Contacts of the helix formed by residues 81 - 90 (chain B) in PDB entry 1PU5
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 HIS 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A THR* 3.9 23.1 + - + +
103A TYR* 5.2 1.4 + - - -
119A PRO* 5.1 0.2 - - - +
120A LYS* 3.2 53.7 + - + +
121A SER 4.5 0.4 - - - -
122A GLU* 4.7 10.1 + - - -
49B SER* 5.7 2.2 - - - -
50B PRO* 4.0 27.8 - - + +
51B LEU 3.6 4.7 - - - +
79B PHE 3.3 0.2 - - - -
80B GLU* 1.3 96.1 + - + +
82B PHE* 1.3 65.7 + - - +
83B CYS* 3.1 3.4 - - + +
84B ASP* 2.9 17.6 + - + +
85B VAL* 3.0 14.8 + - - +
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Residues in contact with PHE 82 (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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51B LEU* 2.7 34.6 + - + +
53B VAL* 3.6 33.4 - - + -
79B PHE* 3.9 31.3 + + + -
80B GLU 3.8 0.4 - - - -
81B HIS* 1.3 73.9 - - - +
83B CYS* 1.3 61.0 + - - +
85B VAL* 3.5 18.9 - - + +
86B LEU* 2.9 60.5 + - + +
111B PHE* 5.8 1.8 - + - -
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Residues in contact with CYS 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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48B SER 4.0 0.7 - - - -
49B SER* 3.6 34.1 - - - -
51B LEU* 3.8 16.7 + - - +
81B HIS* 3.1 1.7 + - + -
82B PHE* 1.3 76.6 - - - +
84B ASP* 1.3 62.0 + - - +
86B LEU* 3.3 6.1 + - - +
87B ASP* 3.1 28.9 + - - +
109B CYS* 2.0 56.9 + - + -
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Residues in contact with ASP 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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38A SER* 3.7 1.7 + - - -
119A PRO* 3.3 10.5 - - - +
120A LYS* 2.8 61.7 + - + +
81B HIS* 2.9 12.5 + - + +
83B CYS* 1.3 78.2 - - - +
85B VAL* 1.3 64.6 + - - +
87B ASP* 3.2 14.2 + - - +
88B MET* 2.9 45.5 + - - +
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Residues in contact with VAL 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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103A TYR* 3.8 19.7 - - + +
119A PRO* 3.7 27.6 - - + -
73B TYR* 4.3 13.2 - - + -
79B PHE* 4.2 17.3 - - + -
81B HIS 3.0 15.8 + - - +
82B PHE* 3.1 25.1 + - + +
84B ASP* 1.3 75.6 - - - +
86B LEU* 1.3 59.7 + - + +
88B MET* 3.3 1.6 + - - +
89B LEU* 3.0 51.2 + - + +
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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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82B PHE* 2.9 54.6 + - + +
83B CYS 3.6 5.2 - - - +
84B ASP 3.2 0.2 - - - -
85B VAL* 1.3 76.3 - - + +
87B ASP* 1.3 61.5 + - - +
89B LEU* 4.8 6.3 - - + -
90B ILE* 2.9 48.1 + - + +
107B CYS* 3.9 19.5 - - + +
108B HIS* 4.0 7.0 + - + -
109B CYS* 4.4 9.2 - - - -
111B PHE* 3.9 31.4 - - + -
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Residues in contact with ASP 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 CYS* 3.1 21.0 + - - +
84B ASP* 3.2 19.5 + - - +
86B LEU* 1.3 77.0 - - - +
88B MET* 1.3 60.7 + - + +
90B ILE 3.2 20.5 - - - +
91B PRO* 3.8 7.1 - - - +
92B THR* 3.9 15.8 + - + +
108B HIS* 3.0 26.5 - - - +
109B CYS 5.3 1.0 + - - +
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Residues in contact with MET 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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21A SER* 4.7 4.5 - - - +
38A SER* 3.8 13.7 - - - +
39A VAL 4.4 1.6 - - - +
40A VAL* 3.6 30.1 - - + -
117A SER* 4.1 15.1 + - - -
118A LEU 3.6 15.9 - - - +
119A PRO* 3.6 28.0 - - + -
73B TYR* 5.9 0.7 - - - +
84B ASP* 2.9 43.7 + - - +
85B VAL* 3.8 4.9 - - - +
87B ASP* 1.3 78.5 - - + +
89B LEU* 1.3 67.4 + - + +
90B ILE 3.3 0.2 - - - -
91B PRO* 4.8 6.2 - - - +
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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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73B TYR* 4.3 31.4 - - + +
85B VAL* 3.0 38.5 + - + +
86B LEU* 4.3 5.4 - - + +
88B MET* 1.3 80.9 - - + +
90B ILE* 1.3 70.6 + - + +
91B PRO* 4.0 5.7 - - - +
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Residues in contact with ILE 90 (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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86B LEU* 2.9 24.1 + - + +
87B ASP 3.2 9.4 - - - +
89B LEU* 1.3 90.2 - - + +
91B PRO* 1.3 67.8 - - + +
92B THR 3.5 0.2 + - - -
94B GLU* 5.4 0.9 - - + +
95B PRO 4.8 7.2 - - - +
97B PRO* 4.2 34.1 - - + -
100B LEU* 6.2 0.4 - - + -
107B CYS* 4.3 24.7 - - + +
108B HIS* 2.8 43.3 + - + +
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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