Contacts of the helix formed by residues 58 - 77 (chain F) 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 HIS 58 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F HIS* 3.2 44.6 + + + -
55F ASP* 2.9 29.3 + - + +
56F THR 3.4 0.2 - - - -
57F SER* 1.3 77.6 - - - +
59F PRO* 1.3 85.2 - - + +
60F ALA* 2.7 45.0 + - + +
61F PHE* 2.8 14.9 + - - -
62F ILE* 2.9 10.4 + - - -
158M HIS* 6.0 5.6 - + - -
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Residues in contact with PRO 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F SER 3.6 4.8 - - - +
58F HIS* 1.3 104.0 - - + +
60F ALA* 1.3 62.0 + - - +
62F ILE* 2.9 12.1 + - + +
63F ALA* 2.7 25.5 + - - +
87G ASP* 4.8 0.7 - - - +
89G PRO* 3.5 25.4 - - + +
90G ALA* 3.4 32.1 - - + +
93G ALA* 4.4 1.3 - - + -
158M HIS* 5.8 7.9 - - + -
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Residues in contact with ALA 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F VAL* 3.2 19.6 - - + +
52F HIS* 3.8 17.0 - - + +
58F HIS* 2.7 30.0 + - + +
59F PRO* 1.3 74.2 - - - +
61F PHE* 1.3 56.4 + - - +
63F ALA* 3.2 4.3 - - - +
64F HIS 3.0 21.1 + - - -
67F ARG* 4.6 1.0 + - - -
93G ALA* 3.9 17.3 - - + +
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Residues in contact with PHE 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F GLN* 5.2 1.8 - - - -
34F TRP* 3.7 35.4 - + + -
38F PHE* 3.6 32.3 - + - -
48F PHE* 4.6 3.8 - + + -
51F VAL* 3.4 18.5 + - + +
52F HIS 3.4 21.5 - - - +
53F GLY* 4.3 6.1 - - - -
55F ASP 4.0 3.4 - - - +
56F THR* 3.0 44.0 - - - -
58F HIS* 2.8 13.1 + - + +
60F ALA* 1.3 73.8 - - - +
62F ILE* 1.3 57.6 + - + +
64F HIS* 3.0 26.6 + + - +
65F ALA* 2.7 36.7 + - + +
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Residues in contact with ILE 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F GLU* 4.0 34.3 - - + +
30F SER* 5.1 1.6 + - - +
31F GLN* 3.6 41.1 - - + +
56F THR 3.9 6.1 - - - +
57F SER* 4.0 12.6 - - - +
58F HIS 2.9 16.8 + - - +
59F PRO* 3.3 11.9 - - + +
61F PHE* 1.3 75.7 - - + +
63F ALA* 1.3 65.9 + - - +
65F ALA* 3.3 7.0 + - + +
66F ASP* 2.9 24.3 + - - +
84G LEU* 4.8 7.0 - - + -
87G ASP* 5.1 2.5 - - - +
90G ALA* 3.8 18.2 - - + -
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Residues in contact with ALA 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F PRO 2.7 11.2 + - - +
60F ALA 3.2 11.2 - - - +
62F ILE* 1.3 79.9 - - - +
64F HIS* 1.3 66.6 + - - +
66F ASP* 3.0 2.1 + - - +
67F ARG* 2.7 38.8 + - - +
80G LEU* 4.8 1.0 - - - +
84G LEU* 4.2 13.7 - - - -
90G ALA* 3.9 3.6 - - - +
93G ALA* 4.3 2.9 - - + -
94G ALA* 3.7 31.0 - - + +
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Residues in contact with HIS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F TRP* 4.1 3.4 - + - -
48F PHE* 3.2 20.6 - + - -
51F VAL* 3.4 25.8 - - + +
60F ALA 3.0 2.0 + - - -
61F PHE* 3.0 34.1 + + - +
63F ALA* 1.3 79.3 - - - +
65F ALA* 1.3 53.6 + - - +
