Contacts of the helix formed by residues 77 - 88 (chain E) in PDB entry 1H4O
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 77 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E PRO* 5.8 2.7 - - + -
76E ASN* 1.3 78.8 + - - +
78E ALA* 1.3 58.7 - - - +
79E PHE* 2.9 29.7 + - + +
80E VAL* 3.0 28.5 + - - +
81E THR* 3.1 23.4 + - - +
98E ALA* 3.7 0.9 - - - -
100E PRO* 4.3 13.2 - - + +
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Residues in contact with ALA 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E PHE* 4.0 11.9 - - + -
17E GLY 3.3 15.9 - - - +
18E GLU 3.5 35.7 - - - +
19E PRO* 3.6 7.3 - - + +
77E ASP* 1.3 72.4 - - - +
79E PHE* 1.3 64.9 + - - +
81E THR* 3.3 11.0 + - - +
82E GLY 3.0 17.2 + - - -
98E ALA* 3.5 14.3 - - + +
100E PRO* 5.6 0.8 - - - +
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Residues in contact with PHE 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E GLY 4.2 9.0 - - - +
18E GLU* 4.3 12.6 - - + -
19E PRO* 3.4 37.0 - - + -
77E ASP* 2.9 13.9 + - - +
78E ALA* 1.3 78.3 - - - +
80E VAL* 1.3 63.4 + - + +
82E GLY* 3.4 0.5 + - - -
83E GLU* 3.1 32.1 + - + +
86E ARG* 4.8 0.7 + - - -
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Residues in contact with VAL 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ALA* 3.7 24.5 - - + +
43E PHE* 3.5 19.4 - - + -
76E ASN* 3.9 16.8 - - + +
77E ASP* 3.0 31.8 + - - +
79E PHE* 1.3 77.0 - - + +
81E THR* 1.3 58.1 + - - +
83E GLU* 3.3 3.5 + - - -
84E TRP* 2.9 27.0 + - - +
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Residues in contact with THR 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E GLY 4.6 2.9 + - - -
42E ALA* 4.6 3.4 - - + -
74E SER* 3.5 25.1 - - - +
76E ASN* 3.8 9.6 - - + -
77E ASP 3.1 12.5 + - - +
78E ALA* 3.3 17.5 + - - +
80E VAL* 1.3 76.4 - - - +
82E GLY* 1.3 60.1 + - - +
84E TRP* 3.3 9.1 + - + +
85E GLY 3.0 23.0 + - - -
96E LEU* 3.7 29.3 + - + +
97E LEU 4.3 2.0 - - - +
98E ALA* 3.5 24.3 + - + +
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Residues in contact with GLY 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E GLY* 4.1 14.8 - - - -
78E ALA 3.0 16.7 + - - -
79E PHE 3.9 0.2 - - - -
81E THR* 1.3 78.6 + - - +
83E GLU* 1.3 61.8 + - - +
85E GLY* 3.4 2.3 + - - -
86E ARG* 3.2 43.9 + - - +
96E LEU* 5.2 3.8 - - - -
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Residues in contact with GLU 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E PHE* 3.9 11.6 - - + -
79E PHE* 3.1 19.9 + - + +
80E VAL* 3.9 3.4 - - - +
82E GLY* 1.3 76.3 - - - +
84E TRP* 1.3 63.0 + - - +
86E ARG* 2.2 40.8 + - - +
87E ALA* 3.0 22.2 + - - +
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Residues in contact with TRP 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E VAL* 3.9 24.7 - - + -
42E ALA* 3.6 17.9 - - + -
43E PHE* 3.1 46.1 - + + +
47E CYS* 3.7 34.5 - - + -
48E SER* 3.0 21.3 + - - -
52E LEU* 3.7 26.5 - - + -
72E CYS* 3.9 11.4 - - - -
74E SER* 5.1 3.4 - - - -
80E VAL 2.9 18.3 + - - +
81E THR* 3.5 4.5 - - - +
83E GLU* 1.3 74.3 - - - +
85E GLY* 1.3 64.8 + - - +
87E ALA* 3.1 13.7 + - - +
88E HIS* 3.2 30.3 + + - -
96E LEU* 3.6 31.2 - - + -
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Residues in contact with GLY 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 4.8 3.6 - - - -
81E THR 3.0 10.9 + - - -
82E GLY 3.4 3.3 + - - -
84E TRP* 1.3 75.7 - - - +
86E ARG* 1.3 62.3 + - - +
88E HIS 3.0 11.4 + - - -
90E ALA* 3.1 25.9 + - - +
91E GLU 5.5 0.4 - - - -
96E LEU* 3.7 31.5 - - - +
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Residues in contact with ARG 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E GLY* 4.0 14.5 + - - -
79E PHE* 4.8 0.8 + - - +
82E GLY* 3.2 34.6 + - - +
83E GLU* 2.2 62.4 + - - +
84E TRP 3.2 0.2 - - - -
85E GLY* 1.3 76.7 - - - +
87E ALA* 1.3 62.3 + - - +
88E HIS 3.3 0.5 + - - -
89E LYS* 3.4 15.5 + - - +
90E ALA 5.0 0.7 - - - +
91E GLU* 6.5 1.6 - - + -
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Residues in contact with ALA 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E PHE* 4.6 12.3 - - + -
83E GLU 3.0 13.8 + - - +
84E TRP* 3.1 11.9 + - - +
86E ARG* 1.3 77.5 - - - +
88E HIS* 1.3 73.3 + - + +
89E LYS* 3.5 3.3 + - - +
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Residues in contact with HIS 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E PHE* 6.0 0.6 - - - -
48E SER* 2.9 45.6 + - - -
52E LEU* 3.9 27.8 - - + -
53E PRO* 4.1 11.6 - - + +
56E VAL* 3.9 17.2 - - + +
84E TRP* 3.2 39.0 + + - +
85E GLY 3.0 4.5 + - - +
87E ALA* 1.3 85.6 + - + +
89E LYS* 1.3 73.7 + - - +
90E ALA* 3.2 4.0 + - + +
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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