Contacts of the helix formed by residues 51 - 72 (chain F) in PDB entry 2FYU
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 PRO 51 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ARG 3.6 1.7 - - - +
50F LEU* 1.4 88.1 - - + +
52F GLU* 1.3 67.4 + - - +
53F ASN* 3.3 21.1 - - - +
54F LEU* 3.2 22.4 + - + -
55F TYR* 3.0 20.8 + - - +
93F TYR* 3.4 27.1 - - + +
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Residues in contact with GLU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F LEU 3.9 0.4 + - - -
51F PRO* 1.3 72.2 - - - +
53F ASN* 1.3 64.4 + - - +
55F TYR* 3.4 6.9 + - - +
56F ASP* 3.1 50.9 + - - +
9G ARG* 4.8 8.3 + - - -
11G ARG* 2.8 39.2 + - - +
12G HIS* 4.5 1.8 + - - +
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Residues in contact with ASN 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D TYR* 4.2 0.4 + - - -
241D LYS* 5.9 5.4 - - - +
51F PRO* 3.6 27.1 - - - +
52F GLU* 1.3 77.1 - - - +
54F LEU* 1.3 75.4 + - - +
56F ASP* 3.5 3.9 + - - +
57F ASP* 3.1 41.2 + - - +
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Residues in contact with LEU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F LEU* 4.1 22.6 - - + +
51F PRO* 3.2 27.5 + - + +
53F ASN* 1.3 96.8 - - - +
55F TYR* 1.3 60.6 + - - +
57F ASP* 3.5 11.2 + - - +
58F ARG* 2.9 32.2 + - - +
61F ARG* 4.8 7.4 + - - +
89F TYR* 4.2 32.2 - - + +
93F TYR* 4.6 5.2 - - + +
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Residues in contact with TYR 55 (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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215C VAL* 5.7 0.2 - - - +
47F ILE* 3.7 41.3 - - + -
48F ARG* 5.8 1.3 - - - -
50F LEU* 4.2 16.3 - - + +
51F PRO 3.0 17.5 + - - +
52F GLU* 3.6 9.0 - - - +
54F LEU* 1.3 76.2 - - - +
56F ASP* 1.3 77.6 + - - +
58F ARG* 3.3 6.0 + - - +
59F VAL* 3.1 43.1 + - + +
8G THR* 3.3 16.1 + - - -
9G ARG* 3.0 49.4 + - + +
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Residues in contact with ASP 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D TYR* 3.2 30.5 + - + +
52F GLU* 3.1 42.0 + - - +
53F ASN* 4.0 3.0 - - - +
55F TYR* 1.3 92.9 - - - +
57F ASP* 1.3 55.9 + - - +
59F VAL* 3.4 9.6 + - - +
60F PHE* 3.1 23.2 + - - +
9G ARG* 5.7 0.3 + - - -
11G ARG* 3.9 29.8 + - - +
12G HIS* 3.8 14.1 + - + -
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Residues in contact with ASP 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D TYR* 2.8 40.2 + - - -
239D PRO* 5.0 2.8 - - - +
53F ASN* 3.1 28.1 + - - +
54F LEU* 3.7 11.6 - - - +
56F ASP* 1.3 70.7 - - - +
58F ARG* 1.3 58.2 + - - +
60F PHE* 3.4 3.6 + - - +
61F ARG* 2.9 57.5 + - - +
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Residues in contact with ARG 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ILE* 4.9 4.8 - - - +
212C SER* 5.8 1.2 - - - -
34F ASP 3.5 19.4 + - - -
35F ASP* 3.7 12.4 + - - +
37F ILE* 4.0 12.5 + - - +
39F GLU* 3.9 18.0 + - - -
43F VAL* 5.1 0.6 - - - +
47F ILE* 3.5 47.3 - - - +
50F LEU* 4.4 6.5 - - - -
54F LEU 2.9 14.9 + - - +
55F TYR* 3.3 12.8 - - - +
57F ASP* 1.3 73.7 - - - +
59F VAL* 1.3 59.9 + - - +
61F ARG* 3.2 15.2 + - - +
62F ILE* 3.0 55.2 + - + +
89F TYR* 3.2 30.1 + - + +
90F LEU* 5.3 0.2 - - - +
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Residues in contact with VAL 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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215C VAL* 3.5 26.3 - - + +
