Contacts of the helix formed by residues 82 - 88 (chain A) in PDB entry 1H9T
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 ILE 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ASP* 5.6 3.6 - - + +
60A TRP* 3.8 31.2 - - + +
74A PHE* 3.8 35.2 - - + -
75A TRP* 6.4 0.2 - - + -
78A SER* 4.1 17.9 - - - +
79A GLY 3.0 11.0 + - - +
80A LEU 2.5 8.1 + - - -
81A ASN* 1.3 79.0 - - - +
83A LEU* 1.3 73.1 + - + +
84A GLU* 3.2 3.1 - - - -
85A THR* 2.6 43.4 + - + +
86A LEU* 2.8 18.4 + - + +
163B LEU* 4.0 17.3 - - + -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TRP* 6.1 1.3 - - + -
80A LEU* 3.1 43.7 - - + +
82A ILE* 1.3 79.1 - - + +
84A GLU* 1.3 69.9 + - - +
86A LEU* 2.5 23.0 + - + +
87A ALA* 2.8 11.6 + - - +
97A LEU* 4.4 17.6 - - + +
101A LEU* 4.7 21.1 - - + -
167A GLY 4.8 6.3 - - - +
168A MET* 4.9 4.0 - - - -
171A LEU* 3.8 22.2 - - + -
160B ILE* 4.5 20.6 - - + -
163B LEU* 4.2 15.7 - - + -
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU 4.7 0.4 + - - -
81A ASN 5.4 2.0 - - - +
82A ILE 2.8 3.7 + - - -
83A LEU* 1.3 81.6 - - - +
85A THR* 1.3 55.2 - - - +
86A LEU 2.6 8.0 + - - -
87A ALA* 2.8 17.0 + - - +
88A ARG* 3.2 10.2 + - - +
170A GLY* 3.7 24.0 - - - +
171A LEU* 3.4 27.8 - - - +
174A ARG* 4.0 20.7 + - - +
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Residues in contact with THR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 4.8 10.2 - - - +
58A ASP* 5.8 3.8 - - - +
60A TRP* 4.7 12.8 - - + +
81A ASN 4.7 2.2 - - - +
82A ILE* 2.6 48.8 + - + +
84A GLU* 1.3 75.5 - - - +
86A LEU* 1.3 56.2 - - - -
88A ARG* 4.0 28.3 + - - +
89A LEU* 3.5 24.7 + - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TRP* 4.4 16.8 - - + -
74A PHE* 4.6 15.7 - - + -
75A TRP* 4.0 24.2 - - + +
82A ILE* 2.8 18.3 + - + +
83A LEU* 2.5 26.5 + - + +
85A THR* 1.3 72.2 - - - +
87A ALA* 1.3 56.5 + - - +
88A ARG 2.9 4.7 - - - -
89A LEU* 2.8 23.9 + - + -
90A ASP* 3.2 23.7 + - + +
93A SER 6.2 0.2 - - - +
97A LEU* 3.5 34.5 - - + -
163B LEU* 6.4 0.2 - - + -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU 2.8 11.7 + - - +
84A GLU* 2.8 9.4 + - - +
86A LEU* 1.3 76.6 - - - +
88A ARG* 1.3 58.9 + - - +
89A LEU 3.3 0.7 + - - -
90A ASP* 4.1 6.6 + - - -
91A HIS* 4.2 5.4 + - - -
94A VAL* 3.6 33.9 - - + +
97A LEU* 4.1 15.0 - - + +
171A LEU* 4.6 16.8 - - + -
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.3 44.3 + - - +
17A ILE* 4.5 17.9 - - - +
18A GLU* 5.7 4.4 - - - +
84A GLU 3.2 11.2 + - - +
85A THR* 4.1 26.1 + - - +
86A LEU 2.9 1.0 - - - -
87A ALA* 1.3 78.6 - - - +
89A LEU* 1.3 74.1 + - - +
91A HIS* 4.2 16.2 + - + -
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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