Contacts of the helix formed by residues 58 - 73 (chain F) in PDB entry 1RFU
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 58 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F LEU* 1.3 76.1 - - - +
59F SER* 1.3 59.3 + - - +
60F ASP* 2.7 29.7 + - - +
61F GLU* 2.7 48.7 + - - +
62F LEU* 2.9 10.2 + - - +
87F ASP* 3.3 16.2 - - - +
89F SER* 5.8 0.2 - - - -
90F PHE* 4.2 5.4 - - - -
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Residues in contact with SER 59 (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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58F ASN* 1.3 73.3 - - - +
60F ASP* 1.3 60.6 + - - +
62F LEU* 3.4 2.9 + - - +
63F GLN* 2.9 24.0 + - - +
87F ASP* 4.2 1.8 + - - -
89F SER* 2.9 37.7 + - - -
90F PHE* 4.3 10.5 - - - +
93F MET* 3.2 27.6 - - - +
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Residues in contact with ASP 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F ASN* 2.7 23.8 + - - +
59F SER* 1.3 74.7 - - - +
61F GLU* 1.3 57.7 + - + +
63F GLN* 3.1 8.3 + - - +
64F GLU* 2.9 31.6 + - - +
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Residues in contact with GLU 61 (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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55B GLN* 3.8 34.3 + - - +
56F VAL 3.0 25.6 - - - +
57F LEU* 3.1 20.3 - - + -
58F ASN* 2.7 37.1 + - - +
60F ASP* 1.3 73.8 - - + +
62F LEU* 1.3 61.1 + - - +
64F GLU* 3.4 18.0 - - - +
65F LEU* 3.4 20.4 - - - +
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Residues in contact with LEU 62 (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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10F ILE* 5.0 5.6 - - + -
38F VAL* 3.9 32.5 - - + -
57F LEU* 4.5 1.2 - - - +
58F ASN 2.9 6.3 + - - -
59F SER 3.8 7.6 - - - +
61F GLU* 1.3 73.9 - - - +
63F GLN* 1.3 67.0 + - - +
65F LEU* 3.3 10.1 + - + +
66F TYR* 3.0 21.5 + - + +
90F PHE* 3.4 35.4 - - + +
93F MET* 3.9 13.2 - - + -
94F VAL* 3.8 24.9 - - + -
97F ILE* 3.9 28.3 - - + -
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Residues in contact with GLN 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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59F SER 2.9 18.3 + - - +
60F ASP* 3.1 9.6 + - - +
62F LEU* 1.3 76.7 - - - +
64F GLU* 1.3 54.6 + - - +
66F TYR* 3.0 17.2 + - - -
67F ASP* 2.6 72.7 + - - +
93F MET* 2.5 36.8 - - + +
97F ILE* 6.3 0.2 - - - +
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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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53B LYS* 3.8 26.9 - - + +
54B GLY 3.4 22.0 + - - +
55B GLN* 2.5 31.7 - - - +
197C ASP* 4.6 11.5 - - - +
198C TYR* 4.8 11.1 + - - -
224C HIS* 5.1 4.9 - - - -
60F ASP 2.9 12.9 + - - +
61F GLU* 3.4 13.4 - - - +
63F GLN* 1.3 77.0 - - - +
65F LEU* 1.3 52.6 + - - +
67F ASP* 3.3 6.9 + - - +
68F GLY* 2.7 32.7 + - - -
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Residues in contact with LEU 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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15B VAL* 3.9 15.5 - - + -
42B GLN* 3.7 50.3 - - + +
43B PHE 3.9 18.6 - - - -
44B SER* 3.7 7.7 - - - +
53B LYS 5.1 0.4 - - - -
54B GLY* 4.1 9.2 - - - -
55B GLN* 3.9 9.0 - - - +
38F VAL* 3.9 21.1 - - + -
57F LEU* 4.0 5.8 - - + -
61F GLU 3.4 16.4 - - - +
62F LEU* 3.5 9.4 - - + +
63F GLN 3.2 0.6 - - - -
64F GLU* 1.3 79.6 - - - +
66F TYR* 1.3 64.5 + - - +
68F GLY* 2.8 12.2 + - - +
69F LEU* 2.8 19.4 + - + +
