Contacts of the helix formed by residues 163 - 175 (chain A) in PDB entry 2XMS
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 GLY 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A ALA 3.5 2.8 + - - -
162A LYS* 1.3 75.0 - - - +
164A TRP* 1.3 67.8 + - - -
165A MET 3.2 2.9 - - - -
166A ASP* 2.8 16.8 + - - -
167A TRP* 3.0 23.5 + - - -
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Residues in contact with TRP 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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163A GLY* 1.3 73.0 - - - -
165A MET* 1.3 107.9 + - + +
167A TRP* 3.5 9.2 + - - +
168A ALA* 3.0 31.4 + - + +
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Residues in contact with MET 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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163A GLY* 3.2 1.2 - - - -
164A TRP* 1.3 118.5 - - + +
166A ASP* 1.3 67.7 + - - +
168A ALA* 3.6 4.8 + - - +
169A ALA* 3.2 23.7 + - - +
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Residues in contact with ASP 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 ALA 4.2 2.6 - - - +
162A LYS* 3.5 25.8 + - + +
163A GLY* 2.8 26.8 + - - +
165A MET* 1.3 78.9 - - - +
167A TRP* 1.3 64.4 + - - +
169A ALA* 3.3 5.8 + - - +
170A HIS* 3.0 25.6 + - - +
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Residues in contact with TRP 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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162A LYS* 3.6 32.6 + - + +
163A GLY 3.0 25.8 + - - +
164A TRP* 3.9 7.2 - - - +
166A ASP* 1.3 76.8 - - - +
168A ALA* 1.3 56.2 + - - +
170A HIS* 3.4 27.8 + + - +
171A LYS* 2.9 67.6 + - - +
224A ASN* 3.4 37.2 - - + -
225A ASN* 3.4 28.5 - - - -
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Residues in contact with ALA 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 TRP* 3.0 20.3 + - + +
165A MET* 3.8 7.2 - - - +
166A ASP 3.3 0.2 - - - -
167A TRP* 1.3 74.5 - - - +
169A ALA* 1.3 56.7 + - - +
171A LYS* 3.9 5.8 - - - +
172A LEU* 3.0 31.0 + - - +
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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 MET 3.2 16.0 + - - +
166A ASP* 3.3 5.8 + - - +
168A ALA* 1.3 74.9 - - - +
170A HIS* 1.3 59.5 + - - +
172A LEU* 3.3 7.6 + - - +
173A THR* 2.9 35.1 + - - +
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Residues in contact with HIS 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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162A LYS* 3.8 19.7 + - - +
166A ASP 3.0 17.6 + - - +
167A TRP* 3.6 27.6 - + - +
169A ALA* 1.3 73.7 - - - +
171A LYS* 1.3 67.1 + - + +
173A THR* 3.3 7.5 + - - -
174A GLY* 2.9 26.4 + - - -
182A MET* 3.5 28.3 - - + +
220A TRP* 3.7 16.6 + + - -
224A ASN* 3.5 30.2 + - - -
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Residues in contact with LYS 171 (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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167A TRP* 2.9 49.6 + - + +
168A ALA* 4.0 4.7 - - - +
170A HIS* 1.3 88.5 - - + +
172A LEU* 1.3 62.6 + - - +
174A GLY* 3.3 10.2 + - - +
175A LEU* 3.4 17.9 + - - +
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Residues in contact with LEU 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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168A ALA 3.0 19.5 + - - +
169A ALA* 3.7 7.9 - - - +
171A LYS* 1.3 74.0 - - - +
173A THR* 1.3 67.4 + - - +
175A LEU* 3.2 31.9 + - + +
176A THR* 4.3 3.6 + - - +
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Residues in contact with THR 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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169A ALA* 2.9 18.9 + - - +
170A HIS* 3.5 6.9 - - - -
172A LEU* 1.3 75.9 - - - +
174A GLY* 1.3 63.7 + - - +
175A LEU 3.1 1.6 + - - -
176A THR* 3.2 15.4 + - - -
177A SER* 3.2 24.2 + - - +
182A MET* 4.0 20.2 - - + -
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Residues in contact with GLY 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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170A HIS* 2.9 13.4 + - - -
171A LYS* 3.3 6.7 + - - -
172A LEU 3.2 0.8 - - - -
173A THR* 1.3 75.9 - - - +
175A LEU* 1.3 61.9 + - - +
176A THR 3.2 0.2 - - - -
177A SER 3.2 15.0 - - - +
182A MET* 3.7 20.2 - - - -
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Residues in contact with LEU 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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171A LYS 3.5 15.0 - - - +
172A LEU* 3.5 25.6 - - + +
173A THR 3.1 1.4 + - - -
174A GLY* 1.3 78.6 - - - +
176A THR* 1.3 69.6 + - + +
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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