Contacts of the helix formed by residues 64 - 82 (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 GLY 64 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E GLU 3.1 5.0 + - - -
63E SER* 1.3 81.4 + - - +
65E GLU* 1.3 63.9 + - - +
66E PHE 3.0 1.7 - - - +
67E LYS* 3.6 24.9 - - - +
68E SER* 3.0 25.8 + - - -
88H ASP* 4.3 11.7 - - - -
89H MET* 4.3 6.3 - - - -
92H ALA* 3.9 9.3 - - - +
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Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E VAL* 3.6 20.7 - - - +
57E LYS* 3.9 34.3 + - + +
63E SER* 3.9 17.1 - - - +
64E GLY* 1.3 77.3 - - - +
66E PHE* 1.3 57.2 + - - +
68E SER* 3.0 15.8 + - - -
69E HIS* 3.7 6.4 + - - +
72E ARG* 4.2 3.5 + - - -
88H ASP 5.2 2.1 - - - +
92H ALA* 4.2 20.1 - - - +
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Residues in contact with PHE 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ARG* 3.7 22.9 - - + -
39E PHE* 5.8 3.1 - + + -
43E PHE* 5.3 11.0 - + - -
53E PHE* 5.1 1.8 - + + -
56E VAL* 3.4 29.4 - - + +
57E LYS 3.5 7.0 - - - +
58E ILE* 3.2 31.0 - - + -
60E GLU 4.3 0.2 - - - -
61E PRO* 3.3 28.3 - - + -
63E SER* 2.7 17.0 + - - +
65E GLU* 1.3 78.4 - - - +
67E LYS* 1.3 64.1 + - - +
68E SER 3.2 0.9 - - - -
69E HIS* 2.8 38.7 + + - +
70E LEU* 2.9 28.2 + - + +
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Residues in contact with LYS 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E VAL* 4.8 12.7 - - + +
36E ARG* 4.0 11.0 - - - +
61E PRO 3.9 16.8 - - - +
62E GLU* 3.7 36.0 + - - +
64E GLY* 3.5 10.1 + - - +
66E PHE* 1.3 78.6 - - - +
68E SER* 1.3 63.5 + - - +
70E LEU* 2.9 23.8 + - + +
71E VAL* 3.0 13.9 + - - +
86H THR* 5.7 4.0 - - - +
88H ASP* 3.7 21.0 + - - -
89H MET* 3.3 32.0 - - + -
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Residues in contact with SER 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLY 3.0 15.3 + - - -
65E GLU* 3.0 13.2 + - - -
67E LYS* 1.3 76.0 - - - +
69E HIS* 1.3 65.9 + - - +
71E VAL* 3.1 5.5 + - - +
72E ARG* 2.9 42.4 + - - -
83H MET* 3.5 29.8 - - - +
89H MET* 3.5 10.6 - - - +
92H ALA* 4.5 3.2 - - - +
93H GLN* 4.1 14.2 + - - +
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Residues in contact with HIS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E PHE* 4.7 2.3 - + - -
53E PHE* 3.4 18.9 - + - -
56E VAL* 3.9 11.9 - - + +
65E GLU 4.0 7.4 - - - +
66E PHE* 2.8 37.8 + + - +
68E SER* 1.3 80.0 + - - +
70E LEU* 1.3 69.3 + - + -
72E ARG* 2.6 48.6 + - - +
73E VAL* 2.9 22.2 + - + +
160E HEM 3.7 28.8 - + + +
161E CMO 3.3 28.2 + - - -
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Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E VAL* 4.4 14.4 - - + -
35E VAL* 3.7 16.9 - - + +
36E ARG* 4.0 35.9 - - + +
39E PHE* 3.5 33.0 - - + -
66E PHE* 2.9 43.5 + - + +
67E LYS* 2.9 19.4 + - - +