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Residues in contact with TYR 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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8F LEU* 5.1 7.6 - - + -
62F LEU* 3.0 15.8 + - + +
63F GLN* 3.6 20.2 - - - +
65F LEU* 1.3 75.5 - - - +
67F ASP* 1.3 54.2 + - - +
69F LEU* 3.0 18.0 + - + +
70F LYS* 2.5 45.1 + - + +
75F ASN* 3.5 22.0 + - + -
77F TYR* 5.3 1.1 - + - -
97F ILE* 3.5 50.1 + - + +
100F GLU* 3.3 35.3 + - - +
101F LEU* 3.3 30.2 - - + +
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Residues in contact with ASP 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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53B LYS* 4.8 9.0 - - + +
63F GLN* 2.6 58.2 + - - +
64F GLU* 3.4 6.8 - - - +
66F TYR* 1.3 73.8 - - - +
68F GLY* 1.3 55.4 + - - +
70F LYS* 2.8 9.7 + - - +
71F LEU* 2.5 48.7 + - + +
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Residues in contact with GLY 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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44B SER* 3.7 20.0 - - - -
52B TRP* 5.5 1.3 - - - -
53B LYS* 4.5 8.5 - - - +
64F GLU 2.7 19.5 + - - -
65F LEU 2.8 5.6 + - - -
67F ASP* 1.3 74.8 - - - +
69F LEU* 1.3 62.9 + - - +
71F LEU* 3.4 11.9 + - - +
72F ASN* 3.2 27.8 + - - -
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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
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15B VAL* 4.0 20.4 - - + -
16B ARG* 3.8 29.4 - - + -
44B SER* 3.9 16.5 - - - +
45B ASN* 5.1 2.0 - - - +
8F LEU* 5.1 5.2 - - + -
36F ASP* 4.8 0.2 - - - +
38F VAL* 5.4 2.5 - - + -
65F LEU 2.8 18.6 + - - +
66F TYR* 3.5 21.5 - - + +
68F GLY* 1.3 71.5 - - - +
70F LYS* 1.3 71.5 + - - +
72F ASN* 3.0 2.8 + - - -
73F HIS 3.0 14.6 + - - -
74F VAL* 3.2 28.4 + - + +
75F ASN* 4.4 11.0 - - + +
77F TYR* 3.6 23.8 - - + +
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Residues in contact with LYS 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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66F TYR* 2.5 25.9 + - + +
67F ASP* 2.8 17.9 + - - +
69F LEU* 1.3 72.1 - - - +
71F LEU* 1.3 58.0 + - + +
73F HIS* 2.7 37.3 + - - -
75F ASN* 3.0 37.5 + - - +
100F GLU* 3.9 18.5 + - - +
104F GLN* 3.9 8.1 + - - +
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Residues in contact with LEU 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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51B HIS* 4.3 39.7 + - + +
53B LYS* 3.6 35.9 - - + +
67F ASP* 2.5 29.4 + - + +
68F GLY* 3.5 8.7 - - - +
70F LYS* 1.3 74.0 - - + +
72F ASN* 1.3 62.1 + - - +
73F HIS* 3.3 15.8 + - - -
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Residues in contact with ASN 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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45B ASN* 3.5 12.9 + - - +
49B TYR* 3.9 22.3 - - + +
50B SER* 4.4 3.8 + - - -
51B HIS* 3.2 48.4 + - - +
287B ALA* 6.0 1.3 - - + +
68F GLY 3.2 18.2 + - - -
69F LEU 3.0 3.2 + - - +
70F LYS 2.9 0.2 + - - -
71F LEU* 1.3 76.6 - - - +
73F HIS* 1.3 79.7 + - - +
74F VAL* 3.6 23.1 + - + +
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Residues in contact with HIS 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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70F LYS* 2.7 27.6 + - - -
71F LEU* 3.9 14.3 + - - -
72F ASN* 1.3 81.2 - - - +
74F VAL* 1.3 61.2 + - - +
75F ASN* 3.5 9.6 - - - -
76F GLN* 3.6 17.8 - - - +
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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
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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