Contacts of the helix formed by residues 77 - 88 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H ASN* 1.3 78.5 + - - +
78H ALA* 1.3 57.5 + - - +
79H PHE* 3.0 24.6 + - + +
80H VAL* 2.9 46.2 + - - +
81H THR* 3.1 22.9 + - - +
98H ALA* 3.8 0.9 - - - -
100H PRO* 4.2 13.2 - - + +
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Residues in contact with ALA 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H PHE* 3.7 35.2 - - + -
17H GLY* 4.0 13.8 - - - +
19H PRO* 3.9 25.3 - - + +
20H GLY 4.2 1.1 - - - +
77H ASP* 1.3 71.0 - - - +
79H PHE* 1.3 65.9 + - + +
81H THR* 3.3 11.1 + - - +
82H GLY* 3.0 20.8 + - - -
86H ARG* 5.4 0.5 + - - -
98H ALA* 3.7 5.5 - - + +
100H PRO* 5.6 0.2 - - - +
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Residues in contact with PHE 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H PRO* 3.1 43.3 - - + -
77H ASP* 3.0 21.3 + - + +
78H ALA* 1.3 77.2 - - - +
80H VAL* 1.3 65.0 + - + +
82H GLY* 4.0 0.7 - - - -
83H GLU* 3.1 30.3 + - + +
86H ARG* 4.6 2.6 + - - +
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Residues in contact with VAL 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H ALA* 3.8 23.3 - - + +
43H PHE* 3.5 19.4 - - + -
76H ASN* 3.8 17.9 - - + +
77H ASP* 2.9 32.6 + - - +
79H PHE* 1.3 76.8 - - + +
81H THR* 1.3 60.3 + - - +
83H GLU* 3.3 3.6 + - - -
84H TRP* 2.9 27.5 + - - +
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Residues in contact with THR 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H PHE 5.2 0.5 + - - -
16H GLU 6.1 0.5 - - - -
17H GLY* 5.9 1.0 + - - -
42H ALA* 4.8 3.6 - - + -
74H SER* 4.5 12.3 - - - -
76H ASN* 3.6 20.9 - - + +
77H ASP 3.1 12.6 + - - +
78H ALA* 3.3 16.5 + - - +
80H VAL* 1.3 74.5 - - - +
82H GLY* 1.3 61.9 + - - +
84H TRP* 3.2 9.2 + - + +
85H GLY 2.9 25.3 + - - -
96H LEU* 3.7 29.3 + - + +
97H LEU 4.6 1.3 - - - +
98H ALA* 3.6 25.8 + - + +
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Residues in contact with GLY 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLY* 5.3 10.5 - - - -
78H ALA 3.0 18.1 + - - -
81H THR* 1.3 79.4 + - - +
83H GLU* 1.3 61.3 + - - +
85H GLY* 3.4 1.5 + - - -
86H ARG* 3.2 42.0 + - - +
96H LEU* 5.2 4.7 - - - -
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Residues in contact with GLU 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H PHE* 4.0 12.0 - - + -
79H PHE* 3.1 21.9 + - + +
80H VAL* 3.3 4.0 + - - +
82H GLY* 1.3 76.2 - - - +
84H TRP* 1.3 59.3 + - - +
86H ARG* 2.3 38.0 + - - +
87H ALA* 2.9 28.9 + - - +
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Residues in contact with TRP 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H VAL* 3.9 24.0 - - + -
42H ALA* 3.6 21.1 - - + -
43H PHE* 3.1 42.0 - + + +
47H CYS* 3.6 42.8 - - + -
48H SER* 2.9 20.5 + - - -
52H LEU* 3.8 31.4 - - + -
72H CYS* 3.9 4.7 - - - -
74H SER* 5.3 2.7 - - - -
80H VAL 2.9 17.7 + - - +
81H THR* 3.5 5.6 - - - +
83H GLU* 1.3 76.9 - - - +
85H GLY* 1.3 62.7 + - - +
87H ALA* 3.1 9.1 + - - +
88H HIS* 3.2 41.2 + + - -
96H LEU* 3.6 26.9 - - + -
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Residues in contact with GLY 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H LEU* 4.7 2.9 - - - -
81H THR 2.9 12.9 + - - -
82H GLY 3.4 2.2 + - - -
83H GLU 3.3 0.2 - - - -
84H TRP* 1.3 75.9 - - - +
86H ARG* 1.3 61.6 + - - +
88H HIS 3.0 8.1 + - - -
90H ALA* 3.0 29.2 + - - +
91H GLU 5.5 0.7 - - - -
96H LEU* 3.7 31.1 - - - +
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Residues in contact with ARG 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H GLY 5.6 4.4 + - - -
18H GLU* 5.9 1.0 + - - -
19H PRO* 5.9 6.1 - - - +
78H ALA 5.4 0.4 + - - -
79H PHE* 4.6 3.0 + - - +
82H GLY* 3.2 35.9 + - - +
83H GLU* 2.3 66.0 + - - +
84H TRP 3.2 0.2 - - - -
85H GLY* 1.3 75.8 - - - +
87H ALA* 1.3 62.8 + - - +
88H HIS 3.1 1.0 + - - -
89H LYS* 3.2 15.7 + - - +
90H ALA 5.0 1.1 - - - +
91H GLU* 6.1 1.1 - - + +
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Residues in contact with ALA 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H PHE* 4.7 11.4 - - + -
83H GLU 2.9 14.2 + - - +
84H TRP* 3.1 11.8 + - - +
86H ARG* 1.3 74.8 - - - +
88H HIS* 1.3 75.1 + - + +
89H LYS* 3.5 5.0 - - - +
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Residues in contact with HIS 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H PHE* 5.7 1.4 - - - -
48H SER* 3.1 34.5 + - - -
52H LEU* 3.8 26.7 - - + -
53H PRO* 4.3 10.6 - - + +
56H VAL* 3.9 16.1 - - + +
84H TRP* 3.2 49.1 + + - +
85H GLY 3.0 4.3 + - - +
87H ALA* 1.3 89.0 + - + +
89H LYS* 1.3 76.0 + - - +
90H ALA* 3.2 3.6 + - - +
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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