69E HIS* 1.3 80.7 - - + +
71E VAL* 1.3 57.6 + - + +
73E VAL* 3.0 10.1 + - - +
74E ALA* 2.8 29.1 + - - +
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Residues in contact with VAL 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E THR* 4.0 12.1 - - + -
31E ARG* 4.5 13.9 - - - +
32E VAL* 3.8 19.1 - - + +
67E LYS 3.0 12.6 + - - +
68E SER* 3.2 9.2 - - - +
70E LEU* 1.3 75.7 - - - +
72E ARG* 1.3 51.0 + - - +
74E ALA* 2.9 8.2 + - - +
75E ASN* 2.6 47.4 + - - +
79H ILE* 3.4 30.5 - - + -
83H MET* 4.3 1.3 - - + -
89H MET* 3.7 21.5 - - + -
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Residues in contact with ARG 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ARG* 5.1 1.4 - - - +
56E VAL* 4.3 4.6 - - - +
65E GLU 4.2 3.4 + - - -
68E SER* 2.9 34.3 + - - +
69E HIS* 2.6 42.6 + - - +
71E VAL* 1.3 72.4 - - - +
73E VAL* 1.3 56.4 + - + +
75E ASN* 3.9 0.7 - - - +
76E GLY* 2.8 27.0 + - - -
160E HEM 3.7 49.6 + - + +
79H ILE* 3.9 21.9 - - + +
93H GLN* 3.0 26.8 + - - +
96H HIS* 3.4 41.8 + - + +
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Residues in contact with VAL 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E VAL* 4.3 6.7 - - + -
39E PHE* 4.0 18.2 - - + -
69E HIS* 2.9 31.8 + - + +
70E LEU* 3.2 8.7 - - - +
72E ARG* 1.3 74.5 - - + +
74E ALA* 1.3 72.1 + - - +
76E GLY* 3.0 9.4 + - - -
77E LEU* 3.0 12.8 + - + +
115E ILE* 5.5 2.9 - - + -
119E PHE* 6.0 4.7 - - + -
160E HEM 3.9 32.6 - - + +
161E CMO 3.2 29.8 - - - +
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Residues in contact with ALA 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E TRP* 5.7 0.7 - - - -
23E TRP* 3.2 27.8 - - + -
31E ARG* 4.6 5.2 - - + +
35E VAL* 3.3 30.7 - - + +
70E LEU 2.8 8.0 + - - +
71E VAL* 3.1 13.0 - - - +
73E VAL* 1.3 75.4 - - - +
75E ASN* 1.3 55.3 + - - +
77E LEU* 2.7 32.5 + - - +
78E LYS* 2.8 10.2 + - - +
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Residues in contact with ASN 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E TRP* 3.2 10.5 - - - -
31E ARG* 3.1 25.3 + - - -
71E VAL* 2.6 21.3 + - - +
72E ARG 3.9 1.1 - - - +
74E ALA* 1.3 72.0 - - - +
76E GLY* 1.3 56.3 + - - +
78E LYS* 3.3 12.5 - - - +
79E LEU* 2.8 30.7 + - - +
75H SER* 3.3 27.3 + - - +
78H ASP* 3.7 17.0 + - - +
79H ILE* 3.2 38.6 - - + +
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Residues in contact with GLY 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ARG 2.8 19.6 + - - -
73E VAL 3.0 4.8 + - - -
75E ASN* 1.3 73.9 - - - +
77E LEU* 1.3 60.1 + - - +
79E LEU* 3.6 8.5 - - - +
80E LEU* 3.3 25.3 + - - +
93E HIS* 4.5 5.3 + - - -
97E LEU* 5.0 4.3 - - - +
160E HEM 4.3 20.8 - - - +
75H SER* 5.4 0.2 - - - -
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Residues in contact with LEU 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E TRP* 3.8 24.7 - - + -
