Contacts of the helix formed by residues 105 - 118 (chain A) in PDB entry 6AF6
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 SER 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A PHE 3.7 1.0 + - - -
104A GLY* 1.3 75.6 - - - -
106A SER* 1.3 65.3 + - - +
107A GLU* 3.2 17.2 + - - +
108A LEU* 3.0 32.5 + - - +
109A LYS* 2.9 24.1 + - - +
224A SER 4.8 0.7 + - - -
226A ARG 5.4 1.5 + - - -
228A GLY 5.1 2.4 - - - +
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Residues in contact with SER 106 (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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105A SER* 1.3 72.5 - - - +
107A GLU* 1.3 57.2 + - - +
109A LYS* 3.9 14.9 + - - +
110A ASP* 2.8 43.6 + - - +
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Residues in contact with GLU 107 (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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105A SER* 3.2 18.6 + - - +
106A SER* 1.3 79.8 - - - +
108A LEU* 1.3 63.1 + - + +
110A ASP* 3.7 7.1 - - - +
111A LYS* 3.1 24.1 + - - +
224A SER* 3.5 35.7 - - - +
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Residues in contact with LEU 108 (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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100A LEU* 4.3 11.5 - - + +
105A SER* 3.0 26.6 + - - +
107A GLU* 1.3 76.5 - - + +
109A LYS* 1.3 65.1 + - - +
111A LYS* 3.3 3.1 + - + -
112A TYR* 3.0 57.6 + - + +
187A LEU* 4.7 9.6 - - + -
224A SER 3.1 22.2 - - - +
225A GLN* 4.0 17.0 - - + +
226A ARG 3.2 33.0 - - - +
227A ILE* 4.2 14.6 - - + -
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Residues in contact with LYS 109 (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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59A PHE* 3.8 34.2 - - + -
100A LEU* 3.6 28.3 - - + +
101A TYR* 3.8 20.3 + - + +
104A GLY* 3.4 20.0 + - - +
105A SER 2.9 20.0 + - - +
106A SER* 4.0 11.1 + - - +
108A LEU* 1.3 76.2 - - - +
110A ASP* 1.3 62.7 + - - +
113A LEU* 2.9 47.2 + - + +
114A GLU 4.2 1.0 + - - -
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Residues in contact with ASP 110 (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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58A GLN* 4.5 7.6 + - - -
59A PHE* 3.8 19.4 - - - -
106A SER* 2.8 36.7 + - - +
107A GLU* 3.7 7.2 - - - +
109A LYS* 1.3 73.4 - - - +
111A LYS* 1.3 61.6 + - - +
114A GLU* 5.7 2.3 + - - +
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Residues in contact with LYS 111 (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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107A GLU 3.1 18.5 + - - +
108A LEU* 4.5 1.3 - - + -
110A ASP* 1.3 77.9 - - - +
112A TYR* 1.4 104.3 + - + +
115A SER* 4.6 8.1 + - - -
121A LEU* 5.7 0.2 - - - +
189A GLU* 4.2 7.2 + - - -
225A GLN* 5.1 7.5 - - - +
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Residues in contact with TYR 112 (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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100A LEU* 4.1 13.7 - - + -
108A LEU* 3.0 42.7 + - + +
111A LYS* 1.4 114.6 + - + +
113A LEU* 1.3 65.9 + - - +
114A GLU 3.5 1.8 - - - -
115A SER* 3.2 10.1 + - - -
116A LEU* 3.1 24.7 + - + +
121A LEU* 4.1 20.0 - - + -
167A VAL* 4.2 13.7 - - + -
187A LEU* 3.7 27.5 - - + +
189A GLU* 2.5 35.8 + - - +
225A GLN* 4.5 10.4 + - + -
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Residues in contact with LEU 113 (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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55A VAL* 4.4 1.3 - - + -
59A PHE* 3.6 35.9 - - + -
97A VAL* 3.8 30.7 - - + +
100A LEU* 3.9 19.2 - - + +
101A TYR* 3.8 29.2 - - + +
109A LYS* 2.9 33.0 + - + +
112A TYR* 1.3 76.6 - - - +
114A GLU* 1.3 66.0 + - - +
116A LEU* 3.0 5.5 + - + -
117A VAL* 2.9 38.5 + - + +
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Residues in contact with GLU 114 (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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58A GLN 4.4 8.9 - - - +
59A PHE* 3.2 37.4 + - + +
60A GLY* 4.5 7.2 - - - +
109A LYS 4.2 3.0 + - - +
110A ASP 5.7 2.0 + - - +
112A TYR 3.5 0.4 - - - -
113A LEU* 1.3 78.9 - - - +
115A SER* 1.3 56.3 + - - +
117A VAL* 3.6 0.3 - - - +
118A THR* 3.0 44.5 + - + +
120A LYS* 4.5 7.6 + - - +
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Residues in contact with SER 115 (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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111A LYS 4.6 6.4 + - - -
112A TYR* 3.2 13.4 + - - -
114A GLU* 1.3 78.0 - - - +
116A LEU* 1.3 61.0 + - - +
118A THR* 3.9 5.4 - - - -
119A GLY 3.2 1.7 + - - -
120A LYS* 2.9 44.1 + - - +
121A LEU* 3.1 32.6 + - - +
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Residues in contact with LEU 116 (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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51A ALA* 3.8 2.3 - - - +
92A HIS* 2.9 31.6 + - + -
96A CYS* 5.1 2.5 - - + +
97A VAL* 3.8 21.3 - - + -
100A LEU* 3.5 33.4 - - + -
112A TYR* 3.1 15.4 + - + +
113A LEU* 3.0 9.2 + - + +
115A SER* 1.3 75.7 - - - +
117A VAL* 1.3 64.0 + - - +
119A GLY* 3.2 8.1 + - - -
121A LEU* 3.5 32.5 - - + +
123A ALA* 3.8 19.3 - - + -
167A VAL* 3.8 14.6 - - + -
169A ILE* 5.7 2.5 - - + -
187A LEU* 5.1 2.7 - - + -
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Residues in contact with VAL 117 (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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46A ALA 3.6 1.4 - - - +
51A ALA* 3.5 17.1 - - - +
52A HIS* 3.1 46.4 + - + +
55A VAL* 3.9 23.8 - - + -
59A PHE 3.5 20.9 - - - +
60A GLY* 3.8 16.8 - - - +
61A GLY* 4.1 2.0 - - - +
97A VAL* 4.0 12.1 - - + -
113A LEU* 2.9 31.5 + - + +
114A GLU 3.2 2.2 + - - +
116A LEU* 1.3 78.1 - - - +
118A THR* 1.3 60.4 + - + +
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Residues in contact with THR 118 (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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43A LYS* 4.0 4.2 - - - +
46A ALA* 4.2 4.0 - - - -
47A ALA* 3.6 29.2 + - + +
52A HIS* 4.8 2.7 - - - +
60A GLY* 5.4 4.3 - - - +
114A GLU* 3.0 28.6 + - + +
115A SER 3.6 1.0 + - - -
117A VAL* 1.3 83.1 - - + +
119A GLY* 1.3 60.0 + - - +
120A LYS* 2.5 45.3 + - - +
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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