Contacts of the helix formed by residues 103 - 111 (chain C) in PDB entry 1A9N
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 LEU 103 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLU* 1.3 70.2 - - - +
104C GLY* 1.3 60.9 + - - +
106C LEU* 3.0 18.3 + - + +
107C ASP 3.9 0.5 + - - -
125C VAL* 3.4 29.7 - - + +
128C LYS* 4.3 16.6 - - + +
129C LYS 4.2 8.7 - - - +
130C HIS 4.6 0.9 - - - +
131C TYR* 4.1 23.6 - - + -
134C TYR* 3.3 46.0 - - + -
174C ILE* 3.6 55.0 - - + +
175C ALA* 4.4 1.6 - - - +
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Residues in contact with GLY 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLU* 3.1 2.0 + - - -
103C LEU* 1.3 75.9 - - - +
105C ASP* 1.3 61.2 + - - +
106C LEU 3.2 0.2 - - - -
107C ASP* 3.2 35.0 - - - +
108C PRO* 4.2 1.9 - - - +
134C TYR* 4.0 4.2 + - - -
175C ALA* 3.2 24.1 - - - +
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Residues in contact with ASP 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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78A ARG* 2.5 50.3 + - - -
77C CYS 3.9 13.8 - - - +
78C ARG* 4.5 6.6 - - - +
79C ILE* 4.0 19.0 + - - +
100C LEU* 4.7 9.9 - - + -
101C VAL* 4.3 3.4 + - - +
102C GLU* 2.8 29.6 + - - +
104C GLY* 1.3 77.5 - - - +
106C LEU* 1.3 59.2 + - + +
107C ASP 3.2 0.2 - - - -
108C PRO* 3.3 16.6 - - - +
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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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79C ILE* 4.7 7.4 - - + -
100C LEU* 3.9 37.7 - - + -
102C GLU 4.3 2.5 - - - +
103C LEU* 3.0 17.8 + - + +
105C ASP* 1.3 80.0 - - - +
107C ASP* 1.3 61.9 + - - +
108C PRO* 3.5 1.1 - - - -
109C LEU* 3.3 27.1 + - + +
120C ILE* 3.7 21.8 - - + -
125C VAL* 3.9 26.7 - - + -
131C TYR* 4.1 2.7 - - + -
134C TYR* 5.1 4.9 - - + -
135C VAL* 3.5 32.8 - - + -
138C LYS* 5.7 0.9 - - - -
139C VAL* 4.6 8.6 - - + +
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Residues in contact with ASP 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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104C GLY* 3.2 22.4 + - - +
105C ASP 3.2 0.4 - - - -
106C LEU* 1.3 76.5 - - - +
108C PRO* 1.3 67.0 - - + +
109C LEU 3.0 2.1 + - - -
110C ALA* 3.2 22.7 + - - +
134C TYR* 2.6 30.4 + - - -
138C LYS* 3.1 36.4 + - - +
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Residues in contact with PRO 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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79C ILE* 3.2 28.7 - - + +
80C GLY 3.2 22.2 - - - +
81C GLU* 3.9 30.6 - - - +
83C LEU* 5.5 3.1 - - - +
104C GLY 4.2 1.8 - - - +
105C ASP* 3.3 16.6 - - - +
106C LEU 3.5 1.6 - - - -
107C ASP* 1.3 92.5 - - + +
109C LEU* 1.3 60.0 + - - +
110C ALA* 3.1 2.6 + - + -
111C SER* 3.4 21.1 + - - +
112C LEU* 4.4 3.3 + - - +
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Residues in contact with LEU 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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79C ILE* 3.7 39.3 - - + -
83C LEU* 4.7 0.4 - - + -
93C LEU* 3.6 26.2 - - + -
95C LEU* 5.0 2.0 - - + -
106C LEU* 3.6 23.1 - - + +
107C ASP 3.0 1.8 + - - -
108C PRO* 1.3 74.8 - - - +
110C ALA* 1.3 62.0 + - - +
111C SER 3.2 0.7 - - - -
112C LEU* 3.2 32.8 + - + +
115C LEU* 4.3 8.5 - - + +
118C LEU* 3.9 31.2 - - + -
120C ILE* 4.8 5.6 - - + -
135C VAL* 6.3 0.2 - - + -
139C VAL* 3.8 17.2 - - + +
141C GLN* 3.4 8.7 + - - -
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Residues in contact with ALA 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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107C ASP 3.2 15.6 + - - +
108C PRO 3.1 0.6 - - - -
109C LEU* 1.3 77.9 - - - +
111C SER* 1.3 57.4 + - - +
113C LYS* 5.2 0.3 - - - -
138C LYS* 3.5 33.4 - - + +
139C VAL* 4.3 3.6 - - - +
141C GLN* 2.9 22.3 + - - +
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Residues in contact with SER 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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81C GLU 4.4 12.4 + - - -
83C LEU* 4.6 1.6 + - - -
84C ASP* 3.0 50.6 + - - +
108C PRO* 3.4 12.7 + - - -
109C LEU 3.2 0.6 - - - -
110C ALA* 1.3 77.8 - - - +
112C LEU* 1.3 59.3 + - - +
113C LYS* 3.0 11.4 + - - +
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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