Contacts of the helix formed by residues 108 - 127 (chain A) in PDB entry 2GTL
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 THR 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLY 4.0 4.5 - - - +
107A VAL* 1.3 84.1 - - - +
109A LYS* 1.3 63.1 + - - +
110A GLU* 3.1 15.6 + - + +
111A TYR* 2.8 58.6 + - + +
112A PHE* 3.9 9.9 + - - -
150A LEU* 4.1 5.5 - - - +
151A PRO* 4.5 7.4 - - - +
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Residues in contact with LYS 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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108A THR* 1.3 75.6 - - - +
110A GLU* 1.3 62.2 - - - +
112A PHE* 3.5 6.9 + - - +
113A ARG* 3.5 15.4 + - - +
143A VAL* 5.8 0.3 - - - +
144A ALA* 5.8 1.6 - - - +
147A ALA* 3.6 28.3 - - + +
148A LYS* 4.1 14.3 + - - +
150A LEU* 4.4 5.2 - - - -
151A PRO* 3.5 45.6 - - + +
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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
----------------------------------------------------------
46A TYR* 3.6 33.1 - - + -
108A THR* 3.2 13.2 + - - +
109A LYS* 1.3 76.3 - - - +
111A TYR* 1.3 72.5 + - + +
112A PHE 2.9 2.2 - - - -
113A ARG* 2.8 44.9 + - - +
114A GLY* 2.8 9.5 + - - -
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Residues in contact with TYR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.9 7.1 - - + +
46A TYR* 4.1 20.2 - + + -
48A THR* 3.2 31.4 + - - +
49A SER* 3.5 34.4 + - - -
52A LEU* 3.9 15.3 - - + +
106A GLY 3.2 23.0 + - - -
107A VAL* 4.1 1.3 - - - -
108A THR* 2.8 51.1 + - + +
110A GLU* 1.3 76.6 - - - +
112A PHE* 1.3 56.4 + - - +
114A GLY* 3.1 3.7 + - - +
115A ILE* 2.9 24.1 + - - +
160A HEM 3.5 26.9 - - + +
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Residues in contact with PHE 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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101A HIS* 3.6 15.0 - + - -
107A VAL* 3.8 8.1 - - + -
108A THR 3.9 5.4 - - - -
109A LYS 3.5 9.8 + - - +
110A GLU 2.8 1.4 + - - -
111A TYR* 1.3 75.9 - - - +
113A ARG* 1.3 63.5 + - - +
114A GLY 2.8 5.8 + - - -
115A ILE* 2.9 16.2 + - + +
116A GLY* 3.0 10.2 + - - -
143A VAL* 3.9 36.6 - - + +
146A ILE* 3.4 33.7 - - + -
147A ALA* 4.1 8.5 - - + -
150A LEU* 3.4 28.3 - - + -
160A HEM 3.5 59.2 - + + -
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Residues in contact with ARG 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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46A TYR* 3.6 16.9 + - - -
109A LYS 3.5 7.6 + - - +
110A GLU* 2.8 40.3 + - - +
112A PHE* 1.3 75.8 - - - +
114A GLY* 1.3 57.5 + - - +
116A GLY* 3.6 3.0 + - - +
117A GLU* 2.9 44.7 + - + +
140A HIS* 5.7 7.4 - - + +
143A VAL* 4.7 6.8 - - - +
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Residues in contact with GLY 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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41A ASP* 5.0 1.9 - - - +
42A LEU* 3.9 10.0 - - - +
46A TYR* 3.8 30.5 - - - -
110A GLU 2.8 9.8 + - - -
111A TYR 3.3 5.6 - - - -
112A PHE 2.8 2.8 - - - -
113A ARG* 1.3 76.9 - - - +
115A ILE* 1.3 62.8 + - - -
116A GLY 3.1 1.6 - - - -
117A GLU* 3.3 9.0 + - - +
118A ALA* 3.1 18.0 + - - +
