Contacts of the helix formed by residues 104 - 127 (chain A) in PDB entry 1GQA
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 GLY 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A TYR* 2.9 21.6 + - - -
100A ALA 4.3 0.3 - - - +
102A GLY 3.5 1.0 + - - -
103A ALA* 1.3 80.2 - - - +
105A GLN* 1.3 65.2 + - - -
106A LYS 3.3 2.7 - - - -
107A GLU* 3.5 3.4 + - - -
108A LEU* 3.0 25.5 + - - +
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Residues in contact with GLN 105 (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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27A MET 3.0 25.5 - - - +
28A ALA* 3.2 18.2 - - - +
30A GLY* 4.7 2.9 + - - -
34A TYR* 3.9 38.8 - - + +
104A GLY* 1.3 68.5 - - - -
106A LYS* 1.3 88.6 + - + +
108A LEU* 3.5 3.0 + - + +
109A ALA* 2.8 28.9 + - - +
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLY* 3.3 1.0 - - - -
105A GLN* 1.3 98.3 - - + +
107A GLU* 1.3 65.2 + - + +
109A ALA* 3.3 4.9 + - + +
110A ALA* 3.1 21.7 + - - +
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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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100A ALA* 4.1 15.9 - - + +
103A ALA* 3.5 34.2 - - - +
104A GLY* 3.5 7.5 + - - +
105A GLN 3.3 0.4 - - - -
106A LYS* 1.3 78.4 - - + +
108A LEU* 1.3 64.8 + - - +
110A ALA* 3.1 8.7 + - - +
111A ALA* 3.0 23.0 + - - +
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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
----------------------------------------------------------
24A LEU* 3.9 35.7 - - + +
27A MET* 4.1 13.7 - - + -
28A ALA* 4.0 13.7 - - - +
34A TYR* 4.2 19.5 - - + -
39A ALA* 4.8 3.6 - - + -
97A LEU* 4.0 15.7 - - + -
100A ALA* 4.2 10.6 + - - +
101A ALA* 4.2 14.8 - - - +
104A GLY 3.0 18.2 + - - +
105A GLN* 3.9 4.3 - - - +
107A GLU* 1.3 75.7 - - - +
109A ALA* 1.3 59.2 + - - +
111A ALA* 3.2 3.9 + - - +
112A VAL* 2.8 47.3 + - + +
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Residues in contact with ALA 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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28A ALA* 3.7 36.5 - - + +
105A GLN* 2.8 23.8 + - - +
106A LYS* 3.7 7.6 - - + +
107A GLU 3.2 0.2 - - - -
108A LEU* 1.3 77.7 - - - +
110A ALA* 1.3 56.8 + - - +
112A VAL* 3.5 2.3 + - - +
113A GLY* 2.9 25.3 + - - -
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Residues in contact with ALA 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 LYS 3.1 12.4 + - - +
107A GLU* 3.1 12.2 + - - +
109A ALA* 1.3 75.2 - - - +
111A ALA* 1.4 63.9 + - - +
113A GLY* 3.2 11.1 + - - -
114A LYS* 3.2 19.6 + - - +
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Residues in contact with ALA 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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93A ALA 4.8 1.3 - - - +
96A ALA* 4.6 5.4 - - + +
97A LEU* 3.7 24.9 - - + +
100A ALA* 3.7 19.3 - - + -
107A GLU 3.0 12.4 + - - +
108A LEU 3.6 6.7 - - - +
110A ALA* 1.4 75.1 - - - +
112A VAL* 1.3 64.3 + - - +
114A LYS* 3.2 9.9 + - - +
115A VAL* 3.1 26.0 + - - +
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Residues in contact with VAL 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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21A PHE* 4.1 14.8 - - + -
24A LEU* 3.8 24.9 - - + +
25A ALA* 4.1 15.9 - - + -
28A ALA* 3.8 17.3 - - + -
97A LEU* 4.1 7.4 - - + -
108A LEU* 2.8 42.0 + - + +
109A ALA 3.7 3.8 - - - +
111A ALA* 1.3 75.5 - - - +
113A GLY* 1.3 58.9 + - - +
115A VAL* 3.2 6.9 + - - +
116A GLY* 2.8 27.9 + - - -
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Residues in contact with GLY 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 ALA 2.9 15.5 + - - -
110A ALA 3.2 6.0 + - - -
112A VAL* 1.3 77.6 - - - +
114A LYS* 1.3 64.3 + - - +
116A GLY* 3.5 2.3 + - - -
117A GLY* 3.1 19.2 + - - -
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Residues in contact with LYS 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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93A ALA* 4.2 12.6 - - + +
110A ALA 3.2 14.4 + - - +
111A ALA* 3.2 10.6 + - - +
113A GLY* 1.3 74.8 + - - +
115A VAL* 1.3 70.2 + - - +
117A GLY* 3.2 4.0 + - - -
118A THR* 3.1 22.1 + - + +
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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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21A PHE* 3.5 24.7 - - + -
46A LEU* 5.5 0.7 - - + -
90A PHE* 4.3 2.9 - - + -
93A ALA* 3.6 35.4 - - - +
94A VAL* 4.1 15.9 - - + +
97A LEU* 4.1 20.9 - - + -
111A ALA 3.1 15.2 + - - +
112A VAL 3.6 5.8 - - - +
114A LYS* 1.3 76.1 - - - +
116A GLY* 1.3 60.2 + - - +
118A THR* 2.7 29.3 + - - +
119A CYS* 3.0 5.2 + - - -
131A HEC 3.8 16.6 - - + -
