Contacts of the helix formed by residues 58 - 73 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E LEU* 1.3 75.1 - - - +
59E SER* 1.3 59.0 + - - +
60E ASP* 2.7 29.1 + - - +
61E GLU* 2.6 49.3 + - - +
62E LEU* 3.0 9.2 + - - +
87E ASP* 3.2 16.8 - - - +
90E PHE* 4.2 5.2 - - - -
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Residues in contact with SER 59 (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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58E ASN* 1.3 73.7 + - - +
60E ASP* 1.3 63.0 + - - +
62E LEU* 3.3 2.8 + - - +
63E GLN* 2.8 25.2 + - - +
87E ASP* 4.0 2.8 + - - -
89E SER* 2.9 36.5 + - - -
90E PHE* 4.4 10.1 - - - +
93E MET* 3.2 25.9 - - - +
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Residues in contact with ASP 60 (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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58E ASN* 2.7 23.4 + - - +
59E SER* 1.3 75.9 + - - +
61E GLU* 1.3 64.6 + - + +
63E GLN* 3.1 8.5 + - - +
64E GLU* 2.9 25.5 + - - +
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Residues in contact with GLU 61 (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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55A GLN* 3.7 37.1 + - - +
56E VAL 3.0 24.8 - - - +
57E LEU* 3.1 19.5 - - + +
58E ASN* 2.6 37.4 + - - +
60E ASP* 1.3 74.3 - - + +
62E LEU* 1.3 60.5 + - - +
64E GLU* 3.4 12.3 - - - +
65E LEU* 3.4 20.8 - - - +
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Residues in contact with LEU 62 (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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10E ILE* 4.8 5.8 - - + -
38E VAL* 3.8 33.2 - - + -
57E LEU* 4.5 0.8 - - - +
58E ASN 3.0 5.5 + - - -
59E SER* 3.7 7.4 - - - +
61E GLU* 1.3 76.5 - - - +
63E GLN* 1.3 65.5 + - - +
65E LEU* 3.3 9.1 + - + +
66E TYR* 2.9 21.6 + - + +
90E PHE* 3.4 35.0 - - + +
93E MET* 3.9 22.9 - - + -
94E VAL* 4.0 20.9 - - + -
97E ILE* 3.9 21.1 - - + -
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Residues in contact with GLN 63 (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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59E SER 2.8 17.9 + - - +
60E ASP* 3.4 10.5 - - - +
62E LEU* 1.3 76.4 - - - +
64E GLU* 1.3 53.9 + - - +
66E TYR* 2.9 16.6 + - - +
67E ASP* 2.5 74.5 + - - +
93E MET* 2.7 35.3 - - - +
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Residues in contact with GLU 64 (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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53A LYS* 3.5 27.9 - - + +
54A GLY 2.9 22.6 - - - +
55A GLN* 2.6 30.6 - - - +
197B ASP* 3.2 22.5 - - - +
198B TYR* 5.2 4.9 + - - -
224B HIS* 5.3 4.3 - - - -
60E ASP 2.9 12.9 + - - +
61E GLU* 3.4 11.7 - - - +
63E GLN* 1.3 76.0 - - - +
65E LEU* 1.3 52.5 + - - +
67E ASP* 3.4 6.9 - - - +
68E GLY 2.7 31.2 + - - -
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Residues in contact with LEU 65 (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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15A VAL* 4.1 12.3 - - + -
42A GLN* 3.6 48.5 - - - +
43A PHE 3.8 20.4 - - - +
44A SER* 3.6 7.1 - - - +
53A LYS 5.0 0.4 - - - -
54A GLY* 3.9 10.1 - - - -
55A GLN* 3.7 12.6 - - - +
38E VAL* 4.0 16.6 - - + -
57E LEU* 4.0 8.3 - - + -
61E GLU 3.4 15.9 - - - +
62E LEU* 3.3 10.0 + - + +
64E GLU* 1.3 77.8 - - - +
66E TYR* 1.3 68.0 + - - +
68E GLY* 2.9 11.3 + - - +
69E LEU* 2.9 19.7 + - + +
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Residues in contact with TYR 66 (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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8E LEU* 5.2 6.5 - - + -