35E VAL* 6.3 1.1 - - + -
73E VAL* 3.0 11.0 + - + +
74E ALA* 2.7 19.0 + - - +
76E GLY* 1.3 70.0 - - - +
78E LYS* 1.3 65.1 - - - +
80E LEU* 2.8 29.5 + - + +
81E ILE* 3.0 26.6 + - + +
119E PHE* 3.4 41.1 - - + -
135E TRP* 4.6 2.5 - - + -
139E PHE* 4.2 23.3 - - + -
142E LEU* 5.1 2.9 - - + -
160E HEM 4.1 15.4 - - + +
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Residues in contact with LYS 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E TRP* 3.2 35.4 - - + +
23E TRP* 3.0 40.6 - - + +
74E ALA 2.8 10.4 + - - +
75E ASN* 3.3 19.5 - - - +
77E LEU* 1.3 77.7 - - - +
79E LEU* 1.3 64.2 + - - +
81E ILE* 3.3 1.4 + - - +
82E ASN* 2.8 40.1 + - - +
27H HIS* 5.1 7.6 + - - -
31H ARG* 2.4 48.7 - - - +
75H SER* 5.7 0.9 - - - +
78H ASP* 4.7 5.5 + - - -
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Residues in contact with LEU 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E ASN 2.8 19.8 + - - +
76E GLY* 3.6 8.7 - - - +
77E LEU 3.2 0.2 - - - -
78E LYS* 1.3 75.8 - - - +
80E LEU* 1.3 65.3 + - - +
82E ASN* 3.6 7.3 + - + -
83E LEU* 3.3 28.6 + - + +
93E HIS* 3.5 36.3 - - + +
25H PHE* 6.3 1.3 - - + -
31H ARG* 5.2 7.0 - - - +
71H GLN* 3.3 50.5 - - + +
72H ARG* 4.6 5.2 - - - +
75H SER* 4.1 16.4 - - - +
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Residues in contact with LEU 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E GLY 3.3 14.3 + - - +
77E LEU* 2.8 25.0 + - + +
79E LEU* 1.3 78.5 - - - +
81E ILE* 1.3 54.6 + - - +
83E LEU* 2.7 33.8 + - - +
84E LEU* 3.4 7.7 + - - +
90E LEU* 3.9 13.0 - - + +
93E HIS* 3.6 24.0 - - + +
94E LEU* 3.3 30.7 - - + -
97E LEU* 3.8 19.5 - - + -
139E PHE* 6.3 0.4 - - + -
142E LEU* 4.3 21.5 - - + -
146E ILE* 4.4 6.3 - - + -
160E HEM 4.3 7.4 - - + -
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Residues in contact with ILE 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ILE* 3.9 30.3 - - + -
16E ARG* 4.5 16.1 - - + +
19E TRP* 3.3 61.5 - - + -
77E LEU* 3.0 15.1 + - + +
78E LYS 3.7 6.1 - - - +
80E LEU* 1.3 78.2 - - + +
82E ASN* 1.3 58.6 + - - +
83E LEU 2.7 10.6 + - - -
84E LEU* 3.0 33.4 + - + +
85E ASP 4.9 0.2 + - - -
135E TRP* 4.0 10.8 - - + -
142E LEU* 5.2 6.7 - - + +
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Residues in contact with ASN 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ARG* 5.3 6.0 - - - +
19E TRP* 4.9 2.4 - - - -
20E ASP* 5.1 2.9 - - - +
78E LYS* 2.8 34.1 + - - +
79E LEU* 3.7 6.7 - - + +
80E LEU 3.2 0.2 - - - -
81E ILE* 1.3 76.4 - - - +
83E LEU* 1.3 64.9 + - + +
85E ASP* 5.2 0.6 - - - +
86E ASP* 5.0 1.7 - - - +
27H HIS* 3.6 11.1 - - - +
28H ALA* 2.8 56.3 + - - +
31H ARG* 2.9 45.3 - - - +
32H VAL* 5.3 1.0 - - - +
71H GLN* 5.6 1.2 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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