Contacts of the helix formed by residues 96 - 111 (chain C) in PDB entry 1H88
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 THR 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C PRO 3.7 4.7 + - - +
95C TRP* 1.3 77.2 - - - +
97C LYS* 1.3 64.2 + - - +
98C GLU* 2.9 28.2 + - - +
99C GLU* 3.0 23.3 + - + +
100C ASP* 3.1 18.5 + - - +
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Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C TRP 3.8 0.6 + - - -
96C THR* 1.3 73.7 - - - +
98C GLU* 1.3 58.1 + - - +
100C ASP* 3.8 8.4 - - - +
101C GLN* 2.8 34.9 + - - +
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C THR* 2.9 13.2 + - - +
97C LYS* 1.3 81.1 - - - +
99C GLU* 1.3 69.4 + - + +
101C GLN* 3.5 5.4 - - - +
102C ARG* 3.0 36.2 + - - +
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Residues in contact with GLU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ILE* 4.8 7.4 - - - +
94C PRO 3.5 2.9 - - - +
95C TRP* 3.4 27.9 - - + -
96C THR* 3.0 24.5 + - + +
98C GLU* 1.3 78.9 - - + +
100C ASP* 1.3 64.7 + - - +
102C ARG* 2.8 18.7 + - - +
103C VAL* 3.1 12.9 + - - +
122C LEU* 3.8 21.5 - - + +
123C LYS* 4.3 11.5 - - + +
125C ARG* 3.0 48.0 + - - -
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Residues in contact with ASP 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C TRP* 3.2 16.1 - - - +
96C THR 3.1 20.0 + - - +
97C LYS* 3.8 7.2 - - - +
99C GLU* 1.3 77.7 - - - +
101C GLN* 1.3 64.7 + - - +
103C VAL* 3.3 5.7 + - - +
104C ILE* 3.0 27.0 + - - +
133C ARG* 2.6 49.8 + - - +
138C LEU* 3.2 23.2 - - + +
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Residues in contact with GLN 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LYS 2.8 22.8 + - - +
98C GLU* 3.5 7.2 - - - +
100C ASP* 1.3 74.2 - - - +
102C ARG* 1.3 63.7 - - - +
104C ILE* 3.0 30.4 + - - +
105C LYS* 3.1 24.0 + - + +
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Residues in contact with ARG 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU* 3.0 30.5 + - - +
99C GLU* 2.8 15.7 + - - +
101C GLN* 1.3 71.1 - - - +
103C VAL* 1.3 61.3 + - - +
105C LYS* 3.3 12.3 + - - +
106C LEU* 3.2 33.0 + - + +
121C HIS* 3.9 13.4 + - + +
122C LEU* 4.1 27.1 - - + +
123C LYS* 2.8 34.8 - - - +
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Residues in contact with VAL 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C TRP* 4.1 24.2 - - + -
99C GLU 3.1 12.7 + - - +
100C ASP 3.6 7.4 - - - +
102C ARG* 1.3 75.3 - - - +
104C ILE* 1.3 65.0 + - - +
106C LEU* 3.9 7.0 - - - +
107C VAL* 2.8 43.6 + - + +
115C TRP* 4.5 5.6 - - + -
118C ILE* 5.0 3.6 - - + -
122C LEU* 4.1 15.9 - - + -
130C CYS* 4.5 14.8 - - + +
134C TRP* 4.2 11.2 - - + -
138C LEU* 3.8 22.4 - - + -
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C ASP* 3.0 17.0 - - + +
101C GLN* 3.0 27.5 + - - +
103C VAL* 1.3 77.7 - - - +
105C LYS* 1.3 55.0 + - + +
107C VAL* 3.2 1.6 + - - +
108C GLN* 2.6 60.5 + - - +
134C TRP* 4.1 14.2 - - + -
138C LEU* 3.4 49.1 - - + +
140C PRO* 6.3 3.1 - - + -
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Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C GLN* 3.1 21.1 + - + +
102C ARG* 3.3 15.7 + - + +
104C ILE* 1.3 79.9 - - + +
106C LEU* 1.3 62.9 - - + +
108C GLN* 2.9 11.5 - - - +
109C LYS* 2.8 24.9 + - - +
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ARG* 3.2 22.0 + - + +
103C VAL 3.9 2.2 - - - +
105C LYS* 1.3 78.7 - - + +
107C VAL* 1.3 54.0 + - - +
109C LYS* 3.2 1.0 + - - -
110C TYR* 2.7 63.2 + - + +
118C ILE* 3.6 34.3 - - + -
121C HIS* 3.5 55.2 - - + +
122C LEU* 4.3 4.9 - - + -
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C VAL* 2.8 34.6 + - + +
106C LEU* 1.3 72.2 - - - +
108C GLN* 1.3 64.3 + - - +
111C GLY* 2.6 34.0 + - - +
112C PRO* 3.3 32.3 - - + +
115C TRP* 4.0 16.8 - - + -
118C ILE* 4.2 7.0 - - + -
134C TRP* 3.5 46.2 - - + -
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ILE* 2.6 40.0 + - - +
105C LYS* 2.9 18.3 - - - +
107C VAL* 1.3 75.4 - - - +
109C LYS* 1.3 57.7 + - - +
111C GLY 4.6 0.2 + - - -
134C TRP* 5.0 9.1 - - - -
140C PRO* 5.5 6.4 - - - +
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LYS 2.8 14.7 + - - +
108C GLN* 1.3 79.6 - - + +
110C TYR* 1.3 102.9 + - + +
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Residues in contact with TYR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 2.7 47.6 + - + +
109C LYS* 1.3 117.3 + - + +
111C GLY* 1.3 59.5 + - - +
113C LYS* 3.7 11.3 + - - +
114C ARG* 3.5 30.9 + - - +
118C ILE* 5.9 4.5 - - + -
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Residues in contact with GLY 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C VAL* 2.6 33.6 + - - +
108C GLN 4.6 0.6 + - - -
109C LYS 3.6 1.0 + - - -
110C TYR* 1.3 77.6 - - - +
112C PRO* 1.3 65.4 - - - +
113C LYS* 2.8 26.7 + - - +
118C ILE* 4.2 5.5 - - - +
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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