55F TYR* 3.1 48.2 + - + +
56F ASP* 3.4 8.0 + - - +
58F ARG* 1.3 72.9 - - + +
60F PHE* 1.3 63.5 + - - +
62F ILE* 3.3 8.0 + - - -
63F LYS* 2.9 30.0 + - - +
9G ARG 4.2 4.3 - - - +
10G VAL* 3.8 34.3 - - + -
11G ARG 5.1 2.7 - - - +
13G VAL* 4.8 4.3 - - + -
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Residues in contact with PHE 60 (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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235D LEU* 4.1 29.6 - - + -
236D ALA* 4.3 3.6 - - - -
237D TYR* 3.5 60.8 - + + -
56F ASP 3.1 16.3 + - - +
57F ASP 3.4 3.6 + - - +
59F VAL* 1.3 77.0 - - - +
61F ARG* 1.3 61.4 + - + +
63F LYS* 3.3 6.7 + - + +
64F ARG* 2.9 62.4 + - + +
13G VAL* 4.2 17.5 - - + -
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Residues in contact with ARG 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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30F GLY 3.6 21.5 - - - +
31F LEU* 3.8 4.4 - - + +
32F MET* 3.7 32.4 - - - +
35F ASP* 2.8 48.7 + - - +
54F LEU* 4.8 7.5 + - - +
57F ASP* 2.9 44.1 + - - +
58F ARG* 3.5 13.0 - - - +
60F PHE* 1.3 75.0 - - + +
62F ILE* 1.4 64.4 + - - +
64F ARG* 3.4 25.2 + - - +
65F ALA* 3.1 22.3 + - - +
81F THR* 5.8 0.4 - - - -
89F TYR* 3.4 23.8 - - - -
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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
----------------------------------------------------------
211C ILE* 3.6 14.4 - - + -
212C SER 3.4 25.1 - - - +
215C VAL* 5.0 10.8 - - + -
31F LEU* 4.2 6.5 - - + -
35F ASP* 3.6 35.2 - - + +
58F ARG* 3.0 58.0 + - + +
59F VAL* 3.7 7.4 - - - +
61F ARG* 1.4 73.8 - - - +
63F LYS* 1.3 53.2 + - - +
65F ALA* 3.1 4.4 + - + +
66F LEU* 2.8 47.5 + - + +
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Residues in contact with LYS 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C VAL* 3.5 34.8 + - + +
216C ASP* 3.1 32.0 + - + +
233D ARG* 4.2 8.1 - - - +
235D LEU* 3.9 24.8 - - + +
59F VAL 2.9 16.8 + - - +
60F PHE* 3.6 8.5 - - + +
62F ILE* 1.3 73.9 - - - +
64F ARG* 1.3 57.2 + - - +
66F LEU* 3.3 8.2 + - - +
67F ASP* 2.8 32.6 + - + +
10G VAL* 5.1 4.5 - - + -
13G VAL* 3.8 33.2 - - + -
15G THR* 4.2 7.5 + - - +
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Residues in contact with ARG 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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235D LEU* 4.1 13.0 - - + +
29F LEU 3.2 21.3 + - - -
30F GLY* 3.8 23.5 + - - -
60F PHE* 2.9 46.5 + - + +
61F ARG* 3.4 29.9 + - - +
63F LYS* 1.3 74.4 - - - +
65F ALA* 1.3 54.6 + - - +
67F ASP* 3.5 3.5 - - - +
68F LEU* 3.0 38.8 + - + +
75F LEU* 4.0 28.2 - - - +
79F GLN* 5.7 1.0 + - - -
81F THR* 5.9 0.2 - - - +
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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
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209C THR* 5.1 3.8 - - + -
211C ILE* 5.9 1.1 - - + -
29F LEU* 3.9 26.4 - - + +
31F LEU* 3.7 31.2 - - + -
61F ARG 3.1 15.8 + - - +
62F ILE* 3.4 8.1 - - + +
64F ARG* 1.3 75.2 - - - +
66F LEU* 1.3 59.9 + - + +
68F LEU* 3.4 3.4 + - - +
69F SER* 2.9 28.8 + - - -
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Residues in contact with LEU 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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25C SER* 4.2 5.2 - - - +
