Contacts of the helix formed by residues 108 - 127 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E GLY 4.0 4.5 - - - +
107E VAL* 1.3 83.5 - - - +
109E LYS* 1.3 63.8 + - - +
110E GLU* 3.1 15.0 + - - +
111E TYR* 2.8 58.6 + - + +
112E PHE* 3.8 10.2 + - - -
150E LEU* 4.1 5.7 - - - +
151E PRO* 4.5 7.9 - - - +
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Residues in contact with LYS 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E THR* 1.3 74.3 - - - +
110E GLU* 1.3 64.0 + - - +
112E PHE* 3.5 6.4 + - - +
113E ARG* 3.5 16.3 + - - +
144E ALA* 5.9 1.3 - - - +
147E ALA* 3.6 27.3 - - + +
148E LYS* 4.1 14.3 + - - +
150E LEU* 4.4 4.9 - - - -
151E PRO* 3.5 46.5 - - + +
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Residues in contact with GLU 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E TYR* 3.6 32.3 - - + -
108E THR* 3.2 13.7 + - - +
109E LYS* 1.3 77.0 - - - +
111E TYR* 1.3 72.3 + - + +
112E PHE 3.0 2.2 - - - -
113E ARG* 2.8 46.4 + - - +
114E GLY* 2.8 9.2 + - - -
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Residues in contact with TYR 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E LEU* 3.9 7.2 - - + +
46E TYR* 4.1 22.0 - + + -
48E THR* 3.1 31.6 + - - +
49E SER* 3.5 34.3 + - - -
52E LEU* 4.0 11.4 - - + +
106E GLY 3.2 23.2 + - - -
107E VAL* 4.1 3.8 - - - -
108E THR* 2.8 51.5 + - + +
110E GLU* 1.3 77.8 - - - +
112E PHE* 1.3 57.5 + - - +
114E GLY* 3.1 4.7 + - - +
115E ILE* 2.9 22.9 + - - +
160E HEM 3.5 26.7 - - + +
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Residues in contact with PHE 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E HIS* 3.6 15.0 - + - -
107E VAL* 3.8 8.3 - - + -
108E THR 3.8 5.4 + - - -
109E LYS 3.5 10.5 + - - +
110E GLU 2.8 1.6 + - - -
111E TYR* 1.3 74.3 - - - +
113E ARG* 1.3 64.1 + - - +
114E GLY 2.8 5.5 + - - -
115E ILE* 2.9 16.5 + - + +
116E GLY* 2.9 10.6 + - - -
143E VAL* 3.9 35.2 - - + +
146E ILE* 3.4 33.7 - - + -
147E ALA* 4.1 7.6 - - + -
150E LEU* 3.4 27.4 - - + -
160E HEM 3.4 60.1 - + + -
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Residues in contact with ARG 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E TYR* 3.6 16.9 + - - -
109E LYS 3.5 8.5 + - - +
110E GLU* 2.8 38.8 + - - +
112E PHE* 1.3 76.1 - - - +
114E GLY* 1.3 58.0 + - - +
116E GLY* 3.5 2.6 + - - -
117E GLU* 2.9 45.0 + - + +
140E HIS* 5.7 7.4 - - + +
143E VAL* 4.7 7.0 - - - +
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Residues in contact with GLY 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ASP* 5.0 1.7 - - - +
42E LEU* 3.9 10.0 - - - +
46E TYR* 3.7 30.2 - - - -
110E GLU 2.8 9.7 + - - -
111E TYR 3.4 5.4 - - - -
112E PHE 2.8 3.0 + - - -
113E ARG* 1.3 76.7 - - - +
115E ILE* 1.3 61.6 - - - -
116E GLY 3.0 1.8 - - - -
117E GLU* 3.3 8.5 + - - +
118E ALA* 3.1 17.7 + - - +
121E ARG* 5.2 0.7 + - - -
