Contacts of the helix formed by residues 107 - 121 (chain A) in PDB entry 2GAO
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 ARG 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.5 23.3 - - + +
34A ASP* 3.0 55.6 + - - -
35A ASN* 4.3 7.1 - - - +
104A ASP* 3.1 36.5 + - + +
105A HIS 3.1 0.6 - - - -
106A SER* 1.3 85.9 - - - +
108A LEU* 1.3 58.4 + - - +
109A VAL 3.3 2.9 - - - -
110A GLU* 3.3 41.8 + - - +
111A SER* 3.0 26.9 + - - -
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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 VAL* 3.6 19.1 - - + -
101A ASP 3.6 22.4 - - - +
102A CYS* 4.6 2.5 - - - +
104A ASP 3.7 8.9 + - - +
105A HIS* 3.4 27.1 + - + +
107A ARG* 1.3 78.1 - - - +
109A VAL* 1.3 57.5 + - - +
111A SER* 3.5 2.6 + - - -
112A LYS* 3.0 23.0 + - - +
142A ILE* 3.4 43.5 - - + -
150A ILE* 3.9 23.8 - - + -
151A PHE* 3.5 23.6 - - + -
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A HIS 4.9 1.0 + - - +
106A SER 4.0 16.4 - - - +
108A LEU* 1.3 76.0 - - - +
110A GLU* 1.3 72.8 + - + +
112A LYS* 3.3 20.3 + - - +
113A VAL* 3.0 35.7 + - + +
150A ILE* 5.2 4.2 - - - +
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Residues in contact with GLU 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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33A LEU* 3.7 16.7 - - + +
106A SER 5.2 1.1 - - - +
107A ARG* 3.3 53.8 + - - +
109A VAL* 1.3 82.9 - - + +
111A SER* 1.3 64.0 + - - +
113A VAL* 3.3 11.1 + - - +
114A GLU* 3.3 24.7 + - + +
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Residues in contact with SER 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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33A LEU* 3.7 19.4 + - - +
98A PHE* 3.2 29.0 - - - -
99A LEU 4.6 0.7 + - - -
100A VAL* 3.6 20.5 - - - +
107A ARG 3.0 16.2 + - - -
108A LEU* 3.7 7.0 - - - -
109A VAL 3.3 0.2 - - - -
110A GLU* 1.3 72.4 - - - +
112A LYS* 1.3 67.6 + - - +
114A GLU* 3.0 6.0 + - - +
115A LEU 2.9 18.5 + - - -
151A PHE* 3.7 6.8 - - - -
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Residues in contact with LYS 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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108A LEU 3.0 14.7 + - - +
109A VAL* 3.3 23.3 + - - +
111A SER* 1.3 75.4 + - - +
113A VAL* 1.3 59.1 + - - +
115A LEU* 3.3 2.2 + - + +
116A ASN* 2.8 60.0 + - - +
150A ILE* 3.0 31.0 - - + +
151A PHE* 3.7 36.7 - - + +
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Residues in contact with VAL 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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109A VAL* 3.0 29.2 + - + +
110A GLU* 3.5 10.8 - - - +
111A SER 3.2 0.4 - - - -
112A LYS* 1.3 78.3 - - + +
114A GLU* 1.3 66.7 + - - +
116A ASN* 3.4 10.1 + - - +
117A ALA* 2.8 30.7 + - + +
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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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33A LEU* 4.0 15.0 - - + +
76A LEU* 3.9 39.8 - - + +
98A PHE* 4.1 15.5 - - + -
110A GLU* 3.3 13.4 + - - +
111A SER* 3.0 8.7 + - - +
113A VAL* 1.3 83.9 - - - +
115A LEU* 1.3 58.7 + - - +
117A ALA* 3.3 12.5 + - - +
118A LEU* 3.0 32.1 + - - +
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Residues in contact with LEU 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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98A PHE* 4.0 38.5 - - + -
111A SER 2.9 14.2 + - - +
112A LYS* 3.9 6.1 - - - +
114A GLU* 1.3 73.1 - - - +
116A ASN* 1.3 61.5 + - - +
118A LEU* 3.2 13.3 + - + +
119A MET* 2.8 39.8 + - + +
129A ILE* 4.3 13.0 - - + -
131A ILE* 3.5 27.6 - - + -
151A PHE* 3.7 24.2 - - + -
153A LEU* 4.6 6.1 - - + -
173A MET* 3.9 20.0 - - + -
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Residues in contact with ASN 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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112A LYS* 2.8 55.4 + - - +
113A VAL* 3.5 8.4 - - - +
115A LEU* 1.3 72.4 - - - +
117A ALA* 1.3 66.2 + - - +
119A MET* 3.0 26.9 + - - +
120A THR* 3.0 33.2 + - + +
151A PHE 4.6 5.2 + - - +
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Residues in contact with ALA 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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113A VAL* 2.8 20.4 + - + +
114A GLU* 3.3 19.7 + - - +
116A ASN* 1.3 73.3 - - - +
118A LEU* 1.3 61.6 + - + +
120A THR* 3.4 6.9 + - - -
121A ASP* 3.1 26.1 + - - +
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Residues in contact with LEU 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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31A LEU* 4.1 15.5 - - + -
76A LEU* 4.1 10.8 - - + -
86A TRP* 3.7 30.3 - - + -
96A ILE* 4.3 13.2 - - + -
98A PHE* 3.5 35.0 - - + -
114A GLU 3.0 16.2 + - - +
115A LEU* 3.4 14.4 - - + +
117A ALA* 1.3 77.6 - - + +
119A MET* 1.3 63.2 + - - +
120A THR 3.4 0.2 + - - -
121A ASP* 3.5 9.0 + - - +
124A ILE* 3.6 33.8 - - + +
129A ILE* 4.5 13.0 - - + +
171A ARG* 4.5 4.9 + - - -
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Residues in contact with MET 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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115A LEU* 2.8 26.9 + - + +
116A ASN* 3.0 36.1 + - - +
118A LEU* 1.3 73.2 - - - +
120A THR* 1.3 63.3 + - + +
121A ASP 3.6 2.1 - - - +
122A GLU* 5.4 1.9 - - - +
125A SER* 5.6 1.6 - - - -
129A ILE* 4.4 7.9 - - + -
151A PHE 5.1 4.3 - - - +
153A LEU* 4.7 6.5 - - + -
156A GLN* 4.4 19.1 - - + +
171A ARG* 3.4 24.5 + - - +
173A MET* 3.5 40.2 - - + +
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Residues in contact with THR 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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116A ASN* 3.0 21.7 + - + +
117A ALA* 3.6 7.1 + - - -
119A MET* 1.3 82.2 - - + +
121A ASP* 1.3 64.8 + - - +
122A GLU* 3.3 12.7 + - - +
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Residues in contact with ASP 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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86A TRP* 5.8 1.4 - - - -
87A LYS* 3.9 21.0 + - - -
90A LEU* 5.3 2.5 - - - +
117A ALA 3.1 18.0 + - - +
118A LEU* 3.5 9.7 + - - +
119A MET 4.7 0.9 - - - +
120A THR* 1.3 73.7 - - - +
122A GLU* 1.3 63.8 + - - +
123A THR* 2.4 51.2 + - - +
124A ILE* 3.3 27.2 + - + +
125A SER* 3.5 9.4 + - - -
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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