Contacts of the helix formed by residues 178 - 188 (chain A) in PDB entry 1PZN
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 ARG 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A HIS* 3.2 14.8 + - + +
175A ASN* 2.8 42.7 + - - +
176A THR* 4.2 9.9 - - - +
177A PHE* 1.3 81.2 + - - +
179A PRO* 1.3 58.0 - - - +
180A GLU* 2.8 21.1 - - + +
181A ARG* 2.7 38.9 + - + +
182A ILE* 3.2 7.3 + - - +
103G TYR* 5.0 1.4 + - - -
107G ARG* 3.0 41.4 - - - +
332G HIS* 2.8 53.1 + - + +
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Residues in contact with PRO 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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177A PHE* 3.5 33.7 - - + +
178A ARG* 1.3 78.6 - - - +
180A GLU* 1.3 70.9 + - - +
181A ARG 3.3 0.2 - - - -
182A ILE* 3.2 9.0 - - + +
183A ARG* 2.8 24.8 + - - +
197A LEU* 3.5 12.2 - - + +
100G ALA* 3.9 19.1 - - + +
103G TYR* 3.9 7.4 - - + -
104G LEU* 3.4 35.8 - - + +
107G ARG* 3.7 11.7 - - - -
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Residues in contact with GLU 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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178A ARG* 2.8 30.9 - - + +
179A PRO* 1.3 82.9 - - - +
181A ARG* 1.3 63.7 + - - +
183A ARG* 3.1 8.9 + - - +
184A GLU* 2.9 22.5 + - - +
104G LEU* 3.4 19.3 - - + +
107G ARG* 2.8 35.8 + - - +
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Residues in contact with ARG 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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146A GLN* 2.9 36.7 + - - +
149A HIS* 4.0 14.8 - - + +
178A ARG* 2.7 21.1 + - + +
180A GLU* 1.3 79.5 - - - +
182A ILE* 1.3 63.0 + - - +
184A GLU* 3.3 30.8 + - - +
185A ILE* 2.9 64.4 + - + +
342A ILE* 3.6 15.0 - - - +
343A THR 3.0 23.5 + - - -
344A GLU* 4.3 0.2 - - - +
346A GLY* 3.4 10.9 - - - -
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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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149A HIS* 3.5 44.9 - - + +
152A ALA* 4.1 4.3 - - + -
153A VAL* 4.4 6.3 - - + +
177A PHE* 3.7 24.9 - - + -
178A ARG 3.2 5.1 + - - +
179A PRO* 3.2 10.3 - - + +
181A ARG* 1.3 79.0 - - - +
183A ARG* 1.3 63.9 + - - +
185A ILE* 3.9 3.5 - - - +
186A ALA* 2.9 26.5 + - - +
196A VAL* 3.5 25.4 - - + -
197A LEU* 3.3 22.2 - - + -
200A ILE* 3.9 19.1 - - + -
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Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A PRO 2.8 13.7 + - - +
180A GLU* 3.1 13.4 + - - +
182A ILE* 1.3 78.1 - - - +
184A GLU* 1.3 67.6 + - - +
186A ALA* 3.4 2.7 - - - +
187A GLN* 2.9 38.8 + - - +
193A PRO* 3.5 24.0 - - + +
194A ASP* 3.1 46.5 + - - +
197A LEU* 4.0 16.8 - - + +
104G LEU* 4.3 19.8 - - + +
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Residues in contact with GLU 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 GLU 2.9 13.7 + - - +
181A ARG* 3.4 28.4 + - - +
183A ARG* 1.3 73.5 - - - +
185A ILE* 1.3 58.2 + - - +
186A ALA 2.4 15.6 + - - -
187A GLN* 2.6 30.9 + - - +
188A ASN* 3.2 20.4 + - - +
343A THR 4.7 0.2 - - - -
344A GLU* 3.4 32.5 + - + +
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Residues in contact with ILE 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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146A GLN* 4.9 0.2 - - - +
149A HIS* 4.0 20.4 - - + +
150A THR* 4.3 9.9 - - - +
153A VAL* 3.8 22.7 - - + -
181A ARG* 2.9 62.3 + - + +
182A ILE* 4.0 3.1 - - - +
184A GLU* 1.3 76.1 - - - +
186A ALA* 1.3 59.5 + - - +
188A ASN* 3.6 3.7 + - - +
189A ARG* 3.2 27.4 - - - +
345A LYS* 3.4 31.9 - - - +
346A GLY* 3.4 15.9 - - - +
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Residues in contact with ALA 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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153A VAL* 4.6 8.7 - - + -
182A ILE 2.9 18.9 + - - +
183A ARG 3.4 4.5 - - - +
184A GLU 2.4 11.1 + - - -
185A ILE* 1.3 66.9 - - - +
187A GLN* 1.3 56.7 + - - +
188A ASN 2.9 9.7 + - - -
189A ARG* 3.2 5.8 + - - -
191A LEU* 2.9 33.0 + - + +
193A PRO* 3.9 20.0 - - + -
196A VAL* 4.0 25.1 - - + -
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Residues in contact with GLN 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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183A ARG* 2.9 34.8 + - - +
184A GLU* 2.6 23.8 + - - +
186A ALA* 1.3 70.9 - - - +
188A ASN* 1.3 67.3 + - - +
189A ARG 3.5 0.7 - - - -
190A GLY* 4.3 5.5 + - - -
191A LEU 3.6 9.6 + - - +
193A PRO* 4.0 20.0 - - + +
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Residues in contact with ASN 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 GLU* 3.2 13.5 + - - +
185A ILE 3.9 8.3 - - - +
186A ALA 2.9 1.4 - - - -
187A GLN* 1.3 95.0 - - - +
189A ARG* 1.3 65.0 + - - +
190A GLY 3.5 1.6 - - - -
344A GLU* 2.6 47.2 + - + +
345A LYS* 3.4 31.0 - - + +
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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