Contacts of the helix formed by residues 171 - 183 (chain A) in PDB entry 2ZH8
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A TYR* 4.3 0.7 - - - -
162A GLY* 4.8 1.6 - - - -
163A ALA* 3.6 32.0 - - - +
169A GLY 3.9 0.2 + - - -
170A PHE* 1.3 82.1 - - - +
172A GLY* 1.3 64.6 + - - +
173A TYR* 3.8 8.2 + - - +
174A LEU* 3.3 26.0 + - - +
175A CYS* 3.2 17.8 + - - -
226A VAL* 4.3 10.7 + - - +
33B G 4.9 1.1 - - - -
34B C 4.3 16.2 - - - +
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Residues in contact with GLY 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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152A LYS* 4.1 12.4 - - - -
161A TYR* 3.5 26.7 + - - -
171A SER* 1.3 73.8 - - - +
173A TYR* 1.3 64.9 + - - +
175A CYS* 2.8 16.3 + - - +
176A GLU* 3.2 17.6 + - - +
701A SO4 5.2 1.6 - - - -
34B C 4.8 5.2 - - - +
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Residues in contact with TYR 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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50A ARG* 5.6 3.4 - - - +
133A HIS* 3.1 54.6 + + + +
136A TRP* 5.1 2.3 - + - +
137A LEU* 3.3 34.3 - - + -
171A SER* 3.3 7.5 + - - +
172A GLY* 1.3 74.1 - - - +
174A LEU* 1.3 62.2 + - - +
176A GLU* 3.2 8.2 + - - +
177A LEU* 3.1 35.1 + - + +
218A ASP* 3.0 17.5 + - - -
219A PRO* 3.4 11.8 - - - +
220A VAL* 4.4 2.6 - - - +
224A ARG* 5.7 0.9 - - - -
226A VAL* 3.6 35.4 - - + -
34B C 5.3 7.1 - - - +
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Residues in contact with LEU 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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169A GLY 5.2 1.1 - - - +
170A PHE* 3.6 37.9 - - + -
171A SER* 3.3 21.2 + - - +
173A TYR* 1.3 79.6 - - - +
175A CYS* 1.3 57.9 + - - +
177A LEU* 3.3 4.3 + - + +
178A LEU* 2.9 42.6 + - + +
214A PHE* 5.7 0.9 - - + -
216A VAL* 3.8 34.5 - - + -
226A VAL* 3.6 19.0 - - + +
227A ALA* 3.8 25.6 - - + -
230A LEU* 5.0 2.7 - - + -
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Residues in contact with CYS 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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148A VAL* 4.8 4.9 - - + -
151A LEU* 3.6 19.7 - - + +
152A LYS* 4.2 16.4 - - + -
155A LEU* 3.4 33.4 - - - -
161A TYR* 4.1 11.9 - - - -
170A PHE* 4.0 9.9 - - - -
171A SER 3.2 14.1 + - - -
172A GLY 2.8 9.8 + - - +
174A LEU* 1.3 79.6 - - - +
176A GLU* 1.3 62.4 + - - +
178A LEU* 3.2 6.6 + - - +
179A ILE* 3.1 27.4 + - - +
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Residues in contact with GLU 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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47A SER* 4.7 1.7 + - - -
50A ARG* 2.5 41.9 + - - -
52A THR* 3.1 22.2 + - - +
137A LEU* 3.6 22.1 - - + +
141A ILE* 3.8 13.7 - - + +
148A VAL* 3.7 28.7 - - + -
152A LYS* 4.4 6.1 + - - -
172A GLY 3.2 13.2 + - - +
173A TYR* 3.2 7.3 + - - +
175A CYS* 1.3 72.8 - - - +
177A LEU* 1.3 67.1 + - - +
179A ILE* 3.2 2.9 + - - +
180A VAL* 3.0 28.5 + - - +
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Residues in contact with LEU 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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136A TRP* 3.6 29.2 - - + -
137A LEU* 3.8 9.2 - - + -