121A ARG* 5.2 0.3 + - - -
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Residues in contact with ILE 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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38A VAL* 4.0 12.3 - - + -
39A PHE* 3.8 33.2 - - + -
42A LEU* 3.9 12.5 - - + +
73A VAL* 5.4 2.2 - - + -
111A TYR 2.9 9.0 + - - +
112A PHE* 2.9 15.7 + - + +
114A GLY* 1.3 74.1 - - - +
116A GLY* 1.3 68.7 + - - +
117A GLU 3.3 0.2 - - - -
118A ALA* 3.0 20.2 - - + +
119A PHE* 3.2 34.8 - - + -
139A PHE* 4.6 3.8 - - + -
160A HEM 3.8 51.8 - - + -
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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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112A PHE 3.0 13.1 + - - -
113A ARG* 3.6 4.0 + - - -
114A GLY 3.1 0.4 - - - -
115A ILE* 1.3 76.9 - - - +
117A GLU* 1.3 64.9 + - - +
118A ALA 3.4 0.2 + - - -
119A PHE* 3.5 3.1 + - - +
120A ALA* 3.3 21.0 + - - +
135A TRP* 4.9 0.5 + - - -
136A ASN* 4.5 6.1 + - - -
139A PHE* 3.4 29.9 - - - -
140A HIS* 5.9 6.3 - - - -
143A VAL* 5.5 0.7 - - - -
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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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45A HIS* 5.1 2.3 - - - -
46A TYR* 2.9 37.0 + - - -
113A ARG* 2.9 34.6 + - + +
114A GLY* 3.5 4.2 - - - +
116A GLY* 1.3 74.8 - - - +
118A ALA* 1.3 66.9 + - - +
120A ALA* 3.1 17.7 + - - +
121A ARG* 3.1 42.6 + - - +
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Residues in contact with ALA 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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38A VAL* 3.5 32.8 - - + +
41A ASP* 3.5 19.2 + - - +
42A LEU 4.6 3.6 - - - +
114A GLY 3.1 5.2 + - - +
115A ILE* 3.0 21.8 - - + +
117A GLU* 1.3 77.4 - - - +
119A PHE* 1.3 65.8 + - - +
121A ARG* 2.8 14.2 + - - +
122A VAL* 2.9 18.7 + - - +
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Residues in contact with PHE 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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19A TRP* 5.1 4.5 - + - -
34A ILE* 5.7 2.5 - - + -
35A VAL* 5.6 11.4 - - + -
38A VAL* 3.7 35.9 - - + +
73A VAL* 6.0 4.5 - - + -
77A LEU* 3.4 30.3 - - + -
115A ILE* 3.2 38.7 + - + -
116A GLY 4.0 2.7 - - - +
118A ALA* 1.3 77.2 - - - +
120A ALA* 1.3 58.5 + - - +
121A ARG 2.8 6.4 + - - -
122A VAL* 2.9 4.9 + - - +
123A LEU* 2.8 53.6 + - + +
124A PRO* 3.4 2.3 - - - +
135A TRP* 3.9 24.5 - + - +
139A PHE* 3.8 21.8 - + - -
160A HEM 4.3 3.4 - - + -
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Residues in contact with ALA 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 3.3 11.0 + - - +
117A GLU* 3.1 14.5 + - - +
119A PHE* 1.3 78.0 - - - +
121A ARG* 1.3 56.6 + - - +
124A PRO* 3.3 18.3 - - - +
130A PHE* 4.8 8.1 - - - -
132A VAL* 4.5 14.6 - - + +
135A TRP* 4.6 2.6 - - - +
136A ASN* 3.7 27.8 - - - +
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Residues in contact with ARG 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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41A ASP* 2.7 39.6 + - - +
45A HIS* 3.2 36.5 + - - +
114A GLY 5.2 0.8 + - - -
117A GLU* 3.1 37.7 + - - +
118A ALA 2.8 8.6 + - - +
