Contacts of the helix formed by residues 106 - 114 (chain A) in PDB entry 6B3I
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ALA* 5.1 2.8 - - - +
99A MET* 5.4 0.9 - - - +
102A LEU 4.6 1.6 - - - +
103A GLY 4.5 10.3 - - - +
105A ASP* 1.3 84.8 + - - +
107A SER* 1.3 65.1 + - - +
108A VAL 3.4 2.5 - - - -
109A LEU* 3.6 26.3 - - + +
110A ILE* 3.0 32.3 + - + +
143A ASP* 2.9 34.6 - - - +
144A THR* 3.3 23.1 - - - +
148A LEU* 4.1 17.4 - - + +
231A ASP* 3.4 21.9 + - - +
234A LYS* 4.9 0.4 - - - -
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Residues in contact with SER 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 ASP* 2.8 31.1 + - - -
106A GLU* 1.3 76.6 - - - +
108A VAL* 1.3 62.8 + - - +
110A ILE* 3.9 1.0 - - - +
111A GLU* 3.0 31.8 + - - +
234A LYS* 3.0 26.9 + - - +
253A ARG* 5.0 17.9 + - - -
270A ARG* 5.8 0.4 - - - -
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Residues in contact with VAL 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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94A GLN* 3.8 28.9 - - + +
95A LEU* 3.9 2.8 - - + +
98A ALA* 3.8 23.9 - - + +
106A GLU 3.4 0.2 - - - -
107A SER* 1.3 80.4 - - - +
109A LEU* 1.3 61.7 + - - +
111A GLU* 3.9 4.4 - - - +
112A VAL* 3.3 27.6 + - + +
267A THR* 5.7 0.7 - - - +
270A ARG* 3.9 48.0 - - - +
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Residues in contact with LEU 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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95A LEU* 3.7 26.4 - - + +
98A ALA* 5.3 3.1 - - + +
99A MET* 4.5 18.2 - - - -
106A GLU* 3.4 32.8 + - + +
107A SER 3.3 0.4 - - - -
108A VAL* 1.3 80.3 - - - +
110A ILE* 1.3 60.3 + - - +
112A VAL* 4.4 0.3 - - - +
113A LEU* 3.3 47.3 + - + +
136A LEU* 5.4 0.2 - - + -
140A VAL* 4.1 20.4 - - + -
143A ASP* 5.0 0.4 - - - +
144A THR* 3.7 13.7 - - + -
152A LEU* 3.7 26.5 - - + -
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Residues in contact with ILE 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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106A GLU* 3.0 28.0 + - + +
107A SER 4.0 2.7 - - - +
109A LEU* 1.3 74.8 - - - +
111A GLU* 1.3 67.1 + - - +
114A CYS* 3.1 38.9 + - - +
148A LEU* 4.0 18.4 - - + -
152A LEU* 4.5 7.4 - - + -
231A ASP* 3.4 37.9 - - + +
234A LYS* 4.0 22.4 - - + +
235A ALA* 3.7 23.6 - - + +
238A THR* 3.9 16.4 - - - +
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Residues in contact with GLU 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 SER 3.0 17.7 + - - +
108A VAL 3.9 2.7 - - - +
109A LEU 3.4 0.2 - - - -
110A ILE* 1.3 78.6 - - - +
112A VAL* 1.3 57.0 + - + +
115A THR* 2.5 36.6 + - - +
116A ARG* 4.7 5.9 + - - +
238A THR* 4.7 1.3 - - - -
249A TYR* 4.1 21.1 - - + +
250A PHE* 4.2 19.6 - - + -
253A ARG* 3.2 26.1 + - - +
267A THR* 4.3 0.3 - - - +
270A ARG* 2.9 48.1 + - - +
271A ILE* 3.8 15.3 - - - +
274A THR* 5.6 0.2 + - - -
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Residues in contact with VAL 112 (chain A).
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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91A ALA* 4.4 11.7 - - + +
95A LEU* 4.1 24.2 - - + -
108A VAL* 3.3 27.3 + - + +
111A GLU* 1.3 79.8 - - + +
113A LEU* 1.3 66.8 + - + +
114A CYS 3.3 0.9 + - - -
115A THR* 3.3 8.1 + - - -
116A ARG* 3.1 55.5 - - - +
124A ILE* 3.7 21.8 - - + -
270A ARG* 4.5 13.7 - - + -
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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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95A LEU* 4.9 10.5 - - + -
109A LEU* 3.3 34.5 + - + +
112A VAL* 1.3 85.8 - - + +
114A CYS* 1.3 58.5 + - - +
115A THR 3.7 0.5 + - - -
116A ARG* 4.4 3.8 + - - +
121A ILE* 4.3 22.5 - - + +
124A ILE* 5.8 3.6 - - + -
136A LEU* 5.0 1.6 - - + -
140A VAL* 4.8 1.8 - - + -
152A LEU* 3.7 48.9 - - + +
155A LEU* 3.3 27.3 - - + +
156A LEU* 3.7 31.2 - - + -
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Residues in contact with CYS 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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110A ILE* 3.1 38.3 + - - +
113A LEU* 1.3 76.7 - - - +
115A THR* 1.3 64.3 - - - +
116A ARG 5.4 0.2 - - - -
151A ILE* 6.0 0.2 - - - -
152A LEU* 4.5 7.0 - - - -
155A LEU* 3.6 20.2 - - - -
202A TYR* 4.4 6.2 + - - -
235A ALA* 4.0 10.1 - - - -
238A THR* 3.6 18.6 - - + +
239A LEU* 3.7 32.9 - - + +
242A CYS* 3.8 12.5 - - - +
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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