Contacts of the helix formed by residues 176 - 193 (chain A) in PDB entry 3ZHP
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 THR 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PRO* 5.7 2.8 - - - +
174A LEU* 3.4 4.7 - - - +
175A SER* 1.4 78.0 + - - +
177A PHE* 1.3 67.5 + - - +
178A ASP* 4.2 13.9 - - + +
179A ILE* 3.8 34.8 - - + +
180A ALA* 3.1 23.7 + - - +
88D SER 5.7 2.0 - - - +
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU 5.3 0.4 - - - -
175A SER 3.4 6.1 + - - +
176A THR* 1.3 72.0 - - - +
178A ASP* 1.3 56.2 + - - +
180A ALA* 3.2 8.8 + - + +
181A SER* 2.7 56.5 + - - -
221A ASN* 5.2 4.9 - - - -
223A VAL* 3.7 36.8 - - + -
57D LEU* 5.7 0.7 - - + -
64D ILE* 5.3 2.5 - - + -
68D GLN* 3.7 24.0 - - + -
71D ILE* 4.9 4.5 - - + -
88D SER* 3.2 38.6 + - - +
89D TYR 4.9 0.4 - - - +
90D LEU* 4.1 24.7 - - + +
95D LEU* 3.8 29.4 - - + -
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Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 4.1 19.8 - - + +
176A THR* 3.5 10.0 - - + +
177A PHE* 1.3 76.0 - - - +
179A ILE* 1.4 56.7 + - + +
181A SER* 3.5 6.3 + - - -
182A ASP* 3.0 27.4 + - - +
71D ILE* 3.4 18.2 - - + +
75D SER* 5.7 0.8 - - - -
85D TYR* 2.8 32.7 + - - -
87D GLY* 4.1 2.9 - - - -
88D SER* 2.6 31.3 + - - -
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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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133A TYR* 3.8 39.1 - - + +
136A PRO* 3.8 39.7 - - + +
139A ALA* 3.8 13.7 - - + -
140A LEU* 3.8 16.2 - - + -
174A LEU* 3.8 14.4 - - + -
176A THR* 3.6 32.1 + - + +
177A PHE 3.4 0.4 - - - -
178A ASP* 1.4 71.6 - - + +
180A ALA* 1.4 53.7 - - - +
182A ASP* 3.0 5.0 + - - +
183A ALA* 2.8 33.1 + - - +
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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
----------------------------------------------------------
171A TYR 3.7 14.4 - - - +
172A VAL* 3.7 24.8 - - - +
174A LEU* 3.7 16.0 - - + +
176A THR 3.1 19.6 + - - +
177A PHE* 3.4 9.0 - - + +
179A ILE* 1.4 75.8 - - - +
181A SER* 1.4 56.9 + - - +
183A ALA* 3.4 3.1 + - - +
184A PHE* 3.1 26.5 + - - +
221A ASN* 6.4 0.2 - - - +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 2.7 42.0 + - - -
178A ASP* 3.6 8.3 - - - -
180A ALA* 1.4 69.4 - - - +
182A ASP* 1.4 60.5 + - - +
184A PHE* 3.5 7.0 + - - +
185A ALA* 3.1 25.2 + - - +
223A VAL* 5.4 0.3 - - - +
68D GLN* 3.0 38.2 + - - +
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Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 2.8 26.0 + - + -
140A LEU* 4.1 30.0 - - + +
143A GLY* 3.4 10.6 - - - -
144A ILE* 5.0 1.4 - - - +
147A ARG* 2.7 41.0 + - - -
178A ASP 3.0 13.1 + - - +
179A ILE 3.0 9.5 + - - +
181A SER* 1.4 73.0 - - - +
183A ALA* 1.4 63.6 + - - +
185A ALA* 3.3 19.4 - - - +
186A THR 3.3 4.2 + - - -
72D THR* 5.4 7.1 + - - +
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 3.6 19.9 - - + -
168A PHE* 3.6 9.2 - - + -
171A TYR* 3.5 42.4 - - + +
172A VAL* 3.8 6.7 - - + -
179A ILE 2.8 11.4 + - - +
180A ALA 3.5 6.5 - - - +
181A SER 3.3 0.2 - - - -
182A ASP* 1.4 76.3 - - - +
184A PHE* 1.4 55.6 + - - +
186A THR 3.4 2.3 + - - -
187A PHE* 3.0 27.4 + - - +
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Residues in contact with PHE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 3.5 21.2 - - + +
180A ALA 3.1 15.4 + - - +
181A SER* 3.9 7.4 - - - +
182A ASP 3.4 0.2 - - - -
183A ALA* 1.4 72.7 - - - +
185A ALA* 1.4 57.2 + - - +
187A PHE* 3.9 25.6 - + - -
188A LYS* 2.8 50.5 + - + +
216A LEU* 5.0 0.4 - - + -
224A THR* 5.7 4.5 - - + -
227A GLN* 3.4 50.0 - - + -
228A SER* 3.7 22.7 - - - -
231A LEU* 3.7 23.8 - - + -
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Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG* 4.0 21.1 - - - +
181A SER 3.1 14.0 + - - +