26C ASN* 3.4 30.7 - - - +
207C ASN* 3.6 11.4 - - - +
209C THR* 3.6 25.1 - - + +
211C ILE* 4.3 2.9 - - + +
212C SER 4.6 0.4 - - - +
213C SER* 3.9 24.7 - - - -
215C VAL* 5.2 1.8 - - + -
216C ASP* 3.9 29.4 - - + +
62F ILE* 2.8 43.0 + - + +
63F LYS* 3.9 3.6 - - - +
65F ALA* 1.3 68.7 - - + +
67F ASP* 1.3 59.3 + - - +
69F SER* 3.2 4.4 + - - -
70F MET* 2.9 27.4 + - - +
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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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216C ASP* 4.0 1.6 + - - -
230D LEU 4.4 0.2 - - - +
233D ARG* 2.8 50.5 + - - +
235D LEU* 4.1 19.0 - - + +
63F LYS 2.8 17.3 + - - +
64F ARG 3.5 5.6 - - - +
66F LEU* 1.3 76.5 - - - +
68F LEU* 1.3 60.7 + - - +
70F MET* 3.4 18.8 + - - +
71F ARG* 2.8 53.0 + - - +
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Residues in contact with LEU 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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29F LEU* 3.7 35.0 - - + +
64F ARG* 3.0 27.2 + - + +
65F ALA* 3.4 4.7 + - - +
66F LEU 3.3 0.2 - - - -
67F ASP* 1.3 72.0 - - - +
69F SER* 1.3 50.9 + - - +
71F ARG* 3.0 36.3 + - - +
72F GLN 2.7 30.8 + - - -
73F GLN* 3.1 22.2 + - + +
74F ILE 3.9 23.8 - - - +
75F LEU* 4.0 27.6 - - + +
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Residues in contact with SER 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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26C ASN* 3.0 29.5 + - - +
208C PRO* 3.9 12.6 - - - +
209C THR* 3.8 15.0 - - - +
316C MET* 4.8 11.3 - - - +
29F LEU* 4.9 4.4 - - - +
65F ALA 2.9 18.1 + - - -
66F LEU 3.6 4.7 - - - -
68F LEU* 1.3 74.6 - - - +
70F MET* 1.3 59.8 - - - +
72F GLN* 3.2 29.4 + - - +
73F GLN 5.1 1.8 - - - -
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Residues in contact with MET 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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25C SER* 3.4 28.3 - - - +
26C ASN* 3.6 12.8 - - + +
227D TRP* 4.0 13.5 - - + -
230D LEU* 3.3 48.0 - - - +
231D LYS* 3.7 20.3 + - - -
233D ARG* 4.1 13.5 - - - +
66F LEU 2.9 12.3 + - - +
67F ASP* 3.4 33.4 - - - +
69F SER* 1.3 76.8 - - - +
71F ARG* 1.3 72.4 + - + +
72F GLN* 3.3 8.6 + - - -
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Residues in contact with ARG 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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230D LEU 5.2 0.4 + - - -
231D LYS* 3.3 40.8 - - + +
233D ARG 5.3 4.9 + - - -
67F ASP* 2.8 31.9 + - - +
68F LEU* 3.0 30.7 + - - +
70F MET* 1.3 90.3 - - + +
72F GLN* 1.3 68.8 - - - +
73F GLN* 3.2 42.0 + - + +
36G ASN* 5.1 2.8 + - - -
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Residues in contact with GLN 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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26C ASN 5.8 0.2 - - - +
28C SER* 4.8 18.0 - - - +
208C PRO* 5.6 4.9 - - - +
68F LEU 2.7 5.9 + - - -
69F SER* 3.2 22.8 + - - +
70F MET 3.3 6.7 + - - -
71F ARG* 1.3 79.9 - - - +
73F GLN* 1.3 54.4 + - - +
36G ASN* 3.7 4.7 - - - +
39G ARG* 2.7 27.3 + - - -
40G ARG* 3.4 50.7 + - - +
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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