62E LEU* 2.9 14.1 + - + +
63E GLN* 2.9 21.1 + - - +
65E LEU* 1.3 75.7 - - - +
67E ASP* 1.3 54.6 + - - +
69E LEU* 2.9 19.5 + - + +
70E LYS* 2.5 43.0 + - + +
75E ASN* 3.4 31.4 + - + -
77E TYR* 5.2 1.1 - + - -
97E ILE* 3.6 49.4 - - + +
100E GLU* 3.3 35.8 + - - +
101E LEU* 3.4 23.5 - - + +
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Residues in contact with ASP 67 (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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53A LYS* 4.6 14.6 - - + +
63E GLN* 2.5 58.9 + - - +
64E GLU* 3.4 7.1 - - - +
66E TYR* 1.3 73.3 - - - +
68E GLY* 1.3 55.3 + - - +
70E LYS* 2.9 11.5 + - - +
71E LEU* 2.6 43.8 + - + +
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Residues in contact with GLY 68 (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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44A SER* 3.7 19.5 - - - -
45A ASN* 4.8 0.2 - - - -
52A TRP* 5.3 1.3 - - - -
53A LYS* 4.4 9.6 - - - +
64E GLU 2.7 18.5 + - - -
65E LEU 2.9 5.7 + - - -
67E ASP* 1.3 75.8 - - - +
69E LEU* 1.3 59.8 + - - +
71E LEU* 3.5 11.3 + - - +
72E ASN* 3.2 28.2 + - - -
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Residues in contact with LEU 69 (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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15A VAL* 4.1 18.8 - - + -
16A ARG* 3.8 29.2 - - + -
44A SER* 3.9 17.2 - - - +
45A ASN* 4.9 1.8 - - - +
8E LEU* 5.1 4.9 - - + -
36E ASP* 4.7 0.2 - - - +
38E VAL* 5.4 3.1 - - + -
65E LEU 2.9 18.0 + - - +
66E TYR* 3.4 22.2 - - + +
68E GLY* 1.3 71.7 - - - +
70E LYS* 1.3 71.7 + - - +
72E ASN 3.1 2.1 + - - -
73E HIS 3.0 14.4 + - - -
74E VAL* 3.1 29.2 + - + +
75E ASN* 4.4 10.8 - - + +
77E TYR* 3.5 25.4 - - + +
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Residues in contact with LYS 70 (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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66E TYR* 2.5 25.5 + - + +
67E ASP* 3.1 18.2 - - - +
69E LEU* 1.3 71.5 - - - +
71E LEU* 1.3 56.7 + - + +
73E HIS* 2.6 40.0 + - - -
75E ASN* 3.1 37.4 + - - +
100E GLU* 4.0 13.9 + - - +
104E GLN* 3.8 12.3 + - - +
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Residues in contact with LEU 71 (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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51A HIS* 4.0 46.7 + - + +
53A LYS* 3.6 35.2 - - + +
67E ASP* 2.6 27.8 + - + +
68E GLY* 3.6 7.6 - - - +
70E LYS* 1.3 74.4 - - + +
72E ASN* 1.3 59.3 + - - +
73E HIS* 3.7 15.8 + - - -
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Residues in contact with ASN 72 (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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45A ASN* 3.4 12.9 + - - +
49A TYR* 3.9 23.1 - - + +
50A SER* 4.1 4.7 + - - -
51A HIS* 3.0 47.2 + - - +
287A ALA* 5.9 1.8 - - + +
68E GLY 3.2 18.8 + - - +
69E LEU 3.1 2.0 + - - +
70E LYS 2.8 2.4 + - - -
71E LEU* 1.3 75.5 - - - +
73E HIS* 1.3 80.7 + - - +
74E VAL* 3.9 22.3 - - + +
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Residues in contact with HIS 73 (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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70E LYS* 2.6 30.0 + - - -
71E LEU* 3.9 14.1 + - - -
72E ASN* 1.3 80.9 - - - +
74E VAL* 1.3 61.4 + - - +
75E ASN* 3.4 10.3 - - - -
76E GLN* 3.7 17.5 - - - +
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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