Contacts of the helix formed by residues 62 - 75 (chain F) in PDB entry 3TGX
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 ASN 62 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TRP 5.7 1.1 - - - -
22A ASN* 4.3 15.8 + - - +
23A LEU* 5.3 4.5 - - - +
61F GLY* 1.3 71.9 - - - -
63F ASN* 1.3 81.3 + - - +
64F GLU 3.1 1.8 + - - -
65F ARG* 3.3 18.8 + - - +
66F ILE* 4.3 10.8 + - - +
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Residues in contact with ASN 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E PRO* 5.9 0.3 - - - +
23F TYR* 3.9 24.9 + - + -
26F ASP* 3.5 28.4 + - + +
60F THR* 5.0 1.1 - - - +
61F GLY 2.9 3.5 + - - +
62F ASN* 1.3 93.6 + - - +
64F GLU* 1.3 58.3 - - - +
65F ARG 3.1 0.2 - - - -
66F ILE* 2.9 18.4 + - - +
67F ILE* 2.8 43.2 + - + +
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Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F SER* 4.0 10.9 + - - +
58F ALA 3.6 9.0 - - - +
59F ASN* 2.9 17.6 + - - -
60F THR* 2.3 54.9 + - - +
61F GLY 3.7 7.0 - - - +
62F ASN 3.1 1.0 + - - -
63F ASN* 1.3 77.6 - - - +
65F ARG* 1.3 57.6 + - - +
67F ILE* 4.3 7.9 - - + -
68F ASN* 2.7 45.7 + - - +
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Residues in contact with ARG 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E GLN* 5.7 3.6 - - - +
65E ASP* 5.1 4.4 + - - -
67E PHE* 3.7 29.3 - - - -
68E HIS* 4.7 7.7 + - - -
127E ALA* 6.1 2.4 - - - +
62F ASN 3.3 11.2 + - - +
63F ASN 3.1 0.2 - - - -
64F GLU* 1.3 79.9 - - - +
66F ILE* 1.3 63.4 + - + +
68F ASN* 4.3 3.7 - - - +
69F VAL* 3.4 30.5 + - + +
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Residues in contact with ILE 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E ASP* 5.3 0.2 - - - +
126E PRO* 3.6 25.1 - - + +
127E ALA* 3.6 40.8 - - + +
129E TYR* 5.3 1.7 - - + -
19F GLN* 3.9 17.0 - - - +
23F TYR* 3.8 24.2 - - + +
62F ASN* 4.9 9.2 - - - +
63F ASN* 2.9 25.4 + - - +
65F ARG* 1.3 80.0 - - + +
67F ILE* 1.3 62.0 + - - +
69F VAL* 3.7 6.0 + - - +
70F SER* 3.5 21.1 + - - -
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Residues in contact with ILE 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F GLN* 5.6 0.2 - - - +
20F LEU* 4.4 10.9 - - + +
23F TYR* 3.7 35.2 - - + +
26F ASP* 3.7 30.3 - - + -
27F LEU* 3.8 13.5 - - + -
57F SER* 3.6 28.3 - - - -
60F THR* 5.4 0.7 - - - +
63F ASN* 2.8 27.2 + - + +
64F GLU* 3.8 3.6 - - - +
66F ILE* 1.3 71.3 - - - +
68F ASN* 1.3 60.6 + - - +
69F VAL 3.2 0.2 - - - -
70F SER* 3.1 4.2 + - - +
71F ILE* 2.9 46.1 + - + +
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Residues in contact with ASN 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F SER* 3.6 23.4 + - - +
64F GLU* 2.7 39.0 + - - +
65F ARG* 4.3 4.3 - - - +
67F ILE* 1.3 73.5 - - - +
69F VAL* 1.3 61.7 + - - +
71F ILE* 3.9 12.2 - - - +
72F LYS* 3.2 41.2 + - - +
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Residues in contact with VAL 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E PHE* 4.4 13.2 - - + +
