Contacts of the helix formed by residues 82 - 90 (chain B) in PDB entry 1XHU
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 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PHE* 3.2 6.0 - - - +
81B ASN* 1.3 81.9 - - - +
83B PRO* 1.3 70.6 - - - +
85B LEU* 2.9 29.3 + - - +
86B LEU* 3.0 22.7 + - - +
160B GLU* 3.1 16.7 + - - -
163B LEU* 3.1 27.3 - - - +
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Residues in contact with PRO 83 (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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81B ASN 4.6 1.1 - - - -
82B SER* 1.3 83.5 - - - +
84B THR* 1.3 56.6 + - - +
86B LEU* 3.3 16.7 - - + +
87B PHE* 3.1 27.5 + - - +
154B LYS* 4.0 8.0 - - + +
158B ASN* 3.2 34.1 - - + +
160B GLU* 3.5 17.3 - - - +
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Residues in contact with THR 84 (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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82B SER* 3.0 2.3 - - - -
83B PRO* 1.3 73.1 - - - +
85B LEU* 1.3 68.1 + - - +
86B LEU 2.9 0.9 - - - -
87B PHE* 2.8 16.3 + - - +
88B LEU* 2.9 14.0 + - + +
151B THR* 3.8 31.6 - - + +
154B LYS* 3.6 30.4 + - + +
155B MET* 3.9 10.4 + - + -
158B ASN* 4.4 0.7 + - - -
160B GLU* 2.7 26.2 + - - +
163B LEU* 5.2 1.6 - - - -
164B PHE* 4.0 21.1 - - + -
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Residues in contact with LEU 85 (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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80B PHE* 4.7 13.9 - - + +
82B SER* 2.9 19.8 + - - +
84B THR* 1.3 73.7 - - - +
86B LEU* 1.3 52.2 + - - +
88B LEU* 3.6 7.4 - - + +
89B LEU* 2.5 76.8 + - + +
123B TYR* 3.4 53.8 - - + +
125B LEU* 4.6 6.3 - - + -
163B LEU* 3.3 30.5 - - + -
164B PHE* 4.6 6.1 - - + -
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Residues in contact with LEU 86 (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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77B TYR* 3.3 43.5 - - + +
80B PHE* 3.6 24.2 - - + -
82B SER 3.0 18.1 + - - +
83B PRO* 3.3 17.3 - - + +
84B THR 2.8 0.6 + - - -
85B LEU* 1.3 75.7 - - - +
87B PHE* 1.3 63.0 + - - +
90B SER* 2.7 49.8 + - - +
13H G 3.9 29.2 - - + +
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Residues in contact with PHE 87 (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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83B PRO 3.1 10.2 + - - +
84B THR 2.8 12.3 + - - +
86B LEU* 1.3 79.3 - - + +
88B LEU* 1.3 63.9 + - + +
89B LEU 5.1 0.3 - - - -
90B SER* 4.7 5.0 + - - +
147B LYS* 3.7 29.0 - - + -
150B GLN* 3.5 42.4 - - + -
151B THR* 3.6 25.6 - - - -
154B LYS* 3.4 27.4 - - + -
6E T 5.7 0.9 - - - -
13H G 5.0 8.6 - - - +
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Residues in contact with LEU 88 (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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56B GLN* 3.5 4.3 + - - -
84B THR* 2.9 16.2 + - + +
85B LEU* 3.8 11.0 - - + +
87B PHE* 1.3 82.6 - - + +
89B LEU* 1.3 67.2 + - + +
90B SER 5.1 0.4 - - - +
112B THR* 3.2 40.5 + - + +
125B LEU* 3.8 17.5 - - + -
143B ILE* 5.4 2.0 - - + -
147B LYS* 4.3 11.7 - - + -
151B THR* 3.5 34.1 - - + +
164B PHE* 3.4 37.5 - - + -
166B ILE* 4.6 9.0 - - + -
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Residues in contact with LEU 89 (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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56B GLN* 3.0 33.6 + - + +
59B TYR* 4.3 10.1 - - + -
60B LEU* 3.7 15.9 - - + +
80B PHE* 4.3 10.1 - - + -
85B LEU* 2.5 45.6 + - + +
88B LEU* 1.3 83.8 - - + +
90B SER* 1.3 71.3 + - - +
91B ARG* 5.3 0.3 - - - -
111B ASP* 5.1 0.5 - - - +
113B ALA* 5.7 0.2 - - + -
116B LEU* 3.6 29.8 - - + -
123B TYR* 4.2 9.2 - - + -
125B LEU* 3.7 31.4 - - + -
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLN* 4.8 0.9 + - - -
60B LEU* 4.2 2.7 - - - -
77B TYR* 3.8 10.9 - - - -
80B PHE* 3.8 18.8 - - - -
86B LEU* 2.7 50.9 + - - +
87B PHE* 4.7 2.3 + - - +
88B LEU 5.1 0.9 - - - +
89B LEU* 1.3 84.0 - - - +
91B ARG* 1.3 63.5 + - - +
111B ASP* 5.6 0.5 - - - +
13H G 3.0 24.8 + - - +
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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