182A ASP* 3.3 15.5 + - - +
184A PHE* 1.4 75.7 - - - +
186A THR* 1.4 55.6 + - - +
188A LYS* 3.8 7.1 - - - +
189A ASP* 3.2 25.8 + - - +
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Residues in contact with THR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 2.8 17.0 + - - -
143A GLY 4.0 1.7 + - - -
146A LEU* 3.8 20.9 - - + -
147A ARG* 2.8 39.2 + - - +
150A ILE* 3.8 18.8 - - + +
168A PHE* 3.7 21.3 - - + -
182A ASP 3.3 1.4 + - - -
183A ALA 3.8 4.5 - - - -
185A ALA* 1.4 71.7 - - - +
187A PHE* 1.4 56.9 + - - +
189A ASP* 3.1 5.6 + - - +
190A LEU* 2.9 36.5 + - + +
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Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PHE* 3.9 20.2 - + - -
168A PHE* 3.7 34.7 - + + -
169A PHE* 3.8 37.2 - + - -
172A VAL* 4.4 4.7 - - + -
183A ALA 3.0 18.2 + - - +
184A PHE* 3.6 32.3 - + - +
186A THR* 1.4 75.0 - - - +
188A LYS* 1.4 62.4 + - - +
190A LEU* 3.3 8.8 + - - +
191A LEU* 3.3 45.9 + - + +
213A TYR* 3.9 20.6 - + - -
216A LEU* 4.2 8.1 - - + -
231A LEU* 4.0 8.1 - - + -
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Residues in contact with LYS 188 (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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184A PHE* 2.8 34.1 + - + +
185A ALA* 3.8 6.5 - - - +
187A PHE* 1.4 69.3 - - - +
189A ASP* 1.3 60.0 + - - +
191A LEU 3.3 2.6 + - - -
192A THR* 2.7 41.6 + - - +
230A LYS* 6.3 1.0 - - - +
231A LEU* 3.8 33.0 - - + -
234A GLU* 4.0 21.9 + - - -
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Residues in contact with ASP 189 (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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147A ARG* 4.8 12.3 - - + +
150A ILE* 3.4 24.7 - - + +
185A ALA 3.2 11.8 + - - +
186A THR* 3.1 10.8 + - - +
188A LYS* 1.3 76.9 - - - +
190A LEU* 1.4 58.7 - - - +
192A THR* 3.1 5.5 + - - -
193A ARG* 2.9 79.5 + - - +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 5.8 0.4 - - + -
150A ILE* 3.8 17.0 - - + -
156A ALA* 3.5 38.8 - - + +
159A ILE* 3.8 21.8 - - + -
160A LEU* 3.8 26.0 - - + +
165A PHE* 4.0 11.9 - - + -
168A PHE* 3.7 33.7 - - + -
186A THR* 2.9 23.5 + - + +
187A PHE* 3.3 8.3 + - - +
189A ASP* 1.4 75.3 + - - +
191A LEU* 1.3 57.9 + - - +
193A ARG* 4.8 1.0 + - - -
194A HIS* 5.3 3.8 + - - -
197A LEU* 5.9 0.3 - - - +
198A VAL* 3.1 18.7 - - - +
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Residues in contact with LEU 191 (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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160A LEU* 4.5 8.5 - - + -
165A PHE* 4.1 18.8 - - + -
187A PHE* 3.3 53.1 + - + +
188A LYS* 3.3 4.4 + - - +
189A ASP 3.2 0.6 - - - -
190A LEU* 1.3 75.2 - - - +
192A THR* 1.4 61.2 + - + +
195A LYS* 6.0 0.2 - - - -
198A VAL* 3.3 29.9 - - + +
201A PHE* 4.5 3.4 - - + -
202A LEU* 4.0 28.0 - - + -
209A ILE* 5.9 0.9 - - + -
213A TYR* 4.9 3.4 - - + -
231A LEU* 4.5 8.5 - - + -
235A LEU* 3.4 30.1 - - + +
241A ASN* 5.4 0.3 + - - -
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Residues in contact with THR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LYS* 2.7 36.0 + - + +
189A ASP* 3.6 4.3 + - - -
190A LEU 3.5 0.2 - - - -
191A LEU* 1.4 83.8 - - - +
193A ARG* 1.4 68.4 + - - +
194A HIS 3.9 0.9 - - - -
195A LYS* 2.8 39.4 + - - +
198A VAL* 5.0 0.2 - - - -
231A LEU* 3.8 24.7 - - + -
234A GLU* 5.6 5.6 - - + +
235A LEU* 4.9 5.6 - - + +
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Residues in contact with ARG 193 (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 ILE 3.7 7.6 - - - +
151A ARG* 3.8 41.8 + - - +
189A ASP* 2.9 55.5 + - - +
190A LEU* 4.8 0.6 - - - -
192A THR* 1.4 80.7 + - - +
194A HIS* 1.4 91.0 + - + +
195A LYS* 3.1 11.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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