173A TYR* 3.1 34.9 + - + +
174A LEU* 3.3 8.5 + - + +
176A GLU* 1.3 76.1 - - - +
178A LEU* 1.3 63.9 + - - +
180A VAL* 3.3 5.6 + - - +
181A PHE* 3.1 24.3 + - - +
203A VAL* 4.1 18.4 - - + +
216A VAL* 4.8 6.3 - - + -
217A VAL 4.8 0.2 - - - +
219A PRO* 3.7 24.0 - - + -
226A VAL* 3.7 38.4 - - + -
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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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151A LEU* 4.2 19.1 - - + -
170A PHE* 4.1 17.0 - - + -
174A LEU* 2.9 41.4 + - + +
175A CYS* 3.5 9.0 - - - +
176A GLU 3.2 0.4 - - - -
177A LEU* 1.3 78.0 - - - +
179A ILE* 1.3 56.1 + - - +
181A PHE* 3.5 2.4 + - + +
182A TYR* 3.0 43.6 + - + -
188A THR* 3.5 12.7 + - + -
195A TRP* 3.7 38.4 - - + -
201A ILE* 4.3 15.9 - - + -
216A VAL* 5.2 4.0 - - + -
238A PHE* 5.6 0.4 - - + -
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Residues in contact with ILE 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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141A ILE* 4.0 8.7 - - + -
144A LYS* 3.6 37.4 - - + +
147A GLU* 3.8 22.7 - - + +
148A VAL* 3.7 21.1 - - + +
151A LEU* 4.0 11.4 - - + -
175A CYS 3.1 14.3 + - - +
176A GLU 3.2 6.0 + - - +
178A LEU* 1.3 72.1 - - - +
180A VAL* 1.3 61.4 + - - +
181A PHE 3.0 2.0 - - - -
183A GLY* 2.6 34.4 + - - +
184A SER 3.6 24.7 - - - -
185A PHE* 3.8 2.5 - - - +
188A THR* 3.7 9.4 - - - +
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Residues in contact with VAL 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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136A TRP* 3.9 33.0 - - + -
137A LEU* 4.4 4.7 - - + -
140A ARG* 4.1 33.2 - - + +
141A ILE* 3.8 17.3 - - + -
144A LYS* 4.8 11.0 + - - +
176A GLU 3.0 22.2 + - - +
177A LEU* 3.7 5.6 - - - +
179A ILE* 1.3 77.5 - - - +
181A PHE* 1.3 61.3 + - - +
183A GLY* 4.4 1.4 + - - -
203A VAL* 4.3 5.8 - - + -
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Residues in contact with PHE 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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177A LEU 3.1 16.0 + - - +
178A LEU* 3.7 6.7 - - - +
179A ILE 3.0 0.4 - - - -
180A VAL* 1.3 82.6 - - - +
182A TYR* 1.3 95.9 + + + +
201A ILE* 4.0 17.0 - - + -
202A ASP 3.7 21.1 - - - -
203A VAL* 3.8 23.6 - - + -
206A GLY* 3.8 10.8 - - - -
207A GLU 3.5 16.8 - - - -
208A VAL* 3.5 32.8 - - + -
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Residues in contact with TYR 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 28.2 + - + -
181A PHE* 1.3 104.9 - + - +
183A GLY* 1.3 57.5 + - - +
184A SER 3.3 2.2 + - - -
187A GLU* 3.1 24.0 - - + +
188A THR* 3.3 45.3 - - + +
191A ASN* 3.5 38.3 - - + +
195A TRP* 3.0 44.3 + + - -
201A ILE* 3.8 9.3 - - + +
208A VAL* 4.8 6.8 - - + +
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Residues in contact with GLY 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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144A LYS* 3.0 36.9 - - - +
147A GLU* 4.3 1.7 - - - +
179A ILE* 2.6 24.4 + - - -
180A VAL 4.3 1.3 - - - -
181A PHE 3.4 2.4 + - - -
182A TYR* 1.3 71.5 - - - +
184A SER* 1.3 60.9 + - - +
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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