Contacts of the helix formed by residues 162 - 170 (chain A) in PDB entry 3ATI
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 SER 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ALA* 3.6 18.8 - - - +
161A LEU* 1.3 77.3 - - - +
163A ASP* 1.3 63.3 + - - +
164A SER* 3.1 12.8 + - - -
165A SER* 2.9 42.1 + - - -
166A CYS* 3.0 9.9 + - - +
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Residues in contact with ASP 163 (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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130A ALA* 5.1 0.2 - - - +
161A LEU 3.7 1.8 + - - -
162A SER* 1.3 72.2 - - - +
164A SER* 1.3 57.9 + - - +
166A CYS* 3.4 5.7 + - - +
167A LYS* 2.6 71.1 + - - +
174A ILE* 4.2 12.0 - - - +
175A THR 5.2 1.7 - - - +
178A MET 5.1 4.0 - - - +
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Residues in contact with SER 164 (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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162A SER* 3.1 13.1 + - - -
163A ASP* 1.3 80.1 + - - +
165A SER* 1.3 60.2 + - - +
167A LYS* 3.8 6.9 - - - +
168A SER* 2.8 35.0 + - - -
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Residues in contact with SER 165 (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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161A LEU* 3.5 14.6 - - - +
162A SER* 2.9 30.7 + - - -
164A SER* 1.3 78.8 + - - +
166A CYS* 1.3 63.2 + - - +
168A SER* 3.3 6.7 + - - -
169A ALA* 2.9 30.0 + - - +
184A LEU* 4.6 23.4 - - - +
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Residues in contact with CYS 166 (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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161A LEU 5.2 0.2 - - - +
162A SER 3.0 13.8 + - - +
163A ASP* 3.6 8.1 - - - +
165A SER* 1.3 81.7 + - - +
167A LYS* 1.3 62.5 + - - +
169A ALA* 3.2 6.1 + - - +
170A TYR* 3.0 19.1 + - - -
174A ILE* 3.7 34.9 - - + +
179A PHE* 4.1 2.9 - - - -
180A CYS* 2.0 64.2 - - + +
221A PRO* 5.6 0.7 - - - -
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Residues in contact with LYS 167 (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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163A ASP* 2.6 53.1 + - - +
164A SER* 3.8 6.1 - - - +
166A CYS* 1.3 73.5 - - - +
168A SER* 1.3 61.9 + - - +
170A TYR 3.2 1.7 - - - -
171A PRO* 3.1 28.1 - - - +
172A GLY 6.2 0.7 - - - +
174A ILE* 3.9 37.5 - - + +
175A THR 5.9 1.9 - - - -
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Residues in contact with SER 168 (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 SER* 2.8 23.9 + - - -
165A SER* 3.7 7.9 - - - -
167A LYS* 1.3 76.9 - - - +
169A ALA* 1.3 62.2 + - - +
171A PRO* 3.6 13.1 - - - +
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Residues in contact with ALA 169 (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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165A SER 2.9 16.7 + - - +
166A CYS* 3.2 8.3 + - - +
168A SER* 1.3 78.6 - - - +
170A TYR* 1.3 64.5 + - + +
171A PRO* 3.5 4.0 - - - +
184A LEU* 4.8 4.9 - - + -
219A ASN* 3.5 23.5 - - - +
220A LYS* 2.8 32.7 + - - -
221A PRO* 3.9 12.8 - - + -
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Residues in contact with TYR 170 (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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166A CYS 3.0 9.9 + - - -
167A LYS* 3.2 7.3 - - - +
169A ALA* 1.3 87.2 - - + +
171A PRO* 1.3 69.1 - - - +
172A GLY 3.3 0.5 + - - -
173A GLN* 3.3 26.9 + - - +
174A ILE* 3.8 23.6 + - + +
180A CYS* 4.2 4.0 - - - -
211A TRP* 3.6 27.4 - + + -
212A GLY* 3.6 0.5 - - - -
213A SER* 3.2 28.9 + - - -
220A LYS* 3.2 35.8 + - + +
221A PRO* 2.6 42.9 + - + -
223A VAL* 3.6 20.0 - - + -
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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