67F ARG* 2.9 29.5 + - - +
68F VAL* 2.8 48.6 + - + +
160F HEM 3.7 36.4 + - + +
161F CMO 3.3 22.5 + - - -
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Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F SER* 3.9 15.5 - - - +
31F GLN* 5.1 2.2 - - + +
34F TRP* 3.5 35.9 - - + +
61F PHE* 2.7 21.7 + - + +
62F ILE* 3.5 12.3 - - + +
64F HIS* 1.3 72.5 - - - +
66F ASP* 1.3 57.7 + - - +
68F VAL* 2.7 23.6 + - - +
69F LEU* 3.0 18.4 + - - +
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Residues in contact with ASP 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F TYR* 4.3 2.8 + - - -
23F GLY 5.2 0.5 - - - +
26F ARG* 3.2 32.1 + - - +
27F GLU* 3.7 28.4 + - - +
30F SER* 4.3 8.4 + - - -
62F ILE* 2.9 17.3 + - - +
63F ALA 3.5 3.4 - - - +
65F ALA* 1.3 76.6 - - - +
67F ARG* 1.3 59.0 + - - +
69F LEU* 3.9 4.8 + - - +
70F GLY* 3.3 16.5 + - - -
80G LEU* 3.6 22.8 - - + +
83G ASN* 4.9 2.9 - - - +
84G LEU* 3.5 26.0 - - + +
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Residues in contact with ARG 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F ARG* 4.9 1.6 - - - +
51F VAL* 4.4 6.7 - - - +
60F ALA 4.6 1.4 + - - -
63F ALA* 2.7 26.6 + - - +
64F HIS* 3.0 57.7 + - - +
65F ALA 2.8 0.2 + - - -
66F ASP* 1.3 71.8 - - - +
68F VAL* 1.3 64.4 + - + +
70F GLY* 3.4 8.4 + - - -
71F GLY 3.6 7.3 + - - -
160F HEM 3.9 33.6 + - + +
80G LEU* 3.9 26.2 - - + +
93G ALA 5.0 0.6 + - - -
94G ALA* 4.4 5.5 - - - +
97G HIS* 3.5 57.6 + - - +
98G LEU* 5.9 4.3 - - - -
101G GLN* 5.9 0.2 - - - -
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Residues in contact with VAL 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F TRP* 4.2 5.2 - - + +
64F HIS* 2.8 37.4 + - + +
65F ALA* 2.7 13.4 + - - +
67F ARG* 1.3 69.0 - - - +
69F LEU* 1.3 71.2 + - + +
70F GLY 2.9 1.6 - - - -
71F GLY* 2.8 14.2 + - - -
72F LEU* 3.2 9.4 + - + +
109F PHE* 4.2 18.8 - - + -
160F HEM 3.6 38.9 - - + +
161F CMO 3.2 29.4 - - - +
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TRP* 3.7 27.2 - - + -
20F TYR* 4.0 22.9 - - + +
26F ARG* 5.8 0.4 - - + -
29F PHE* 3.9 15.7 - - + -
30F SER* 3.6 29.4 - - - -
33F ILE* 4.0 15.7 - - + -
34F TRP* 4.4 9.9 - - + +
65F ALA 3.0 17.5 + - - +
66F ASP* 4.1 4.7 - - - +
68F VAL* 1.3 84.5 - - + +
70F GLY* 1.3 51.6 + - - +
72F LEU* 2.9 16.5 + - + +
73F ASP* 2.7 34.5 + - - +
109F PHE* 5.4 6.5 - - + -
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Residues in contact with GLY 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F TYR* 3.9 10.7 + - - -
66F ASP 3.3 13.1 + - - -
67F ARG* 3.6 6.5 - - - -
68F VAL 2.9 2.8 - - - -
69F LEU* 1.3 77.9 - - - +
71F GLY* 1.3 61.5 + - - -
73F ASP* 3.0 20.0 - - - +
74F ILE* 3.1 11.0 + - - +
76G ASN* 3.5 20.7 + - - -
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Residues in contact with GLY 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ARG 3.6 6.3 + - - -
68F VAL 2.8 13.4 + - - -