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Residues in contact with ILE 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E VAL* 4.0 11.7 - - + -
39E PHE* 3.8 32.5 - - + -
42E LEU* 3.9 13.2 - - + +
73E VAL* 5.5 2.2 - - + -
111E TYR 2.9 9.3 + - - +
112E PHE* 2.9 15.0 + - + +
114E GLY* 1.3 73.8 - - - +
116E GLY* 1.3 70.3 + - - +
118E ALA* 3.0 21.0 + - + +
119E PHE* 3.2 30.3 - - + -
139E PHE* 4.6 3.6 - - + -
143E VAL* 5.5 0.2 - - + -
160E HEM 3.8 52.7 - - + -
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Residues in contact with GLY 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E PHE 2.9 12.7 + - - -
113E ARG* 3.9 4.0 - - - -
114E GLY 3.0 0.2 - - - -
115E ILE* 1.3 79.1 - - - +
117E GLU* 1.3 63.7 - - - +
119E PHE* 3.5 3.8 + - - +
120E ALA* 3.3 20.5 + - - +
135E TRP* 5.0 0.7 + - - -
136E ASN* 4.6 5.7 + - - -
139E PHE* 3.5 28.3 - - - -
140E HIS* 5.9 6.3 - - - -
143E VAL* 5.5 0.4 - - - -
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Residues in contact with GLU 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E HIS* 5.1 2.1 - - - -
46E TYR* 3.0 36.9 + - - -
113E ARG* 2.9 34.1 + - + +
114E GLY* 3.5 3.3 - - - +
116E GLY* 1.3 75.4 - - - +
118E ALA* 1.3 66.4 + - - +
120E ALA* 3.1 17.0 + - - +
121E ARG* 3.1 43.2 + - - +
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Residues in contact with ALA 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E VAL* 3.5 32.5 - - + +
41E ASP* 3.5 19.0 + - - +
42E LEU 4.6 3.8 - - - +
114E GLY 3.1 5.5 + - - +
115E ILE* 3.0 21.5 - - + +
116E GLY 3.1 0.2 - - - -
117E GLU* 1.3 77.4 - - - +
119E PHE* 1.3 64.8 + - - +
121E ARG* 2.8 13.2 + - - +
122E VAL* 2.9 18.4 + - - +
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Residues in contact with PHE 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E TRP* 5.2 4.3 - + - -
34E ILE* 5.7 2.2 - - + -
35E VAL* 5.6 11.9 - - + -
38E VAL* 3.7 34.1 - - + -
73E VAL* 6.0 4.5 - - + -
77E LEU* 3.4 30.1 - - + -
115E ILE* 3.2 39.0 + - + -
116E GLY 4.0 2.9 - - - +
117E GLU 3.4 0.2 - - - -
118E ALA* 1.3 77.6 - - - +
120E ALA* 1.3 53.6 + - - +
121E ARG 2.8 10.9 + - - -
122E VAL* 2.8 4.9 + - - +
123E LEU* 2.8 58.5 + - + +
124E PRO* 3.4 2.3 - - - +
135E TRP* 3.9 18.2 - + - +
139E PHE* 3.9 21.8 - + + -
160E HEM 4.3 3.8 - - + -
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Residues in contact with ALA 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E GLY 3.3 10.9 + - - +
117E GLU* 3.1 14.5 + - - +
119E PHE* 1.3 76.5 - - - +
121E ARG* 1.3 57.9 + - - +
124E PRO* 3.3 17.8 - - - +
130E PHE* 4.8 9.2 - - - -
132E VAL* 4.4 14.4 - - + +
135E TRP* 4.7 3.1 - - + +
136E ASN* 3.7 28.3 - - - +
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Residues in contact with ARG 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ASP* 2.7 38.7 + - - +
45E HIS* 3.3 35.6 + - - +
46E TYR* 5.9 0.2 - - - -
114E GLY 5.2 0.6 + - - -
117E GLU* 3.1 37.4 + - - +
118E ALA 2.8 8.2 + - - +
