Contacts of the helix formed by residues 112 - 122 (chain A) in PDB entry 3IXE
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 GLN 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ALA 3.5 15.9 - - - +
76A SER 3.0 21.0 + - - -
77A HIS* 3.6 4.8 + - - +
78A GLY* 3.4 20.6 - - - +
107A ALA* 2.8 22.2 + - - +
110A TRP* 3.7 22.9 + - + +
111A GLY* 1.3 71.4 - - - +
113A ASP* 1.3 64.0 + - - +
114A GLN 3.4 2.5 - - - -
115A VAL* 3.2 21.9 + - + -
116A ALA* 2.9 22.8 + - - +
56B ARG* 4.4 3.6 - - - +
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Residues in contact with ASP 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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111A GLY* 3.1 17.2 + - - +
112A GLN* 1.3 71.3 - - - +
114A GLN* 1.3 76.5 + - - +
116A ALA* 3.3 4.5 + - - +
117A GLU* 2.9 32.1 + - + +
144A LEU* 3.5 41.0 - - + +
147A LEU* 5.5 6.0 - - + +
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Residues in contact with GLN 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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80A ARG* 3.6 40.2 - - - +
112A GLN 3.4 0.4 - - - -
113A ASP* 1.3 87.0 - - - +
115A VAL* 1.3 60.3 + - - +
117A GLU* 2.9 31.2 + - - +
118A ASP* 2.8 34.5 + - - +
147A LEU* 5.9 1.8 - - - +
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Residues in contact with VAL 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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75A ALA* 3.8 34.3 - - + +
78A GLY* 4.1 19.3 - - - +
80A ARG* 3.8 35.4 - - + +
83A VAL* 3.9 14.1 - - + -
107A ALA* 3.9 9.0 - - + -
112A GLN* 3.2 13.8 + - + +
114A GLN* 1.3 76.3 - - + +
116A ALA* 1.3 63.7 + - - +
118A ASP* 3.2 9.6 + - - +
119A LEU* 3.0 27.0 + - + +
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Residues in contact with ALA 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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104A LEU* 3.6 22.4 - - + +
107A ALA* 4.0 11.0 - - + +
108A CYS* 4.5 1.6 - - - -
112A GLN 2.9 13.8 + - - +
113A ASP 3.4 8.7 - - - +
114A GLN 3.3 0.2 - - - -
115A VAL* 1.3 75.7 - - - +
117A GLU* 1.3 63.9 + - - +
119A LEU* 3.2 4.1 + - - +
120A VAL* 3.0 27.4 + - - +
144A LEU* 4.3 10.3 - - + -
148A LEU* 3.7 20.9 - - + -
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Residues in contact with GLU 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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80A ARG* 5.8 1.1 - - - +
113A ASP 2.9 15.9 + - - +
114A GLN* 2.9 39.6 + - - +
116A ALA* 1.3 77.6 - - - +
118A ASP* 1.3 57.5 + - - +
120A VAL 3.5 0.3 + - - -
121A ALA* 2.9 31.0 + - - +
144A LEU* 5.0 3.4 - - + -
147A LEU* 4.0 27.1 - - + +
148A LEU* 3.9 17.0 - - + -
151A ARG* 3.4 36.7 + - - +
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Residues in contact with ASP 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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80A ARG* 2.8 38.3 + - - +
83A VAL* 4.7 5.9 - - + +
84A GLN* 2.8 33.1 + - + +
87A LEU* 3.8 11.9 - - + +
114A GLN 2.8 17.2 + - - +
115A VAL* 3.2 10.2 + - - +
117A GLU* 1.3 73.2 - - - +
119A LEU* 1.3 60.6 + - - +
121A ALA* 3.6 5.2 + - - +
122A ASN* 2.9 34.1 + - - +
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Residues in contact with LEU 119 (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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71A LEU* 4.2 13.9 - - + -
75A ALA* 4.2 4.5 - - + -
83A VAL* 4.2 15.3 - - + -
87A LEU* 4.1 12.6 - - + -
93A ILE* 3.0 29.5 - - + +
103A PRO* 4.1 6.1 - - + -
104A LEU* 3.9 33.0 - - + +
107A ALA* 4.0 16.6 - - + -
115A VAL* 3.0 23.6 + - + +
116A ALA 3.5 5.6 - - - +
117A GLU 3.2 0.2 - - - -
118A ASP* 1.3 74.7 - - - +
120A VAL* 1.3 65.7 + - - +
122A ASN 3.0 9.4 + - - -
124A ALA* 3.0 29.0 + - + -
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Residues in contact with VAL 120 (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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104A LEU* 3.8 15.5 - - + -
116A ALA 3.0 16.0 + - - +
119A LEU* 1.3 72.9 - - - +
121A ALA* 1.3 62.5 + - - +
122A ASN 3.0 0.2 - - - -
123A GLY* 3.0 14.4 + - - -
124A ALA 3.8 8.2 + - - +
126A VAL* 3.6 22.2 - - + -
148A LEU* 3.9 18.6 - - + +
151A ARG* 3.8 17.5 - - + -
152A ALA* 3.7 37.0 - - + +
155A MET* 4.6 9.2 - - + +
157A GLN* 4.1 7.9 + - - +
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Residues in contact with ALA 121 (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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117A GLU 2.9 19.6 + - - +
118A ASP* 3.7 8.5 - - - +
119A LEU 3.3 0.2 - - - -
120A VAL* 1.3 74.9 - - - +
122A ASN* 1.3 64.8 + - - +
123A GLY 3.5 0.2 - - - -
151A ARG* 3.7 26.5 - - - +
155A MET* 3.6 24.9 - - - +
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Residues in contact with ASN 122 (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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87A LEU* 3.8 22.4 - - + +
93A ILE* 3.6 25.7 - - + +
118A ASP* 2.9 27.0 + - - +
119A LEU 3.0 5.6 + - - -
121A ALA* 1.3 85.3 - - - +
123A GLY* 1.3 57.7 + - - +
124A ALA 3.7 0.2 - - - -
155A MET* 6.1 0.4 - - - -
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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