Contacts of the helix formed by residues 102 - 112 (chain o) in PDB entry 6AH0
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 GLU 102 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100o LEU* 5.6 0.5 - - - -
101o VAL* 1.3 76.0 - - - +
103o LEU* 1.3 56.4 + - - +
104o GLY 3.1 3.6 - - - +
105o ASP* 2.6 32.1 + - - +
106o LEU 3.8 2.1 + - - -
125o VAL* 5.5 2.0 - - - -
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Residues in contact with LEU 103 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101o VAL 4.1 1.6 + - - -
102o GLU* 1.3 69.0 - - - +
104o GLY* 1.3 60.4 + - - +
106o LEU* 3.1 17.0 + - - -
107o ASP 3.9 2.3 + - - -
125o VAL* 5.6 3.5 + - - +
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Residues in contact with GLY 104 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102o GLU 2.9 1.8 + - - -
103o LEU* 1.3 74.2 - - - +
105o ASP* 1.3 58.9 + - - +
106o LEU 3.2 0.9 - - - -
107o ASP* 3.3 14.5 + - - -
108o PRO 5.0 0.3 - - - -
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Residues in contact with ASP 105 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77o CYS 5.7 4.9 - - - -
78o ARG* 5.2 2.6 - - - +
79o ILE* 4.3 19.9 + - - +
102o GLU* 2.6 20.9 + - - +
104o GLY* 1.3 71.1 - - - +
106o LEU* 1.3 56.8 + - - +
107o ASP 3.3 0.4 - - - -
108o PRO 4.6 3.7 - - - -
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Residues in contact with LEU 106 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102o GLU 3.8 2.0 + - - -
103o LEU 3.1 11.4 + - - -
105o ASP* 1.3 76.1 - - - +
107o ASP* 1.3 63.3 + - - +
108o PRO 3.4 1.8 - - - -
109o LEU* 3.2 15.6 + - - -
110o ALA 4.5 0.5 + - - -
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Residues in contact with ASP 107 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103o LEU 3.9 2.6 + - - -
104o GLY* 3.3 14.1 + - - -
105o ASP 3.3 3.0 - - - -
106o LEU* 1.3 76.2 - - - +
108o PRO* 1.3 56.9 - - - +
109o LEU 2.8 7.1 + - - -
110o ALA* 3.0 14.6 + - - -
111o SER 4.6 0.2 + - - -
138o LYS 5.4 0.5 - - - +
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Residues in contact with PRO 108 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79o ILE* 5.2 6.5 - - - +
80o GLY 4.7 15.9 - - - +
81o GLU* 5.2 9.6 - - - +
104o GLY 5.0 0.4 - - - -
105o ASP 4.6 4.0 - - - +
106o LEU 3.3 2.2 - - - -
107o ASP* 1.3 72.7 - - - +
109o LEU* 1.3 58.8 + - - -
110o ALA 3.2 1.0 + - - -
111o SER* 3.6 11.4 + - - +
112o LEU 4.6 1.2 + - - -
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Residues in contact with LEU 109 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106o LEU 3.2 11.0 + - - -
107o ASP 2.8 2.8 + - - -
108o PRO* 1.3 72.5 - - - +
110o ALA* 1.3 63.2 + - - +
111o SER 3.2 2.5 - - - -
112o LEU* 3.3 17.4 + - - +
139o VAL* 5.2 5.3 - - - -
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Residues in contact with ALA 110 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106o LEU 4.5 0.8 + - - -
107o ASP 3.0 12.7 + - - -
109o LEU* 1.3 77.7 - - - +
111o SER* 1.3 59.0 + - - +
112o LEU 3.4 4.7 + - - +
113o LYS* 4.8 1.4 + - - -
138o LYS 3.6 24.2 + - - -
139o VAL* 4.6 4.9 - - - +
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Residues in contact with SER 111 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84o ASP* 4.3 16.6 - - - -
107o ASP 4.6 0.6 + - - -
108o PRO 3.6 9.9 + - - -
109o LEU 3.2 1.2 - - - -
110o ALA* 1.3 76.1 - - - +
112o LEU* 1.3 56.3 + - - +
113o LYS 3.2 7.4 + - - -
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Residues in contact with LEU 112 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84o ASP* 5.0 9.6 - - - +
87o LEU 5.8 2.0 - - - -
88o PRO 5.9 0.2 - - - -
90o LEU 5.4 2.2 - - - -
108o PRO 4.6 1.4 + - - -
109o LEU* 3.3 17.8 + - - +
110o ALA 3.3 3.0 - - - +
111o SER* 1.3 72.2 - - - +
113o LYS* 1.3 65.7 + - - +
114o SER 3.4 2.5 - - - -
115o LEU* 3.2 18.5 + - - +
141o GLN* 5.9 1.7 - - - -
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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