120A ALA* 1.3 77.4 - - - +
122A VAL* 1.3 63.6 + - - +
124A PRO* 3.4 12.1 - - - +
125A GLN* 3.3 18.9 - - - +
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Residues in contact with VAL 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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34A ILE* 4.3 11.2 - - + +
37A ALA* 3.8 28.0 - - + +
38A VAL* 3.7 38.6 - - + -
41A ASP* 4.6 8.3 - - + +
118A ALA 2.9 17.2 + - - +
119A PHE 2.9 1.7 + - - +
121A ARG* 1.3 75.8 - - + +
123A LEU* 1.3 57.4 + - - +
124A PRO* 3.2 2.0 - - - -
125A GLN* 2.6 40.8 + - - +
126A VAL* 3.4 5.4 + - + -
7B LEU* 4.4 14.6 - - + -
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Residues in contact with LEU 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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18A ILE* 5.6 1.1 - - + -
19A TRP* 5.0 6.7 - - + -
22A VAL* 4.3 19.5 - - + -
34A ILE* 4.4 15.3 - - + -
119A PHE* 2.8 33.5 + - + +
122A VAL* 1.3 73.8 - - + +
124A PRO* 1.3 59.1 - - + +
125A GLN 2.6 11.4 + - - -
126A VAL* 2.9 26.9 + - + -
127A LEU* 2.9 18.7 + - + +
130A PHE* 3.5 35.2 - - + -
135A TRP* 3.6 35.9 - - + -
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Residues in contact with PRO 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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119A PHE 3.4 9.0 - - - +
120A ALA 3.3 21.5 - - - +
121A ARG* 3.4 15.0 - - - +
122A VAL 3.2 1.8 - - - -
123A LEU* 1.3 92.7 - - + +
125A GLN* 1.3 58.7 + - + +
127A LEU 3.5 14.3 - - - +
130A PHE* 3.8 25.5 - - + -
132A VAL* 5.8 2.2 - - + -
11B LYS* 3.7 9.7 + - - -
184M LYS* 6.3 0.9 - - - +
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Residues in contact with GLN 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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121A ARG 3.3 19.7 - - - +
122A VAL* 2.6 17.4 + - - +
123A LEU 2.6 0.8 + - - -
124A PRO* 1.3 75.8 - - + +
126A VAL* 1.3 58.0 + - - +
127A LEU 3.4 2.0 - - - -
2B LYS* 5.4 11.9 - - - +
7B LEU* 3.3 40.9 - - + +
8B GLU* 4.4 15.9 + - - +
11B LYS* 2.8 30.8 - - - +
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Residues in contact with VAL 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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22A VAL* 5.7 0.2 - - + -
30A ARG* 3.8 16.3 + - - +
34A ILE* 4.0 34.8 - - + -
122A VAL* 3.7 5.8 - - + +
123A LEU* 3.1 37.2 - - + +
125A GLN* 1.3 77.7 - - - +
127A LEU* 1.3 73.5 - - + +
7B LEU* 3.8 30.3 - - + -
10B LEU* 4.2 13.9 - - + -
11B LYS* 3.9 20.1 + - - +
14B SER* 5.2 1.6 - - - -
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Residues in contact with LEU 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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18A ILE* 3.7 39.5 - - + +
21A ASP* 3.2 29.6 - - + +
22A VAL* 3.8 17.5 - - + -
30A ARG* 5.2 1.3 - - - +
123A LEU* 2.9 38.4 - - + +
124A PRO* 3.5 19.8 - - - +
125A GLN 3.4 1.0 - - - -
126A VAL* 1.3 93.7 - - + +
128A SER* 1.3 69.3 + - - +
129A CYS 5.2 1.6 - - - +
130A PHE* 4.3 10.6 - - + +
11B LYS* 4.2 8.4 - - - +
15B GLU* 6.5 0.2 - - - -
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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