Contacts of the helix formed by residues 80 - 88 (chain H) in PDB entry 1I3R
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 GLY 80 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G ARG* 4.3 4.3 - - - -
63H ASN* 3.6 29.5 + - - +
64H LEU* 3.8 8.9 - - - +
75H ALA* 3.8 6.5 - - - -
77H THR 2.8 6.7 + - - -
78H GLU 2.7 1.8 + - - -
79H LEU* 1.3 75.1 - - - +
81H ARG* 1.3 65.5 + - - +
82H PRO* 3.3 4.0 - - - -
83H ASP* 3.3 10.3 + - - +
84H ALA* 3.2 16.8 + - - +
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Residues in contact with ARG 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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152F ASN* 5.8 1.7 - - - +
153F ILE* 3.2 34.3 + - - +
154F GLU* 4.1 17.6 + - - +
173F LEU* 6.2 1.6 - - - +
75H ALA* 3.7 15.3 - - + -
77H THR 3.6 3.2 + - - -
78H GLU* 2.6 51.7 + - - +
80H GLY* 1.3 72.2 - - - +
82H PRO* 1.3 64.4 - - + +
84H ALA* 3.2 3.7 + - + +
85H GLU* 2.9 60.8 + - + +
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Residues in contact with PRO 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G ARG* 3.8 21.8 - - - +
14H GLY 5.6 0.7 - - - +
15H GLY 4.7 7.0 - - - +
16H GLY 3.4 28.5 - - - +
17H GLY* 3.7 16.2 - - - +
78H GLU 3.5 7.0 - - - +
79H LEU 3.7 6.7 - - - +
80H GLY 3.3 4.7 - - - -
81H ARG* 1.3 96.4 - - + +
83H ASP* 1.3 57.2 + - - +
85H GLU* 3.4 10.3 + - - +
86H ASN* 2.9 30.5 + - - +
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Residues in contact with ASP 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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76G ARG* 2.8 41.2 + - - -
13H LYS* 3.1 42.6 + - - +
14H GLY 4.4 2.1 + - - -
63H ASN* 4.9 1.4 - - - +
64H LEU* 3.6 23.1 - - + +
80H GLY* 3.3 7.1 + - - +
82H PRO* 1.3 72.9 - - - +
84H ALA* 1.3 59.0 + - - +
86H ASN* 4.3 5.4 - - - +
87H TRP* 2.7 50.3 + - + +
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Residues in contact with ALA 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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64H LEU* 3.8 24.3 - - + +
73H PHE* 4.2 9.4 - - - +
74H ARG* 4.5 0.4 - - - -
75H ALA* 4.1 13.5 - - + +
80H GLY 3.2 5.5 + - - +
81H ARG* 3.2 11.1 + - + +
83H ASP* 1.3 79.3 - - - +
85H GLU* 1.3 58.6 + - + +
88H ASN* 2.7 49.2 + - - +
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Residues in contact with GLU 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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154F GLU* 5.7 1.7 - - - +
81H ARG* 2.9 57.5 + - + +
82H PRO* 3.8 8.2 - - - +
84H ALA* 1.3 77.8 - - + +
86H ASN* 1.3 64.4 + - - +
88H ASN* 4.1 3.9 - - - +
89H SER* 3.5 20.6 + - - -
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Residues in contact with ASN 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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12H LEU 4.0 7.9 + - - -
13H LYS* 4.8 0.6 - - - +
14H GLY* 4.2 16.6 - - - +
82H PRO 2.9 18.9 + - - +
83H ASP* 3.2 4.7 + - - +
85H GLU* 1.3 74.5 - - - +
87H TRP* 1.3 88.9 + - - +
89H SER* 2.9 26.3 + - - -
90H GLN* 2.6 29.8 + - - +
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Residues in contact with TRP 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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11H GLY* 3.1 37.8 - - - -
12H LEU 2.8 27.7 + - - +
13H LYS* 3.8 21.1 - - + -
56H TYR* 3.6 39.9 - + - -
64H LEU* 3.9 14.8 - - + -
73H PHE* 3.5 34.8 - + + -
83H ASP* 2.7 25.9 + - + +
86H ASN* 1.3 87.8 - - - +
88H ASN* 1.3 59.8 + - - +
89H SER 3.1 1.3 + - - -
90H GLN* 3.3 27.9 + - - +
93H PHE* 3.7 25.9 - + + -
94H LEU* 3.8 12.6 - - - +
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Residues in contact with ASN 88 (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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72H GLU* 3.4 26.3 - - - +
73H PHE* 3.0 50.0 + - - -
74H ARG* 3.8 7.7 - - - +
84H ALA* 2.7 32.9 + - - +
85H GLU* 4.1 4.2 - - - +
86H ASN 3.2 0.2 - - - -
87H TRP* 1.3 77.3 - - - +
89H SER* 1.3 56.9 + - - +
90H GLN 3.3 1.8 - - - -
91H PRO* 5.0 1.4 - - - +
94H LEU* 3.6 20.4 - - - +
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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