68E HIS* 3.9 35.2 - - + +
129E TYR* 5.7 0.7 - - + +
130E MET* 4.9 6.3 - - + -
65F ARG* 3.4 21.1 + - + +
66F ILE* 3.8 7.0 - - - +
67F ILE 3.2 0.4 - - - -
68F ASN* 1.3 78.1 - - - +
70F SER* 1.3 66.2 + - - +
72F LYS* 3.3 12.1 + - - +
73F LYS* 3.2 47.5 + - - +
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Residues in contact with SER 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E TYR* 3.3 11.8 + - - -
16F ILE* 3.8 18.7 - - - +
19F GLN* 2.5 33.1 + - - -
20F LEU* 4.1 15.0 - - - -
66F ILE 3.5 4.7 + - - -
67F ILE 3.1 8.5 + - - -
69F VAL* 1.3 79.8 - - - +
71F ILE* 1.3 60.3 + - - +
73F LYS* 3.4 8.6 + - - +
74F LEU* 3.1 30.0 + - - +
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Residues in contact with ILE 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU* 4.7 5.6 - - + -
27F LEU* 4.5 1.6 - - + -
55F LEU* 3.4 47.8 - - + +
56F LYS* 4.0 14.1 - - + -
57F SER 4.1 2.7 - - - +
67F ILE* 2.9 39.7 + - + +
68F ASN* 4.0 13.5 - - - +
70F SER* 1.3 74.8 - - - +
72F LYS* 1.3 65.9 + - + +
74F LEU* 3.2 18.9 + - + +
75F LYS* 3.3 27.1 + - + +
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Residues in contact with LYS 72 (chain F).
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* 6.1 5.6 - - - -
42E GLU* 5.6 6.3 - - - +
68F ASN* 3.2 33.6 + - - +
69F VAL* 3.3 10.0 + - + +
71F ILE* 1.3 76.3 - - + +
73F LYS* 1.3 64.0 + - + +
75F LYS* 3.2 18.3 + - - +
76F ARG* 3.4 16.3 + - - +
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Residues in contact with LYS 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E TYR* 4.5 1.2 + - - -
67E PHE 3.1 22.7 + - - -
68E HIS 3.3 28.0 - - - +
69E PHE 3.6 11.7 + - - -
70E MET* 3.8 30.4 - - + +
129E TYR* 4.4 5.4 + - - +
130E MET* 3.4 23.4 - - - +
12F GLN* 5.4 2.4 - - - +
13F LEU* 4.2 7.2 - - - +
16F ILE* 3.7 24.5 - - + +
69F VAL* 3.2 23.8 + - + +
70F SER* 3.6 10.1 - - - +
72F LYS* 1.3 75.0 - - + +
74F LEU* 1.3 66.1 + - - +
76F ARG* 3.1 25.9 + - - +
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Residues in contact with LEU 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LEU* 4.1 21.0 - - + +
16F ILE* 3.8 20.4 - - + -
17F VAL* 4.1 22.7 - - + -
20F LEU* 3.5 28.7 - - + -
47F PHE* 5.3 0.9 - - - -
51F GLN* 2.9 32.3 + - + +
55F LEU* 4.2 15.5 - - + -
70F SER 3.1 16.7 + - - +
71F ILE* 3.2 15.2 + - + +
73F LYS* 1.3 76.7 - - - +
75F LYS* 1.3 58.9 + - + +
76F ARG 3.4 1.0 + - - +
108F LEU* 5.5 0.4 - - + -
111F PHE* 4.4 22.1 - - + -
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Residues in contact with LYS 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E GLU* 4.8 1.9 - - - +
51F GLN* 3.7 35.6 + - + +
52F LYS* 6.1 1.3 - - - +
53F ALA 5.7 2.5 - - - +
71F ILE* 3.3 25.1 + - + +
72F LYS* 3.2 12.2 + - - +
73F LYS 3.2 0.8 - - - -
74F LEU* 1.3 77.6 - - + +
76F ARG* 1.3 62.6 + - - +
77F LYS* 3.7 1.6 + - - +
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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