Contacts of the helix formed by residues 58 - 73 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LEU* 1.3 75.2 - - - +
59C SER* 1.3 58.2 + - - +
60C ASP* 2.8 27.4 + - - +
61C GLU* 2.6 50.4 + - - +
62C LEU* 3.0 8.5 + - - +
87C ASP* 3.3 17.3 - - - +
90C PHE* 4.2 4.7 - - - -
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ASN* 1.3 72.6 - - - +
60C ASP* 1.3 63.4 + - - +
62C LEU* 3.4 2.6 + - - -
63C GLN* 2.9 24.3 + - - +
87C ASP* 4.1 2.4 + - - -
89C SER* 2.9 37.1 + - - -
90C PHE* 4.3 11.1 - - - +
93C MET* 3.1 27.3 - - - +
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Residues in contact with ASP 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN* 2.8 23.1 + - - +
59C SER* 1.3 77.3 + - - +
61C GLU* 1.3 58.5 + - + +
63C GLN* 3.1 8.2 + - - +
64C GLU* 2.9 31.7 + - - +
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C VAL 2.8 26.5 - - - +
57C LEU* 3.0 16.4 - - + -
58C ASN* 2.6 36.8 + - - +
60C ASP* 1.3 73.9 - - + +
62C LEU* 1.3 59.8 + - - +
64C GLU* 3.5 9.7 - - - +
65C LEU* 3.4 14.4 - - - +
55H GLN* 3.4 51.2 + - - +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 5.0 6.1 - - + -
38C VAL* 3.8 33.0 - - + -
57C LEU* 4.4 1.0 - - - +
58C ASN 3.0 5.3 + - - -
59C SER 3.7 7.4 - - - +
61C GLU* 1.3 76.7 - - - +
63C GLN* 1.3 65.3 + - - +
65C LEU* 3.3 8.6 + - + +
66C TYR* 3.0 21.6 + - + +
90C PHE* 3.4 36.1 - - + +
93C MET* 3.8 24.0 - - + -
94C VAL* 3.9 20.6 - - + -
97C ILE* 3.9 22.2 - - + -
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Residues in contact with GLN 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C SER 2.9 14.3 + - - +
60C ASP* 3.1 13.2 + - - +
62C LEU* 1.3 74.4 - - - +
64C GLU* 1.3 58.1 + - - +
66C TYR* 3.1 16.4 + - - +
67C ASP* 2.6 73.2 + - - +
93C MET* 2.6 33.9 - - + +
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Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASP 2.9 12.5 + - - +
61C GLU* 3.5 11.1 - - - +
63C GLN* 1.3 75.0 - - - +
65C LEU* 1.3 52.3 + - - +
67C ASP* 3.2 2.3 + - - +
68C GLY 2.7 31.0 + - - -
53H LYS* 2.9 35.6 - - + +
54H GLY* 2.6 33.9 - - - +
55H GLN* 2.7 23.4 - - - +
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C VAL* 3.7 18.8 - - + -
57C LEU* 4.0 3.1 - - + -
61C GLU 3.4 11.7 - - - +
62C LEU* 3.6 9.2 - - + +
63C GLN 3.3 0.6 - - - -
64C GLU* 1.3 80.4 - - - +
66C TYR* 1.3 62.9 + - - +
68C GLY 2.9 2.8 + - - -
69C LEU* 2.9 6.2 + - + +
15H VAL* 3.8 11.7 - - + -
42H GLN* 3.1 59.7 - - - +
43H PHE* 3.3 22.9 - - - +
44H SER* 2.8 29.3 - - - +
53H LYS 4.3 0.2 - - - -
54H GLY* 3.5 8.7 - - - -
55H GLN* 3.8 11.2 - - - +
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Residues in contact with TYR 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 5.2 6.7 - - + -
62C LEU* 3.0 18.5 + - + +
63C GLN* 3.6 17.0 - - - +
65C LEU* 1.3 72.5 - - - +
67C ASP* 1.3 56.8 + - - +
69C LEU* 3.1 18.3 + - + +
70C LYS* 2.6 44.8 + - + +
75C ASN* 3.4 23.5 + - + -
77C TYR* 5.2 1.1 - + - -
97C ILE* 3.5 51.0 + - + +
100C GLU* 3.4 33.9 + - - +
101C LEU* 3.2 31.4 - - + +
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Residues in contact with ASP 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLN* 2.6 59.1 + - - +
64C GLU* 3.4 4.8 + - - +
66C TYR* 1.3 72.8 - - - +
68C GLY* 1.3 56.7 + - - +
70C LYS* 2.9 9.8 + - - +
71C LEU* 2.5 43.0 + - + +
53H LYS* 4.0 22.8 - - + +
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Residues in contact with GLY 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C GLU 2.7 17.4 + - - -
65C LEU 2.9 2.6 + - - -
67C ASP* 1.3 74.8 - - - +
69C LEU* 1.3 61.8 + - - +
71C LEU* 3.4 6.9 + - - +
72C ASN* 3.1 26.3 + - - -
44H SER* 3.1 22.4 - - - -
45H ASN* 3.5 0.4 - - - -
52H TRP* 4.5 1.6 - - - -
53H LYS* 4.0 15.6 - - - +
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 4.9 3.4 - - + -
38C VAL* 5.4 1.1 - - + -
65C LEU 2.9 17.2 + - - +
66C TYR* 3.6 20.4 - - + +
68C GLY* 1.3 71.9 - - - +
70C LYS* 1.3 69.7 + - - +
72C ASN 3.1 1.9 + - - -
73C HIS 3.0 13.9 + - - -
74C VAL* 3.1 27.6 + - + +
75C ASN* 4.4 11.0 - - + +
77C TYR* 3.4 22.2 - - + +
15H VAL* 3.7 19.3 - - + -
16H ARG* 3.3 25.6 - - + +
44H SER* 3.1 30.9 - - - +
45H ASN* 3.9 2.5 - - - +
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Residues in contact with LYS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TYR* 2.6 26.3 + - + +
67C ASP* 2.9 17.2 + - - +
69C LEU* 1.3 70.8 - - - +
71C LEU* 1.3 57.9 + - + +
73C HIS* 2.5 38.6 + - - -
75C ASN* 3.1 38.6 + - + +
100C GLU* 3.8 15.4 + - - +
104C GLN* 3.7 12.1 + - - +
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ASP* 2.5 27.1 + - + +
68C GLY* 3.5 2.9 - - - +
70C LYS* 1.3 73.7 - - + +
72C ASN* 1.3 57.0 + - - +
73C HIS* 3.6 17.3 + - - -
51H HIS* 3.1 64.3 + - + +
53H LYS* 3.5 38.1 - - + +
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Residues in contact with ASN 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C GLY 3.1 7.3 + - - -
69C LEU 3.1 1.8 + - - +
70C LYS 2.8 2.4 + - - -
71C LEU* 1.3 72.7 - - - +
73C HIS* 1.3 80.1 + - - +
74C VAL* 3.8 18.3 - - + +
45H ASN* 3.0 23.8 + - - +
49H TYR* 2.8 38.3 - - + +
50H SER* 3.2 16.8 + - - -
51H HIS 2.5 32.8 + - - -
286H PRO* 5.8 0.2 - - - +
287H ALA* 5.0 4.3 - - - +
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Residues in contact with HIS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C LYS* 2.5 27.8 + - - -
71C LEU* 3.8 15.0 + - - -
72C ASN* 1.3 81.1 - - - +
74C VAL* 1.3 60.2 + - - +
75C ASN* 3.4 11.7 - - - -
76C GLN* 3.5 19.6 + - - +
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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