120E ALA* 1.3 78.5 - - - +
122E VAL* 1.3 65.3 + - + +
124E PRO* 3.5 11.7 - - - +
125E GLN* 3.3 19.5 - - - +
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Residues in contact with VAL 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ILE* 4.4 9.4 - - + +
37E ALA* 3.8 28.9 - - + +
38E VAL* 3.7 37.7 - - + -
41E ASP* 4.6 8.1 - - + +
118E ALA 3.1 17.0 - - - +
119E PHE 2.8 2.9 + - - +
121E ARG* 1.3 76.8 - - + +
123E LEU* 1.3 57.5 + - - +
124E PRO* 3.2 2.7 - - - -
125E GLN* 2.6 40.2 + - - +
126E VAL* 3.4 4.6 + - + -
7F LEU* 4.2 16.8 - - + -
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Residues in contact with LEU 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ILE* 5.6 0.7 - - + -
19E TRP* 5.0 6.5 - - + -
22E VAL* 4.3 19.7 - - + -
34E ILE* 4.4 13.7 - - + -
119E PHE* 2.8 34.4 + - + +
122E VAL* 1.3 73.4 - - + +
124E PRO* 1.3 56.5 - - + +
125E GLN 2.6 12.6 + - - -
126E VAL* 2.8 27.2 + - + -
127E LEU* 2.9 18.7 + - + +
130E PHE* 3.6 33.7 - - + -
135E TRP* 3.6 36.8 - - + -
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Residues in contact with PRO 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E PHE 3.4 11.7 - - - +
120E ALA 3.3 21.1 - - - +
121E ARG* 3.5 14.1 - - - +
122E VAL 3.2 1.6 - - - -
123E LEU* 1.3 90.9 - - + +
125E GLN* 1.3 57.3 + - + +
127E LEU 3.6 13.8 - - - +
130E PHE* 3.8 26.8 - - + -
132E VAL* 5.8 2.5 - - + -
11F LYS* 3.6 9.4 + - - -
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Residues in contact with GLN 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ARG 3.3 20.4 - - - +
122E VAL* 2.6 13.2 + - - +
123E LEU 2.6 5.1 + - - -
124E PRO* 1.3 76.7 - - + +
126E VAL* 1.3 56.4 + - - -
127E LEU 3.4 2.2 - - - -
2F LYS* 5.3 15.4 + - - +
7F LEU* 3.7 35.6 - - + +
8F GLU* 4.2 20.4 + - - +
11F LYS* 3.1 24.9 + - - +
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Residues in contact with VAL 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E VAL* 5.8 0.2 - - + -
30E ARG* 3.8 13.1 + - - +
34E ILE* 3.9 31.4 - - + -
122E VAL* 3.7 2.7 - - + +
123E LEU* 3.0 36.8 - - + +
125E GLN* 1.3 78.0 - - - +
127E LEU* 1.3 74.1 + - + +
7F LEU* 3.1 46.2 - - + +
10F LEU* 4.2 7.9 - - + -
11F LYS* 3.6 20.9 + - - -
14F SER* 5.7 0.3 - - - -
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Residues in contact with LEU 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ILE* 3.7 40.4 - - + +
21E ASP* 3.2 28.5 - - + +
22E VAL* 3.8 17.0 - - + -
30E ARG* 5.2 0.9 - - - +
123E LEU* 2.9 37.2 - - + +
124E PRO* 3.6 19.8 - - - +
125E GLN 3.4 0.8 - - - -
126E VAL* 1.3 93.9 - - + +
128E SER* 1.3 67.5 + - - +
129E CYS 5.2 1.8 - - - +
130E PHE* 4.3 10.6 - - + +
11F LYS* 3.4 11.2 - - - +
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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
------------------------------------------------------------
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