Contacts of the helix formed by residues 169 - 187 (chain A) in PDB entry 4PZ0
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 VAL 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LYS* 3.4 28.7 - - + +
98A SER 3.5 17.0 - - - +
99A THR* 3.5 17.5 - - + +
165A SER* 3.5 23.1 - - - +
166A SER* 3.1 17.5 + - - +
168A THR* 1.3 77.0 + - - +
170A THR* 1.3 70.5 + - - +
171A ASP* 3.6 3.4 - - - +
172A GLN* 3.9 18.4 - - + +
173A ASN* 2.8 30.0 + - - +
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Residues in contact with THR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER 4.4 0.6 + - - -
99A THR 4.6 0.6 + - - -
100A SER* 3.3 23.2 + - - -
101A VAL* 3.3 22.4 + - + -
123A SER* 3.4 6.5 + - - -
124A ASP* 2.9 39.2 + - + +
125A VAL* 5.0 0.9 - - - -
168A THR 3.4 1.4 + - - -
169A VAL* 1.3 78.5 - - - +
171A ASP* 1.3 65.0 + - - +
173A ASN* 4.0 1.6 - - - +
174A GLN* 3.1 50.9 + - + +
319A TYR* 4.2 2.5 - - - +
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 2.8 25.9 + - - -
122A ASP* 3.3 28.7 - - - +
123A SER* 3.2 13.4 + - - +
133A TYR* 4.6 2.9 - - - +
169A VAL* 3.6 3.6 - - - +
170A THR* 1.3 76.1 - - - +
172A GLN* 1.3 80.8 + - - +
174A GLN* 3.1 21.2 + - - +
175A TRP* 3.1 40.4 + - + +
401A PAV 2.6 24.3 + - - -
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Residues in contact with GLN 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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41A LYS* 3.7 5.5 - - - +
164A TYR* 3.4 17.8 - - + +
165A SER* 2.7 39.6 + - - -
169A VAL* 3.9 8.8 + - + -
170A THR 3.5 0.2 - - - -
171A ASP* 1.3 88.7 + - - +
173A ASN* 1.3 59.0 + - - +
175A TRP* 3.4 12.4 + - + +
176A VAL* 2.9 36.5 + - + +
200A ASN* 5.1 0.2 - - - +
225A PRO* 3.1 21.3 + - + +
226A ASP* 2.9 23.0 + - - -
401A PAV 2.9 30.9 + - - +
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Residues in contact with ASN 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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164A TYR* 2.7 26.4 + - - -
166A SER 2.9 23.8 + - - -
167A PRO* 3.2 26.9 + - - +
168A THR 3.7 0.9 - - - -
169A VAL* 2.8 28.3 + - - +
170A THR 4.2 0.9 - - - +
171A ASP 3.2 0.4 - - - -
172A GLN* 1.3 75.4 - - - +
174A GLN* 1.3 63.8 + - - +
176A VAL* 4.6 2.7 - - - -
177A THR* 2.8 33.9 + - - +
197A TYR* 5.2 0.2 + - - -
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Residues in contact with GLN 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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124A ASP* 5.1 1.9 - - - +
133A TYR* 4.9 1.6 + - - -
139A PRO* 3.8 18.2 - - + +
170A THR* 3.1 30.3 + - + +
171A ASP* 3.1 15.1 + - - +
173A ASN* 1.3 76.9 - - - +
175A TRP* 1.3 62.7 + - + +
177A THR* 4.0 3.8 - - - -
178A LYS* 3.3 22.2 + - - +
317A GLN* 2.9 31.4 + - + +
319A TYR* 3.0 40.1 + - - -
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Residues in contact with TRP 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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122A ASP 4.6 0.4 - - - -
133A TYR* 5.1 2.0 + - - -
136A GLN* 3.2 29.2 - - - -
137A GLY 4.5 4.6 + - - -
139A PRO* 4.0 23.1 - - + -
142A LEU* 3.3 36.4 - - + +
143A ALA* 3.6 4.6 - - - +
146A LEU* 4.8 9.9 - - + -
171A ASP* 3.1 43.2 + - + +
172A GLN* 3.8 18.2 - - + +
173A ASN 3.3 0.2 - - - -
174A GLN* 1.3 81.7 - - + +
176A VAL* 1.3 59.7 + - + +
178A LYS* 3.3 4.0 + - - +
179A ALA* 2.8 29.1 + - - +
225A PRO* 4.0 9.0 - - + -
251A PHE* 3.7 28.7 - + - -
272A TRP* 4.0 5.8 - + - -
317A GLN* 4.6 6.7 - - - +
401A PAV 3.5 21.3 - - - -
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Residues in contact with VAL 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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146A LEU* 5.3 1.1 - - + -
162A PHE* 4.0 15.7 - - + -
164A TYR* 3.7 34.3 - - + +
172A GLN 2.9 21.7 + - - +
173A ASN* 4.4 1.6 - - - +
175A TRP* 1.3 75.0 - - + +
177A THR* 1.3 66.8 + - - +
179A ALA* 3.7 4.9 - - - +
180A LYS* 2.9 52.5 + - + +
225A PRO* 3.7 29.6 - - + -
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Residues in contact with THR 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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173A ASN* 2.8 25.3 + - - +
174A GLN* 4.0 5.4 - - - -
