Contacts of the helix formed by residues 159 - 163 (chain A) in PDB entry 6XYU
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 LEU 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ILE 3.9 15.0 - - - +
83A TRP* 3.9 34.5 - - + +
84A ASN 3.4 28.5 - - - +
86A ASN* 3.9 12.8 - - + +
155A GLY* 5.4 2.5 - - - -
156A SER* 3.3 29.2 - - - +
157A ALA 3.4 2.1 - - - +
158A THR* 1.3 81.1 - - - +
160A ASP* 1.3 66.3 + - - +
161A ILE* 3.9 13.5 - - + +
162A TYR* 3.0 39.1 + - + +
163A ASN* 3.7 3.5 + - - -
601A I40 6.2 0.2 - - + -
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Residues in contact with ASP 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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82A ILE 5.5 1.0 + - - -
86A ASN* 3.9 16.1 + - - +
158A THR 3.4 2.6 + - - -
159A LEU* 1.3 72.2 - - - +
161A ILE* 1.3 57.8 + - - +
163A ASN* 2.8 34.5 + - - +
490A GLN* 3.7 3.1 + - - -
2B NAG 5.4 10.4 - - - +
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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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82A ILE* 5.2 13.6 + - + +
83A TRP* 3.8 28.9 - - + -
159A LEU* 3.0 14.0 - - + +
160A ASP* 1.3 79.0 - - - +
162A TYR* 1.3 85.3 + - + +
163A ASN 3.3 0.2 - - - -
484A ILE* 4.4 3.6 - - + -
485A GLU* 3.3 48.2 - - + +
488A PHE* 3.7 12.1 - - - +
490A GLN* 2.9 25.3 + - + +
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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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83A TRP* 3.5 16.2 - + - -
99A TRP* 4.2 11.0 - - - -
146A TRP* 3.4 43.7 - + + +
148A TYR* 3.4 22.6 - - + +
149A GLY 4.3 5.9 + - - -
155A GLY* 5.8 0.2 - - - -
156A SER 3.0 28.9 - - - -
157A ALA* 3.8 15.3 - - - +
159A LEU* 3.0 32.6 + - + +
161A ILE* 1.3 92.9 - - + +
163A ASN* 1.3 64.3 + - - +
164A ALA* 3.0 4.5 + - - +
177A SER* 5.4 1.7 + - - +
484A ILE* 3.8 18.9 - - + +
488A PHE* 3.8 16.3 - + - -
601A I40 4.1 11.4 - - - +
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Residues in contact with ASN 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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99A TRP* 3.6 10.8 + - - -
159A LEU 3.7 1.6 + - - -
160A ASP* 2.8 22.4 + - + +
161A ILE 3.3 1.2 - - - -
162A TYR* 1.3 74.3 - - - +
164A ALA* 1.3 59.0 + - - +
165A ASP* 2.9 51.1 + - - +
166A ILE 4.7 1.9 + - - -
488A PHE* 3.7 8.1 - - - +
490A GLN* 3.2 24.1 + - - +
1B NAG 4.2 24.8 + - - +
2B NAG 6.1 1.4 - - - -
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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