Contacts of the helix formed by residues 171 - 185 (chain X) in PDB entry 1ZV4
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 TYR 171 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113X PHE* 4.5 3.1 - + + -
117X CYS* 3.5 23.6 - - + -
120X LEU* 3.6 25.8 - - + -
133X ALA* 2.6 27.0 + - - -
136X ILE* 3.8 32.8 - - + -
137X TYR* 3.6 11.6 - - - +
141X ILE* 4.1 13.0 - - + -
159X ILE* 3.7 39.9 - - + -
163X LEU* 4.1 2.6 - - - +
168X PRO 5.0 1.2 + - - +
169X HIS* 3.2 1.2 - - - +
170X MET* 1.3 106.5 - - + +
172X GLU* 1.3 53.3 + - - +
173X ASP 3.4 2.2 - - - -
174X ALA* 3.1 7.5 + - - +
175X GLN* 2.7 34.2 + - - +
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Residues in contact with GLU 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X LYS* 5.7 5.6 - - + +
169X HIS* 3.3 40.8 + - + +
170X MET 3.4 1.8 - - - +
171X TYR* 1.3 77.4 - - - +
173X ASP* 1.3 70.3 + - - +
175X GLN* 3.6 15.1 - - - +
176X LEU* 2.8 30.3 + - - +
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Residues in contact with ASP 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155X VAL* 4.3 18.7 - - + +
158X VAL* 4.6 24.9 - - + +
170X MET 5.1 1.2 + - - +
171X TYR 3.4 0.4 - - - -
172X GLU* 1.3 88.2 - - - +
174X ALA* 1.3 60.7 + - - +
176X LEU* 3.5 12.4 + - - +
177X GLN* 3.0 27.9 + - - +
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Residues in contact with ALA 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X PHE* 3.7 20.0 - - + -
151X LEU* 4.0 9.6 - - + -
155X VAL* 3.6 24.6 - - + +
158X VAL* 6.0 0.2 - - - +
159X ILE* 3.9 19.7 - - + +
171X TYR* 3.1 9.9 + - - +
173X ASP* 1.3 76.9 - - - +
175X GLN* 1.3 64.6 + - - +
177X GLN* 3.3 3.5 + - - +
178X ILE* 3.1 27.7 + - - +
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Residues in contact with GLN 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X PHE* 3.8 10.0 - - - -
114X TRP* 3.2 51.1 + - + +
117X CYS* 3.6 19.9 - - + +
118X GLU* 2.7 32.2 + - - +
121X LYS* 3.4 23.7 + - - +
171X TYR 2.7 19.0 + - - +
172X GLU* 3.6 12.1 - - - +
174X ALA* 1.3 74.0 - - - +
176X LEU* 1.3 57.9 + - - +
178X ILE* 3.3 1.0 + - - +
179X TYR* 2.9 30.0 + - + +
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Residues in contact with LEU 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172X GLU 2.8 21.2 + - - +
173X ASP* 3.7 12.6 - - - +
174X ALA 3.3 0.2 - - - -
175X GLN* 1.3 72.3 - - - +
177X GLN* 1.3 54.3 + - - +
179X TYR* 3.5 18.3 + - + -
180X THR* 2.7 46.9 + - - +
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Residues in contact with GLN 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150X SER 3.7 6.3 - - - +
151X LEU* 3.3 17.2 - - + -
152X ASP* 3.0 48.0 + - - -
155X VAL* 3.3 22.4 - - - +
173X ASP 3.0 16.7 + - - +
174X ALA* 3.3 7.5 + - - +
176X LEU* 1.3 76.5 - - - +
178X ILE* 1.3 62.2 + - + +
180X THR* 3.5 6.4 + - - -
181X LEU* 3.2 22.2 + - - +
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Residues in contact with ILE 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X ASN* 3.4 49.6 - - + +
113X PHE* 3.8 20.9 - - + -
114X TRP* 5.0 1.6 - - + -
149X VAL* 4.0 14.6 - - + -
150X SER 3.7 24.5 - - - +
151X LEU* 3.8 13.0 - - + -
174X ALA 3.1 16.6 + - - +
175X GLN 3.9 2.7 - - - +
177X GLN* 1.3 74.6 - - + +
179X TYR* 1.3 61.2 + - - +
181X LEU* 3.5 15.0 + - + +
182X MET* 3.0 31.8 + - + +
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Residues in contact with TYR 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X PHE* 3.6 31.9 - + - +
86X ASP* 3.3 35.3 + - + +
89X MET* 4.2 15.9 - - + -
114X TRP* 3.6 29.4 - + - +
175X GLN 2.9 17.9 + - - +
176X LEU* 3.6 20.4 - - + +
177X GLN 3.3 0.2 - - - -
178X ILE* 1.3 77.4 - - - +
180X THR* 1.3 65.5 + - - +
182X MET* 3.5 12.1 + - - +
183X HIS* 3.0 36.3 + + + +
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Residues in contact with THR 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176X LEU* 2.7 32.9 + - - +
177X GLN* 3.8 6.5 - - - -
178X ILE 3.3 0.2 - - - -
179X TYR* 1.3 77.3 - - - +
181X LEU* 1.3 60.6 + - - +
183X HIS* 3.5 6.2 + - + +
184X ARG* 2.9 36.5 + - + +
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Residues in contact with LEU 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X ASN* 3.4 32.1 - - - +
150X SER* 5.6 6.7 - - - +
177X GLN* 3.2 13.5 + - + +
178X ILE* 3.6 19.3 - - + +
180X THR* 1.3 74.4 - - - +
182X MET* 1.3 58.7 + - - +
184X ARG* 3.2 8.0 + - - +
185X ASP* 2.7 68.6 + - + +
186X SER* 6.1 0.7 - - - +
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Residues in contact with MET 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X PHE* 3.9 12.1 - - + -
89X MET* 3.8 23.8 - - + -
98X PHE* 4.0 23.5 - - + -
102X LEU* 4.4 3.8 - - + -
110X ASN* 4.0 21.5 - - + +
111X LEU* 3.9 26.9 - - - -
114X TRP* 4.0 18.8 - - + -
178X ILE* 3.0 24.3 + - + +
179X TYR* 3.8 14.4 - - - +
181X LEU* 1.3 75.2 - - - +
183X HIS* 1.3 58.5 + - - +
186X SER* 3.1 16.4 + - - +
187X PHE* 2.7 32.4 + - - +
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Residues in contact with HIS 183 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85X PHE* 3.3 43.4 + + + +
179X TYR* 3.0 27.8 + + + +
180X THR* 3.7 7.9 - - - +
182X MET* 1.3 75.2 - - - +
184X ARG* 1.3 60.9 + - - +
187X PHE* 3.6 18.8 - + - +
188X PRO* 3.3 21.7 - - - +
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Residues in contact with ARG 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180X THR* 2.9 23.1 + - + +
181X LEU* 3.2 7.2 + - - +
183X HIS* 1.3 78.3 + - - +
185X ASP* 1.3 78.7 + - - +
188X PRO* 3.7 13.9 - - - +
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Residues in contact with ASP 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181X LEU* 2.7 42.5 + - + +
184X ARG* 1.3 94.0 - - - +
186X SER* 1.3 64.5 + - - +
187X PHE 3.7 0.4 - - - -
188X PRO* 3.8 6.2 - - - +
189X ARG* 2.9 41.1 + - - +
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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