176A VAL* 1.3 76.2 - - - +
178A LYS* 1.3 62.7 + - - +
180A LYS* 3.5 7.4 + - - +
181A GLU* 3.2 38.7 + - + +
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Residues in contact with LYS 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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139A PRO* 3.8 23.1 - - + +
140A ASP* 3.5 28.0 + - - +
143A ALA* 3.8 15.7 - - + -
174A GLN 3.3 11.6 + - - +
175A TRP 3.3 8.0 + - - +
176A VAL 3.2 0.4 - - - -
177A THR* 1.3 80.8 - - - +
179A ALA* 1.3 62.3 + - - +
181A GLU* 3.1 28.5 + - + +
182A ILE* 3.0 38.2 + - + +
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Residues in contact with ALA 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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143A ALA* 3.5 19.4 - - + +
146A LEU* 4.9 5.2 - - + -
147A ILE* 3.5 17.0 - - + +
162A PHE* 3.9 22.4 - - + -
175A TRP 2.8 20.8 + - - +
176A VAL* 3.2 6.7 + - - +
178A LYS* 1.3 72.2 - - - +
180A LYS* 1.3 57.1 + - - +
182A ILE 3.3 1.0 + - - -
183A ILE* 2.9 35.5 + - - +
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PHE* 3.8 18.6 - - + -
164A TYR* 5.1 1.6 + - - -
176A VAL* 2.9 38.8 + - + +
177A THR* 3.9 7.0 - - - +
179A ALA* 1.3 74.9 - - - +
181A GLU* 1.3 63.0 + - - +
183A ILE* 3.8 6.5 - - - +
184A LYS* 3.1 27.1 + - - +
192A ILE* 3.7 26.9 - - + +
195A THR* 2.9 35.6 + - - +
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Residues in contact with GLU 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 THR* 3.2 29.1 + - + +
178A LYS* 3.1 41.0 + - + +
180A LYS* 1.3 76.6 - - + +
182A ILE* 1.3 63.2 + - + +
184A LYS* 3.2 28.6 - - + +
185A GLU* 3.5 9.7 + - - +
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Residues in contact with ILE 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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140A ASP* 4.3 4.7 - - - +
143A ALA* 4.0 10.8 - - + -
144A ASN* 3.8 36.1 - - - +
147A ILE* 3.5 24.5 - - + -
178A LYS* 3.0 37.0 + - + +
179A ALA 3.7 0.4 - - - +
181A GLU* 1.3 73.2 - - + +
183A ILE* 1.3 57.2 + - - +
185A GLU* 3.2 4.5 + - - -
186A LYS* 2.8 59.6 + - + +
187A TYR* 5.5 0.2 - - + -
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Residues in contact with ILE 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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147A ILE* 3.9 15.9 - - + -
160A VAL* 5.1 0.9 - - + -
162A PHE* 3.8 32.8 - - + -
179A ALA 2.9 22.1 + - - +
180A LYS* 3.8 4.7 - - - +
182A ILE* 1.3 76.5 - - - +
184A LYS* 1.3 60.9 + - - +
187A TYR* 2.8 42.4 + - + +
190A TRP* 3.8 56.8 - - + +
192A ILE* 4.4 19.5 - - + -
223A ILE* 4.7 3.1 - - + -
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Residues in contact with LYS 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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180A LYS 3.1 16.2 + - - +
181A GLU* 3.2 25.6 - - + +
183A ILE* 1.3 78.3 - - - +
185A GLU* 1.3 62.6 + - + +
187A TYR 5.0 1.3 - - - -
188A PRO* 4.1 15.6 - - - +
192A ILE* 6.0 0.2 - - - +
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Residues in contact with GLU 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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181A GLU 3.9 9.4 - - - +
182A ILE* 3.2 6.5 + - - +
183A ILE 3.2 0.2 - - - -
184A LYS* 1.3 84.7 - - + +
186A LYS* 1.3 76.4 + - + +
187A TYR 3.5 0.4 - - - -
188A PRO* 3.8 11.1 - - - +
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Residues in contact with LYS 186 (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 ASN* 5.7 2.0 - - - +
156A ASP* 6.0 0.2 - - - +
182A ILE* 2.8 38.5 + - + +
185A GLU* 1.3 89.6 - - + +
187A TYR* 1.3 82.2 + - + +
188A PRO* 3.4 9.0 - - - +
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Residues in contact with TYR 187 (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 ILE* 3.5 29.8 - - + +
148A GLU* 4.4 6.4 + - - -
151A SER* 3.2 33.7 + - - -
155A GLY 4.4 0.4 - - - -
156A ASP* 4.1 24.5 - - + -
182A ILE* 5.5 0.7 - - + -
183A ILE* 2.8 25.2 + - + +
184A LYS* 5.0 0.3 - - - -
186A LYS* 1.3 100.3 - - + +
188A PRO* 1.3 65.9 - - - +
189A ASN 3.1 3.1 - - - -
190A TRP* 3.0 56.4 + + + +
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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