Contacts of the helix formed by residues 102 - 121 (chain Q) in PDB entry 5GJQ
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 ALA 102 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q ALA* 1.3 75.7 - - - +
103Q THR* 1.3 64.1 + - - +
104Q GLY* 4.5 2.9 - - - +
105Q GLN* 3.7 26.1 + - + +
106Q GLU* 2.8 28.9 + - - +
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Residues in contact with THR 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q ALA 3.5 5.0 + - - -
102Q ALA* 1.3 68.7 - - - +
104Q GLY* 1.3 54.6 + - - +
106Q GLU* 3.2 8.1 - - - +
107Q VAL* 2.5 43.4 + - - +
136Q LEU* 6.4 0.9 - - - -
140Q THR* 3.0 39.7 - - - +
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Residues in contact with GLY 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Q ALA* 3.3 2.8 - - - +
103Q THR* 1.3 76.1 - - - +
105Q GLN* 1.3 52.9 + - - +
107Q VAL* 2.6 15.2 + - - -
108Q GLU* 2.2 46.1 + - - -
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Residues in contact with GLN 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Q THR* 4.7 3.0 - - - +
63Q ALA* 2.9 42.1 + - + +
66Q LEU* 5.2 0.2 - - + -
96Q PHE* 3.7 18.4 - - + -
101Q ALA* 4.8 9.5 - - - +
102Q ALA* 3.7 22.1 + - + +
103Q THR 3.6 0.4 - - - -
104Q GLY* 1.3 70.4 - - - +
106Q GLU* 1.3 52.9 + - - +
108Q GLU* 3.9 7.6 - - - +
109Q LEU* 2.2 53.6 + - + +
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Residues in contact with GLU 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96Q PHE* 2.2 62.9 - - + +
97Q LEU* 2.9 33.2 - - + -
99Q MET 4.4 4.2 - - - +
101Q ALA* 3.8 16.7 + - - +
102Q ALA 2.8 25.7 + - - +
103Q THR* 3.2 10.0 + - - +
104Q GLY 2.8 2.8 + - - -
105Q GLN* 1.3 73.1 - - - +
107Q VAL* 1.3 57.0 + - + +
109Q LEU* 3.1 0.9 + - - +
110Q CYS* 2.5 45.0 + - - -
136Q LEU* 4.6 10.9 - - + +
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Residues in contact with VAL 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Q THR* 2.5 35.9 + - - +
104Q GLY* 2.6 5.1 + - - +
106Q GLU* 1.3 72.9 - - + +
108Q GLU* 1.3 60.1 - - - +
110Q CYS* 4.2 5.6 - - - -
111Q LEU* 2.6 47.8 + - + +
133Q LEU* 5.1 4.5 - - + -
136Q LEU* 5.1 10.1 - - + -
137Q TYR* 3.4 45.5 - - + +
140Q THR* 4.9 5.8 - - + -
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Residues in contact with GLU 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Q GLY* 2.2 39.2 + - - +
105Q GLN* 3.9 6.1 - - - +
107Q VAL* 1.3 70.2 - - + +
109Q LEU* 1.3 63.8 + - + +
111Q LEU* 3.6 13.7 - - - +
112Q GLU* 2.8 45.8 + - - +
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Residues in contact with LEU 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Q GLN 4.6 0.9 - - - +
66Q LEU* 2.7 50.3 - - + +
67Q GLY* 4.8 1.1 - - - +
69Q LEU* 5.7 0.2 - - + -
92Q LEU* 5.2 6.3 - - + -
93Q LEU* 4.6 5.8 - - + -
96Q PHE* 3.5 26.9 - - + -
105Q GLN* 2.2 43.2 + - + +
106Q GLU 3.8 0.7 - - - +
108Q GLU* 1.3 75.2 - - + +
110Q CYS* 1.3 71.7 + - - +
112Q GLU* 2.7 33.6 + - - +
113Q CYS* 2.7 20.5 + - - -
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Residues in contact with CYS 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Q LEU* 3.4 32.5 - - - +
97Q LEU* 3.8 25.4 - - - -
106Q GLU* 2.5 38.5 + - - +
107Q VAL* 3.7 4.9 - - - +
109Q LEU* 1.3 72.0 - - - +
111Q LEU* 1.3 55.9 + - - +
113Q CYS* 2.8 1.0 + - - +
114Q ILE* 2.4 51.8 + - + +
129Q LEU* 4.1 5.8 - - + -
133Q LEU* 5.0 3.6 - - + -
136Q LEU* 4.0 11.2 - - + -
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Residues in contact with LEU 111 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Q VAL* 2.6 29.4 + - + +
108Q GLU* 3.6 13.5 - - - +
110Q CYS* 1.3 72.2 - - - +
112Q GLU* 1.3 67.3 + - - +
114Q ILE* 3.3 21.7 - - + +
115Q GLU* 2.8 24.0 + - + +
133Q LEU* 4.9 7.4 - - + +
137Q TYR* 4.3 19.3 - - - +
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Residues in contact with GLU 112 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Q LEU 4.6 7.6 - - - +