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Residues in contact with GLY 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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21A PHE* 4.0 11.2 - - - -
112A VAL 2.8 16.4 + - - -
113A GLY* 3.5 2.9 + - - -
114A LYS 3.2 0.2 - - - -
115A VAL* 1.3 76.5 - - - +
117A GLY* 1.3 61.3 + - - +
119A CYS* 3.1 15.8 + - - +
120A LYS* 3.1 21.7 + - - +
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Residues in contact with GLY 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 GLY 3.1 14.6 + - - -
114A LYS* 3.2 4.2 + - - -
116A GLY* 1.3 73.9 - - - +
118A THR* 1.3 57.2 + - - +
120A LYS* 3.3 6.5 + - - +
121A SER* 2.9 31.3 + - - -
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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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86A LYS* 5.1 2.3 - - - +
89A ALA* 3.8 29.6 - - + +
90A PHE* 3.4 35.4 - - - -
93A ALA* 4.0 8.5 - - + +
114A LYS* 3.1 13.9 + - + +
115A VAL* 2.7 24.3 + - - -
117A GLY* 1.3 69.9 - - - +
119A CYS* 1.3 64.8 + - - +
121A SER* 4.0 5.6 - - - -
122A CYS* 3.2 21.5 + - - +
131A HEC 3.9 5.0 - - - +
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Residues in contact with CYS 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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21A PHE* 4.6 3.8 - - - -
115A VAL 3.0 16.9 + - - -
116A GLY* 3.3 14.1 - - - +
118A THR* 1.3 77.6 + - - +
120A LYS* 1.3 64.0 + - - +
122A CYS* 3.3 1.7 + - - +
123A HIS* 3.1 33.8 + - + -
131A HEC 1.9 76.5 - - + -
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Residues in contact with LYS 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 GLY 3.1 9.1 + - - +
117A GLY* 3.7 9.2 - - - +
119A CYS* 1.3 78.6 - - - +
121A SER* 1.3 56.8 + - - +
123A HIS* 3.1 10.7 + - + +
124A ASP* 2.8 69.6 + - - +
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Residues in contact with SER 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 LYS* 2.7 49.4 + - - +
117A GLY 2.9 18.6 + - - -
118A THR* 4.0 7.0 - - - -
120A LYS* 1.3 78.2 - - - +
122A CYS* 1.3 64.7 + - - +
124A ASP* 3.4 17.1 + - - +
125A ASP 3.7 1.9 + - - -
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Residues in contact with CYS 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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83A PHE* 3.9 11.7 - - - -
86A LYS* 4.2 18.7 - - + +
118A THR 3.2 5.1 + - - +
119A CYS 3.7 2.5 - - - +
120A LYS 3.1 0.2 - - - -
121A SER* 1.3 77.9 - - - +
123A HIS* 1.3 65.3 + - - +
124A ASP 3.1 0.9 + - - -
125A ASP 3.2 2.4 + - - -
126A PHE* 2.9 26.6 + - - +
131A HEC 1.9 76.9 - - + -
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Residues in contact with HIS 123 (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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119A CYS* 3.1 21.0 + - + +
120A LYS* 3.1 12.2 + - + +
122A CYS* 1.3 73.5 - - - +
124A ASP* 1.3 64.4 + - - +
127A ARG* 3.1 76.0 + - - +
129A LYS* 5.9 0.5 - - - +
131A HEC 1.9 79.3 + + + -
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Residues in contact with ASP 124 (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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73A LYS* 4.6 8.0 + - - -
86A LYS* 5.5 0.7 - - - +
120A LYS* 2.8 59.6 + - - +
121A SER* 3.6 10.8 - - - +
122A CYS 3.1 0.6 - - - -
123A HIS* 1.3 79.4 - - - +
125A ASP* 1.3 66.3 + - - +
127A ARG 5.0 0.5 - - - +
129A LYS* 4.3 19.8 + - - +
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Residues in contact with ASP 125 (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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73A LYS* 3.9 15.5 + - - +
75A ALA* 4.1 8.8 - - - +
86A LYS* 2.7 37.5 + - - -
121A SER 3.7 0.8 + - - +
122A CYS 3.2 2.6 + - - +
124A ASP* 1.3 86.8 - - - +
126A PHE* 1.3 86.9 + - + +
127A ARG 3.9 0.7 - - - -
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Residues in contact with PHE 126 (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 ALA 3.9 0.9 - - - +
73A LYS* 3.0 30.4 + - - -
75A ALA* 3.6 26.7 - - + -
76A ILE* 3.5 42.1 - - + +
79A ASP* 4.0 18.6 - - + -
82A GLY 3.9 3.8 - - - -
83A PHE* 3.7 46.4 - + + -
86A LYS* 4.0 16.4 - - + -
122A CYS* 2.9 23.6 + - - +
125A ASP* 1.3 102.7 - - + +
127A ARG* 1.3 59.6 + - - +
131A HEC 4.0 5.2 - - + +
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Residues in contact with ARG 127 (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 ALA* 3.4 19.7 - - + +
73A LYS* 3.7 10.1 - - - -
123A HIS* 3.1 64.3 + - + +
124A ASP 5.0 0.3 - - - +
125A ASP 3.9 0.2 - - - -
126A PHE* 1.3 80.0 - - - +
128A VAL* 1.3 77.2 + - - +
129A LYS* 3.5 7.6 + - - +
131A HEC 3.4 62.6 - - + +
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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
------------------------------------------------------------
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