Contacts of the helix formed by residues 162 - 169 (chain B) in PDB entry 2X5Q
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 TYR 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B HIS* 3.7 21.1 - + + -
45B SER* 2.7 41.6 + - - -
46B GLN* 3.9 22.7 - - - -
47B ILE* 3.3 38.8 - - + -
52B LEU* 5.1 2.7 - - + -
83B ILE* 4.1 5.6 - - + +
85B ILE* 3.4 18.4 - - - +
158B LEU* 2.8 40.0 + - + +
161B ILE* 1.3 93.2 - - + +
163B ALA* 1.3 53.0 + - - +
164B LYS 3.2 3.2 + - - -
165B ILE* 3.3 9.3 + - + +
166B TYR* 2.8 34.3 + - - +
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN* 4.7 8.4 - - - +
159B ALA 3.2 21.5 + - - +
160B LYS* 3.5 12.5 + - - +
161B ILE 3.4 4.0 + - - -
162B TYR* 1.3 73.8 - - - +
164B LYS* 1.3 61.0 + - + +
166B TYR* 4.3 1.6 - - - -
167B ASN* 2.8 46.8 + - - +
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Residues in contact with LYS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN* 5.1 13.7 - - - +
40B ASN* 3.3 25.4 + - - +
162B TYR 3.2 1.2 + - - -
163B ALA* 1.3 80.1 - - + +
165B ILE* 1.3 64.2 + - + +
167B ASN* 3.7 5.6 + - - +
168B SER* 3.3 20.8 + - - -
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLN* 3.4 26.5 - - - +
47B ILE* 3.5 43.7 - - + +
48B ASP* 4.3 2.9 - - - -
162B TYR* 3.3 11.1 + - + +
164B LYS* 1.3 76.0 - - + +
166B TYR* 1.3 66.8 + - - +
168B SER* 2.6 28.3 + - - +
169B LEU* 3.1 19.0 + - + +
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Residues in contact with TYR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.8 8.9 - - + +
154B VAL* 3.7 25.5 - - + +
155B ASP* 3.6 19.7 + - - -
159B ALA* 3.5 35.2 - - + -
162B TYR 2.8 25.2 + - - +
163B ALA 3.8 2.5 - - - +
165B ILE* 1.3 73.3 - - - +
167B ASN* 1.3 74.4 + - - +
169B LEU* 3.0 20.2 + - + +
174B LYS* 3.4 60.0 - - + +
177B LEU* 3.9 21.3 - - + -
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Residues in contact with ASN 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ALA 5.2 1.4 - - - +
163B ALA* 2.8 39.5 + - - +
164B LYS* 4.1 5.5 - - - +
166B TYR* 1.3 84.5 - - - +
168B SER* 1.3 58.6 + - - +
169B LEU 3.6 5.2 + - - +
174B LYS* 4.7 8.3 + - - +
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Residues in contact with SER 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B LYS 3.3 12.8 + - - -
165B ILE* 2.6 29.9 + - - +
167B ASN* 1.3 75.1 - - - +
169B LEU* 1.3 67.1 + - - +
170B ASN 3.8 0.5 + - - -
173B GLN* 4.7 1.0 - - - +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 4.5 10.8 - - + -
48B ASP 3.9 31.6 - - - +
49B ASP* 4.1 7.2 - - + +
165B ILE* 3.4 20.0 - - + +
166B TYR* 3.0 27.8 + - + +
167B ASN 3.9 3.1 - - - +
168B SER* 1.3 83.4 - - - +
170B ASN* 1.3 69.8 + - - +
173B GLN* 3.5 34.1 - - + +
174B LYS* 3.6 25.5 + - + +
177B LEU* 4.8 5.6 - - + -
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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