Contacts of the helix formed by residues 157 - 162 (chain A) 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 VAL 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.7 4.7 - - + -
15A ILE* 5.2 0.9 - - + -
19A ILE* 4.4 29.6 - - + +
20A SER* 4.7 2.7 - - - -
21A SER* 4.2 20.6 - - - +
27A ILE* 4.2 16.4 - - + -
152A THR 4.6 0.2 - - - +
153A ILE* 3.0 26.4 + - + +
156A ASN* 1.3 84.4 - - + +
158A LEU* 1.3 73.2 + - + +
159A ALA 3.2 0.9 - - - -
160A LYS* 3.0 13.2 + - - +
161A ILE* 3.0 35.9 + - + +
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Residues in contact with LEU 158 (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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15A ILE* 5.2 4.3 - - + -
47A ILE* 4.9 1.6 - - + -
52A LEU* 4.3 11.2 - - + -
83A ILE* 3.9 31.6 - - + -
153A ILE* 2.9 22.0 + - + +
154A VAL* 3.9 9.9 - - + +
157A VAL* 1.3 81.7 - - + +
159A ALA* 1.3 54.8 + - - +
161A ILE* 4.7 1.3 - - + -
162A TYR* 2.8 54.7 + - + +
166A TYR* 5.3 2.0 - - - -
177A LEU* 3.9 31.6 - - + -
181A VAL* 3.7 30.5 - - + -
185A PHE* 5.9 0.9 - - + -
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Residues in contact with ALA 159 (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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154A VAL 3.0 20.2 + - - +
155A ASP 3.5 18.2 - - - +
157A VAL 3.2 0.4 - - - -
158A LEU* 1.3 75.6 - - - +
160A LYS* 1.3 64.4 + - + +
163A ALA* 3.0 25.7 - - - +
166A TYR* 3.4 39.2 - - + +
167A ASN* 5.4 1.0 - - - +
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Residues in contact with LYS 160 (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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21A SER* 4.7 9.2 - - - +
37A TYR* 3.7 16.4 - - + +
39A GLN* 3.1 22.2 + - - +
155A ASP 2.8 28.1 + - - -
156A ASN* 3.3 25.9 + - - +
157A VAL* 3.0 8.9 + - - +
159A ALA* 1.3 86.1 - - - +
161A ILE* 1.3 65.3 + - + +
163A ALA* 3.5 11.0 + - + +
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Residues in contact with ILE 161 (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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13A LEU* 3.8 14.6 - - + -
27A ILE* 3.6 23.6 - - + -
37A TYR* 3.8 36.5 - - + -
39A GLN* 3.1 18.9 + - - +
43A HIS* 3.9 28.6 + - + +
83A ILE* 4.1 12.3 - - + -
85A ILE* 4.0 13.0 - - + -
157A VAL* 3.0 26.9 + - + +
158A LEU* 4.7 0.7 - - + -
160A LYS* 1.3 74.1 - - - +
162A TYR* 1.3 80.9 + - + +
163A ALA 3.4 0.2 - - - -
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Residues in contact with TYR 162 (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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43A HIS* 3.8 21.5 - + + +
45A SER* 2.7 39.8 + - - -
46A GLN* 4.2 9.2 - - + -
47A ILE* 3.8 40.4 - - + -
52A LEU* 5.3 1.8 - - + -
83A ILE* 4.1 5.3 - - + +
85A ILE* 3.5 17.7 - - - +
158A LEU* 2.8 44.9 + - + +
159A ALA 4.0 0.2 - - - -
161A ILE* 1.3 92.0 - - + +
163A ALA* 1.3 57.4 + - - +
164A LYS 3.4 2.6 + - - -
165A ILE* 3.5 16.6 + - + +
166A TYR* 2.9 28.4 + - - +
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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