70F GLY* 1.3 71.1 - - - -
72F LEU* 1.3 62.3 + - - -
74F ILE* 2.8 18.9 + - - +
75F ALA* 2.8 21.9 + - - +
88F GLU* 4.3 11.3 - - - +
92F LEU* 4.9 4.7 - - - -
160F HEM 4.6 16.5 - - - +
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TRP* 3.6 28.3 - - + -
68F VAL* 3.2 7.3 + - + +
69F LEU* 2.9 19.4 + - + +
71F GLY* 1.3 74.8 - - - +
73F ASP* 1.3 62.8 + - - +
75F ALA* 3.3 3.8 + - - +
76F ILE* 2.9 49.8 + - + +
109F PHE* 5.1 3.1 - - + -
113F ILE* 3.5 28.9 - - + -
134F ILE* 4.1 14.1 - - + -
137F ILE* 4.1 19.1 - - + -
160F HEM 4.0 24.9 - - + +
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Residues in contact with ASP 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TRP* 3.2 23.2 + - - +
20F TYR* 3.6 29.3 - - + -
69F LEU 2.7 14.7 + - - +
70F GLY* 3.0 13.5 - - - +
72F LEU* 1.3 71.8 - - - +
74F ILE* 1.3 68.7 + - - +
75F ALA 2.9 0.9 + - - -
76F ILE* 4.9 0.2 - - - -
77F SER* 2.6 37.3 + - - -
28G SER* 5.2 1.4 + - - -
32G LYS* 3.0 29.1 + - - -
76G ASN* 3.6 5.5 - - - +
79G ASP* 5.1 1.2 - - - +
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Residues in contact with ILE 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F GLY 3.4 13.7 - - - +
71F GLY* 2.8 11.9 + - - +
73F ASP* 1.3 73.0 - - - +
75F ALA* 1.3 54.8 + - - +
77F SER* 2.8 17.3 + - - -
78F THR* 2.7 27.6 + - + +
84F THR* 6.2 0.2 - - + -
88F GLU* 3.6 42.2 - - + +
69G ALA* 5.1 0.9 - - - +
72G LEU* 3.3 32.5 - - + -
73G ARG* 3.9 30.7 - - + +
76G ASN* 4.1 19.5 - - + +
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Residues in contact with ALA 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F GLY 2.8 11.5 + - - +
72F LEU* 3.3 11.7 - - - +
73F ASP 2.9 0.6 + - - -
74F ILE* 1.3 74.7 - - - +
76F ILE* 1.3 66.7 + - - +
78F THR* 2.8 18.9 + - - -
79F LEU* 3.5 5.9 + - - +
85F LEU* 3.5 20.2 - - + +
88F GLU* 4.3 6.7 - - + +
89F LEU* 4.4 5.2 - - + -
92F LEU* 5.3 2.5 - - + -
137F ILE* 3.5 36.6 - - + -
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Residues in contact with ILE 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 4.1 6.5 - - + -
13F LYS* 3.6 36.0 - - + +
16F TRP* 3.4 50.9 - - + -
72F LEU* 2.9 33.5 + - + +
73F ASP 3.8 1.6 - - - +
75F ALA* 1.3 76.4 - - - +
77F SER* 1.3 54.3 + - - +
78F THR 2.6 12.6 + - - -
79F LEU* 2.9 35.4 + - + +
130F TRP* 4.5 8.5 - - + -
133F CYS* 6.4 0.2 - - + -
134F ILE* 4.5 5.2 - - + -
137F ILE* 3.5 17.2 - - + +
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Residues in contact with SER 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LYS* 3.4 24.6 + - - +
16F TRP* 5.5 1.5 - - - -
73F ASP* 2.6 39.5 + - - -
74F ILE* 2.8 20.1 + - - -
76F ILE* 1.3 70.1 - - - +
78F THR* 1.3 58.8 + - - +
79F LEU 3.8 0.2 - - - -
28G SER* 4.2 17.5 - - - -
29G SER* 3.1 29.2 + - - -
32G LYS* 5.6 2.6 + - - +
72G LEU* 4.9 2.8 - - - +
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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