Contacts of the helix formed by residues 165 - 175 (chain N) in PDB entry 2A3W
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 PRO 165 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163N VAL 3.8 5.6 - - - +
164N LEU* 1.3 87.9 - - + +
166N PRO* 1.3 77.3 - - + +
167N GLU* 3.7 19.3 - - - +
168N ASN* 3.0 43.6 + - - +
169N ILE* 3.1 10.5 + - - +
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Residues in contact with PRO 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202M VAL* 3.9 21.5 - - + -
106N GLU* 5.8 1.1 - - - +
108N TRP* 3.7 32.3 - - + -
164N LEU 4.6 1.1 - - - +
165N PRO* 1.3 87.6 - - + +
167N GLU* 1.3 64.6 + - + +
169N ILE* 3.4 10.4 + - + +
170N LEU* 2.9 37.6 + - + +
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Residues in contact with GLU 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165N PRO* 3.1 16.2 + - - +
166N PRO* 1.3 95.5 - - + +
168N ASN* 1.3 63.7 + - - +
170N LEU* 3.4 8.6 + - - +
171N SER* 2.9 31.5 + - - -
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Residues in contact with ASN 168 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N TRP* 5.9 0.2 - - - -
164N LEU* 3.8 27.0 - - + +
165N PRO* 3.0 34.9 + - + +
167N GLU* 1.3 78.9 - - - +
169N ILE* 1.3 64.3 + - - +
171N SER* 3.5 8.7 + - - -
172N ALA* 3.2 21.8 + - - +
177N PRO* 5.6 1.0 - - - +
178N LEU* 3.4 35.1 + - + +
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Residues in contact with ILE 169 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N THR* 4.0 17.3 - - + -
93N HIS* 6.0 0.2 - - - +
95N CYS* 3.8 25.2 - - + -
97N SER* 5.6 3.6 - - - +
108N TRP* 3.6 53.6 - - + +
111N GLY* 5.1 5.8 - - - -
164N LEU* 3.8 29.6 - - + +
165N PRO 3.1 15.6 + - - +
166N PRO* 3.5 10.5 - - + +
168N ASN* 1.3 76.6 - - - +
170N LEU* 1.3 63.3 + - - +
172N ALA* 3.3 6.1 + - - +
173N TYR* 3.1 21.2 + - + +
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Residues in contact with LEU 170 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108N TRP* 5.5 5.4 - - + -
111N GLY* 4.6 18.4 - - - +
166N PRO* 2.9 23.3 + - + +
167N GLU* 3.5 9.2 - - - +
169N ILE* 1.3 78.0 - - - +
171N SER* 1.3 51.3 + - - +
173N TYR* 3.2 13.2 + - + +
174N GLN* 2.8 66.4 + - - +
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Residues in contact with SER 171 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167N GLU* 2.9 21.1 + - - +
168N ASN* 3.7 11.9 + - - -
170N LEU* 1.3 76.8 - - - +
172N ALA* 1.3 57.1 + - - +
174N GLN* 3.2 7.1 + - - +
175N GLY 3.0 9.2 + - - -
176N THR* 2.9 48.1 + - - -
177N PRO* 5.1 1.1 - - - -
178N LEU* 5.3 5.8 - - - +
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Residues in contact with ALA 172 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N CYS* 4.5 16.2 - - + -
38N ARG* 3.2 14.7 + - - -
93N HIS* 3.5 17.0 + - + +
156N ASP* 5.9 1.2 - - - +
158N TYR* 5.8 1.6 - - + -
160N TRP* 4.5 8.5 - - + -
168N ASN 3.2 11.2 + - - +
169N ILE 3.3 8.7 + - - +
171N SER* 1.3 78.6 - - - +
173N TYR* 1.3 61.4 + - - +
175N GLY* 3.4 6.2 + - - -
177N PRO* 4.0 32.3 - - + +
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Residues in contact with TYR 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ARG* 2.8 25.7 + - - -
93N HIS* 3.5 39.6 - - + +
110N ASN* 3.4 47.0 + - + +
111N GLY* 4.0 12.8 - - - +
169N ILE* 3.1 12.6 + - + +
170N LEU* 3.4 13.9 - - + +
172N ALA* 1.3 76.2 - - - +
174N GLN* 1.3 79.3 + - - +
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Residues in contact with GLN 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ARG* 4.4 0.7 - - - -
170N LEU* 2.8 41.1 + - - +
171N SER* 3.2 9.7 + - - +
173N TYR* 1.3 100.6 - - - +
175N GLY* 1.3 57.6 + - - +
176N THR* 4.5 6.6 - - - +
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Residues in contact with GLY 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ARG* 4.0 9.0 - - - -
156N ASP* 6.1 0.4 - - - -
171N SER 3.0 2.0 + - - -
172N ALA 3.4 8.0 + - - -
173N TYR 3.2 3.4 - - - -
174N GLN* 1.3 79.7 - - - +
176N THR* 1.3 68.0 + - - +
177N PRO* 3.5 11.2 - - - +
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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