 4.0 21.1 - - + -
141A GLU* 4.1 13.3 - - - +
144A ALA* 4.7 0.3 - - - +
155A LEU* 4.9 4.7 - - + -
173A LEU 5.1 0.2 + - - -
174A ALA 3.2 8.6 + - - +
176A PRO* 1.3 79.4 - - - +
178A LEU* 1.3 58.0 + - - +
180A ALA* 3.3 2.6 + - - +
181A VAL* 2.9 34.7 + - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 3.8 27.8 - - + -
171A LEU* 5.3 1.6 - - + +
174A ALA* 2.9 33.1 + - + +
175A GLU* 3.5 7.6 - - - +
177A ALA* 1.3 75.1 - - - +
179A ARG* 1.3 64.7 + - - +
181A VAL* 3.4 3.5 + - + -
182A ALA* 3.0 23.7 + - - +
188A LEU* 4.4 11.7 - - + -
208A LEU* 4.3 18.2 - - + +
211A ARG* 3.5 32.1 - - + -
212A ALA* 4.6 2.9 - - + -
215A LEU* 3.8 13.0 - - + +
217A ILE* 3.5 22.3 - - + +
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Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A GLU* 2.6 55.3 + - - +
176A PRO* 3.7 7.9 - - + +
177A ALA 3.3 0.2 - - - -
178A LEU* 1.3 76.3 - - - +
180A ALA* 1.3 54.4 + - - +
182A ALA* 3.2 6.0 + - - +
183A GLU* 2.6 39.7 + - - +
211A ARG* 4.4 8.1 - - - +
215A LEU* 4.5 10.8 - - + -
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU* 4.0 22.7 - - + +
144A ALA* 3.8 18.5 - - + +
145A ARG* 4.3 15.5 - - + +
176A PRO 3.0 13.5 + - - +
177A ALA* 3.4 9.9 - - - +
179A ARG* 1.3 77.3 - - - +
181A VAL* 1.3 52.7 + - - +
183A GLU* 3.2 6.6 + - - +
184A ALA* 2.8 37.9 + - - +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 5.0 5.8 - - + -
144A ALA* 4.0 11.2 - - + -
152A ILE* 3.9 24.7 - - + -
155A LEU* 5.7 1.3 - - + -
177A ALA 2.9 22.2 + - - +
178A LEU* 3.6 9.9 - - + +
180A ALA* 1.3 75.5 - - - +
182A ALA* 1.3 61.8 + - - +
184A ALA 3.8 0.2 - - - -
185A GLY 3.1 2.9 + - - -
186A LEU* 2.9 60.2 + - + +
187A PHE 4.4 6.1 - - - +
188A LEU* 4.6 10.1 - - + -
217A ILE* 3.7 21.1 - - + -
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU 3.0 17.0 + - - +
179A ARG* 3.6 6.3 - - - +
181A VAL* 1.3 73.9 - - - +
183A GLU* 1.3 66.2 + - - +
185A GLY* 3.1 13.1 + - - -
186A LEU 5.2 0.4 - - - -
215A LEU* 4.0 25.4 - - + +
217A ILE* 3.9 20.6 - - + -
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ARG* 5.7 8.1 - - + +
179A ARG 2.6 23.9 + - - +
180A ALA* 3.5 8.3 - - - +
182A ALA* 1.3 74.3 - - - +
184A ALA* 1.3 61.2 + - - +
185A GLY 3.4 0.3 + - - -
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ALA 3.1 28.3 - - - +
145A ARG* 5.0 5.4 - - + -
180A ALA 2.8 16.5 + - - +
181A VAL* 4.1 2.0 - - - +
183A GLU* 1.3 75.3 - - - +
185A GLY* 1.3 61.1 + - - +
186A LEU* 3.6 17.6 + - + +
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Residues in contact with GLY 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A HIS 4.7 0.2 - - - +
181A VAL 3.1 5.1 + - - -
182A ALA* 3.1 11.2 + - - -
183A GLU 3.3 1.0 + - - -
184A ALA* 1.3 79.6 - - - +
186A LEU* 1.3 65.6 + - - +
187A PHE* 3.9 16.5 - - - -
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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