Contacts of the helix formed by residues 73 - 87 (chain B) in PDB entry 4P5E
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 ASP 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ARG* 3.5 30.5 + - - -
72B GLY* 1.3 78.3 + - - +
74B ARG* 1.3 59.1 + - - +
76B ILE* 3.3 18.8 + - - +
77B HIS* 2.9 30.2 + - - +
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Residues in contact with ARG 74 (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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72B GLY* 3.2 1.8 - - - -
73B ASP* 1.3 79.1 - - - +
75B LEU* 1.3 62.5 + - + +
77B HIS* 3.3 18.8 + - - +
78B GLU* 2.9 67.5 + - + +
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Residues in contact with LEU 75 (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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72B GLY* 3.2 19.1 + - - +
74B ARG* 1.3 82.0 - - + +
76B ILE* 1.3 63.8 + - + +
78B GLU* 3.9 6.3 - - + +
79B GLN* 3.0 26.2 + - - +
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Residues in contact with ILE 76 (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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30B ARG* 5.9 0.7 - - - +
72B GLY 3.1 19.2 + - - +
73B ASP* 3.5 23.6 - - + +
74B ARG 3.3 0.2 - - - -
75B LEU* 1.3 77.7 - - + +
77B HIS* 1.3 64.5 + - - +
79B GLN* 3.9 3.3 - - - +
80B ASP* 2.9 27.1 + - - +
201B N6P 3.3 83.0 - - + +
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Residues in contact with HIS 77 (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 ASP 2.9 17.4 + - - +
74B ARG* 3.7 19.9 + - - +
76B ILE* 1.3 79.6 - - - +
78B GLU* 1.3 82.0 + - - +
80B ASP* 3.8 4.2 - - - -
81B LEU* 2.9 51.1 + - + +
103B TYR* 2.7 46.7 + + - -
107B ARG* 4.3 4.3 - - - -
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Residues in contact with GLU 78 (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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74B ARG* 2.9 52.6 + - + +
75B LEU* 4.0 7.6 - - + +
77B HIS* 1.3 104.1 + - - +
79B GLN* 1.3 64.6 + - - +
81B LEU* 3.3 6.2 + - - +
82B GLU* 3.0 26.3 + - - +
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Residues in contact with GLN 79 (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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75B LEU 3.0 18.2 + - - +
76B ILE* 4.0 4.0 - - - +
78B GLU* 1.3 75.9 - - - +
80B ASP* 1.3 64.1 + - - +
82B GLU* 3.3 25.6 + - - +
83B TRP* 3.1 67.5 + - + +
86B GLN* 5.8 0.2 - - - +
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Residues in contact with ASP 80 (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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24B TYR* 3.3 25.9 + - - +
54B THR* 4.8 1.5 - - - +
76B ILE* 2.9 23.4 + - - +
77B HIS* 3.8 5.6 - - - +
79B GLN* 1.3 76.3 - - - +
81B LEU* 1.3 63.4 + - + +
83B TRP* 3.2 27.7 + - - -
84B LEU* 2.8 25.6 + - - +
104B GLU* 3.8 1.1 - - + +
201B N6P 2.9 50.2 + - - -
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Residues in contact with LEU 81 (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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24B TYR* 5.7 0.9 - - - +
77B HIS* 2.9 46.6 + - + +
78B GLU* 3.9 6.7 - - - +
80B ASP* 1.3 80.1 - - + +
82B GLU* 1.3 64.7 + - - +
84B LEU* 3.4 14.3 + - + -
85B GLN* 3.2 34.7 + - - +
103B TYR* 4.1 12.8 - - + -
104B GLU* 6.1 3.8 - - + -
107B ARG* 3.5 39.9 - - + +
111B PHE* 3.9 18.6 - - + -
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Residues in contact with GLU 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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78B GLU 3.0 14.8 + - - +
79B GLN* 3.4 29.0 + - - +
81B LEU* 1.3 77.9 - - - +
83B TRP* 1.3 62.4 + - - +
85B GLN* 3.4 9.5 + - - +
86B GLN* 3.2 42.7 + - - +
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Residues in contact with TRP 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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24B TYR* 3.8 9.2 - - + -
53B LEU* 3.5 60.3 - - + +
54B THR* 4.0 15.5 - - + -
56B HIS* 5.0 17.5 - + - -
79B GLN* 3.1 45.9 + - + +
80B ASP* 3.4 31.6 - - - +
82B GLU* 1.3 80.6 - - - +
84B LEU* 1.3 63.0 + - - +
86B GLN* 3.1 20.7 + - - -
87B ALA* 3.1 19.2 + - - +
201B N6P 5.8 2.2 - + - -
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Residues in contact with LEU 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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24B TYR* 3.6 30.7 - - + +
80B ASP 2.8 19.9 + - - +
81B LEU* 3.8 15.5 - - + +
82B GLU 3.3 0.4 - - - -
83B TRP* 1.3 73.0 - - - +
85B GLN* 1.3 62.3 + - - +
87B ALA* 3.2 13.6 + - - +
90B VAL* 3.7 31.6 - - + -
104B GLU* 3.7 18.2 - - + +
107B ARG* 3.6 32.3 - - + -
108B ALA* 3.9 11.2 - - + +
111B PHE* 4.2 11.7 - - + -
113B LYS* 3.3 16.0 - - + -
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Residues in contact with GLN 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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81B LEU* 3.2 23.5 + - - +
82B GLU* 3.7 11.3 - - - +
83B TRP 3.2 0.2 - - - -
84B LEU* 1.3 76.3 - - - +
86B GLN* 1.3 59.5 + - + +
107B ARG* 5.7 0.5 + - - -
111B PHE* 3.3 40.7 - - + -
113B LYS* 2.9 24.5 + - - +
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Residues in contact with GLN 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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22B ALA* 3.9 12.5 - - + +
53B LEU* 4.1 12.3 - - + +
79B GLN* 5.8 0.4 - - - +
82B GLU* 3.2 38.3 + - - +
83B TRP* 3.1 22.1 + - - +
85B GLN* 1.3 77.9 - - + +
87B ALA* 1.3 64.0 + - - +
88B ASP* 3.6 7.6 + - - +
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Residues in contact with ALA 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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22B ALA* 3.7 10.8 - - - +
23B LEU 4.5 1.1 - - - -
24B TYR* 3.7 19.7 - - + +
53B LEU* 4.7 1.3 - - + -
83B TRP 3.1 10.0 + - - +
84B LEU 3.2 14.3 + - - +
86B GLN* 1.3 78.9 - - - +
88B ASP* 1.3 63.2 + - - +
89B VAL 3.7 19.3 - - - +
90B VAL* 4.7 4.0 - - + -
113B LYS* 2.8 31.6 + - - +
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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