67Q GLY* 5.6 2.3 - - - -
69Q LEU* 6.0 0.3 - - - +
70Q LEU* 5.5 7.9 + - - +
108Q GLU* 2.8 39.4 + - - +
109Q LEU* 2.7 40.3 + - - +
111Q LEU* 1.3 75.3 - - - +
113Q CYS* 1.3 53.4 + - - +
115Q GLU* 2.9 6.1 + - - +
116Q TRP* 2.7 31.7 + - - +
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Residues in contact with CYS 113 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69Q LEU* 5.2 14.8 - - - -
70Q LEU 6.1 0.7 - - - -
89Q VAL* 4.8 15.3 - - + -
92Q LEU* 5.5 3.1 - - - -
93Q LEU* 3.9 26.2 - - + -
109Q LEU* 2.7 23.0 + - - +
110Q CYS 3.7 3.1 - - - +
112Q GLU* 1.3 77.9 - - - +
114Q ILE* 1.3 65.9 + - - +
116Q TRP* 3.0 27.2 + - + +
117Q ALA* 3.1 14.7 + - - +
129Q LEU* 3.8 6.4 - - + +
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Residues in contact with ILE 114 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q CYS* 2.4 43.3 + - + +
111Q LEU* 3.3 18.8 - - + +
113Q CYS* 1.3 74.0 - - - +
115Q GLU* 1.3 63.3 + - - +
117Q ALA* 3.5 15.4 + - - +
118Q LYS* 3.8 22.2 - - - +
126Q ARG* 4.3 6.6 - - + +
129Q LEU* 3.1 38.1 - - + +
130Q GLU* 3.1 23.1 - - - +
133Q LEU* 3.4 39.0 - - + -
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Residues in contact with GLU 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111Q LEU* 2.8 17.2 + - + +
112Q GLU* 3.5 7.2 - - - +
114Q ILE* 1.3 73.8 - - + +
116Q TRP* 1.3 63.8 + - - +
117Q ALA 3.4 0.2 - - - -
118Q LYS* 3.3 24.1 + - + +
119Q SER* 3.2 19.5 + - - +
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Residues in contact with TRP 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73Q VAL* 4.7 19.8 - - + +
82Q LYS* 6.4 1.1 - - + -
85Q ALA* 3.9 29.8 - - + -
86Q ALA* 5.8 0.9 - - - -
89Q VAL* 4.1 28.5 - - + -
112Q GLU 2.7 11.4 + - - +
113Q CYS* 3.0 28.7 + - + +
115Q GLU* 1.3 71.3 - - - +
117Q ALA* 1.3 92.5 + - + +
119Q SER* 2.6 29.2 + - - -
120Q GLU* 2.9 23.7 + - + +
122Q ARG* 4.6 22.4 - - - -
125Q LEU* 5.5 7.9 - - + -
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Residues in contact with ALA 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Q CYS 3.1 9.8 + - - +
114Q ILE* 3.6 11.7 - - - +
116Q TRP* 1.3 92.4 - - + +
118Q LYS* 1.3 50.6 - - - +
120Q GLU* 3.6 1.7 - - - +
121Q LYS* 2.2 39.1 + - - -
122Q ARG* 3.1 14.3 + - + +
125Q LEU* 4.8 5.2 - - + -
126Q ARG* 3.9 33.2 - - + +
129Q LEU* 5.9 0.9 - - + -
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Residues in contact with LYS 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114Q ILE* 3.8 24.1 - - - +
115Q GLU* 3.4 26.5 - - + +
116Q TRP 3.1 0.6 - - - -
117Q ALA* 1.3 71.5 - - - +
119Q SER* 1.3 64.9 + - - +
120Q GLU 3.0 2.8 + - - -
121Q LYS* 3.2 30.6 + - - +
126Q ARG* 3.0 57.6 - - + +
130Q GLU* 5.5 1.2 + - - -
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Residues in contact with SER 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Q GLU* 3.2 9.9 + - - +
116Q TRP* 2.6 34.6 + - - -
118Q LYS* 1.3 79.0 - - - +
120Q GLU* 1.3 58.0 + - - +
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Residues in contact with GLU 120 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Q LYS* 2.6 50.1 + - + +
116Q TRP* 2.9 32.2 + - + +
117Q ALA* 3.7 4.3 - - - +
119Q SER* 1.3 78.3 + - - +
121Q LYS* 1.3 70.5 + - - +
122Q ARG* 3.9 25.7 + - + +
182i GLU* 3.9 10.7 - - - +
184i GLU* 3.6 17.6 - - - +
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Residues in contact with LYS 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Q ALA 2.2 25.3 + - - -
118Q LYS* 3.4 18.2 - - - +
120Q GLU* 1.3 76.2 - - - +
122Q ARG* 1.3 59.3 - - - +
123Q THR* 3.7 12.7 - - + +
180i ASP 5.5 8.1 - - - +
182i GLU* 3.9 38.2 + - - +
184i GLU* 5.0 0.9 - - - +
185i ASP* 3.9 4.7 - - - +
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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