Contacts of the helix formed by residues 38 - 51 (chain E) in PDB entry 3FZ7
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 ARG 38 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E MET* 1.3 80.2 - - - +
39E ASP* 1.3 66.7 + - - +
40E ASP* 3.2 11.9 - - + +
41E VAL* 3.2 30.7 + - + +
42E ALA* 2.9 19.6 + - - +
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Residues in contact with ASP 39 (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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69D ASP* 4.9 2.8 - - - +
71D ASN* 3.9 7.9 - - - +
329D TYR* 3.6 23.0 + - - +
333D ARG* 3.0 46.1 + - - +
37E MET 3.3 3.6 + - - +
38E ARG* 1.3 72.6 - - - +
40E ASP* 1.3 54.9 + - - +
42E ALA* 3.1 6.2 + - - +
43E PHE* 2.9 30.3 + - - +
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Residues in contact with ASP 40 (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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71D ASN* 3.0 29.2 + - - +
38E ARG* 3.2 14.3 + - + +
39E ASP* 1.3 82.1 - - - +
41E VAL* 1.3 57.2 + - + +
43E PHE* 3.6 5.8 + - + +
44E GLN* 3.0 43.5 + - - +
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Residues in contact with VAL 41 (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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18E PHE* 3.6 48.1 - - + -
23E ILE* 4.8 11.0 - - + -
37E MET* 4.6 6.5 - - + -
38E ARG* 3.2 42.5 + - + +
40E ASP* 1.3 72.6 - - + +
42E ALA* 1.3 61.8 + - - +
43E PHE 3.3 0.2 - - - -
44E GLN* 3.8 2.1 - - - +
45E ILE* 2.8 40.5 + - + +
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Residues in contact with ALA 42 (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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329D TYR* 4.3 8.3 - - + -
332D LEU* 4.3 7.9 - - + -
333D ARG* 3.9 26.5 - - + +
37E MET* 3.8 21.3 - - - -
38E ARG 2.9 12.9 + - - +
39E ASP 3.4 7.9 - - - +
41E VAL* 1.3 78.1 - - - +
43E PHE* 1.3 56.0 + - - +
45E ILE* 3.5 4.6 + - - +
46E ILE* 2.9 35.3 + - - +
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Residues in contact with PHE 43 (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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71D ASN* 3.9 30.3 - - + +
74D LYS* 3.8 47.1 - - + -
75D LEU* 3.7 32.8 - - + -
78D LEU* 4.6 3.4 - - + -
329D TYR* 4.0 9.3 - - + -
39E ASP 2.9 13.7 + - - +
40E ASP* 3.7 8.7 - - + +
41E VAL 3.3 0.2 - - - -
42E ALA* 1.3 76.5 - - - +
44E GLN* 1.3 68.6 + - + +
46E ILE* 3.1 4.4 + - - +
47E ASN* 2.7 63.5 + - + +
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Residues in contact with GLN 44 (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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17E ARG* 4.7 0.4 - - - -
18E PHE* 4.0 25.9 - - + -
40E ASP* 3.0 34.5 + - - +
41E VAL* 4.1 1.6 - - - +
43E PHE* 1.3 87.3 - - + +
45E ILE* 1.3 62.3 + - - +
47E ASN* 4.2 6.3 - - - +
48E ASP* 2.8 42.7 + - - +
67F TRP* 3.4 31.9 - - + -
68F ASP 4.9 1.9 - - - +
69F ASP* 5.6 1.6 - - - -
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Residues in contact with ILE 45 (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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332D LEU* 4.3 8.1 - - + -
15E ASP* 5.6 0.2 - - - +
17E ARG* 3.8 16.8 + - - +
18E PHE* 3.8 20.0 - - + -
23E ILE* 3.9 35.4 - - + +
25E THR* 3.4 31.2 - - + -
37E MET* 4.5 6.3 - - + -
41E VAL* 2.8 38.4 + - + +
42E ALA 3.6 4.9 - - - +
44E GLN* 1.3 78.2 - - - +
46E ILE* 1.3 64.5 + - + +
48E ASP* 3.5 2.9 + - - +
49E GLU* 3.2 25.8 + - + +
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Residues in contact with ILE 46 (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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75D LEU* 4.0 11.4 - - + -
96D ILE* 4.3 10.8 - - + -
325D ILE* 3.9 27.1 - - + +
328D TYR* 3.3 37.0 - - + -
329D TYR* 3.5 34.1 - - + +
332D LEU* 4.0 10.8 - - + -
42E ALA 2.9 22.2 + - - +
43E PHE* 3.7 3.6 - - - +
45E ILE* 1.3 75.7 - - + +
47E ASN* 1.3 64.7 + - - +
49E GLU* 3.1 8.6 + - - +
50E LEU* 3.0 27.3 + - + +
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Residues in contact with ASN 47 (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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75D LEU* 4.7 1.3 - - - +
78D LEU* 3.4 28.9 - - + +
43E PHE* 2.7 48.6 + - + +
44E GLN* 3.8 6.7 + - - +
46E ILE* 1.3 72.5 - - - +
48E ASP* 1.3 71.0 + - - +
50E LEU* 3.2 21.8 + - - +
51E TYR* 3.3 35.5 + - - -
57F ARG* 5.6 0.4 - - - +
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Residues in contact with ASP 48 (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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17E ARG* 2.7 48.1 + - - +
44E GLN* 2.8 22.0 + - - +
45E ILE 3.7 2.2 - - - +
47E ASN* 1.3 85.0 + - - +
49E GLU* 1.3 62.0 + - - +
51E TYR* 3.4 21.1 + - - +
52E LEU 4.3 0.2 + - - -
57F ARG* 3.1 22.4 + - - +
67F TRP* 3.0 17.3 + - - -
68F ASP 5.6 0.2 - - - +
428F GLY 6.0 0.9 - - - +
433F PHE* 3.7 20.2 - - + -
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Residues in contact with GLU 49 (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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92D GLN* 3.0 39.5 + - + +
96D ILE* 4.0 10.4 - - + +
99D ARG* 2.7 26.8 + - - -
328D TYR* 4.8 2.1 - - - -
25E THR* 2.6 36.8 + - - +
26E ILE* 5.9 0.2 - - - +
45E ILE* 3.2 16.2 + - + +
46E ILE* 3.1 9.6 + - - +
48E ASP* 1.3 75.8 - - - +
50E LEU* 1.3 57.5 + - - +
52E LEU* 2.8 24.3 + - + +
432F ASP* 4.4 7.7 - - + +
433F PHE* 4.1 19.7 - - + -
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Residues in contact with LEU 50 (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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75D LEU* 4.2 10.8 - - + -
78D LEU* 4.7 10.5 - - + -
79D SER* 4.8 2.2 - - - +
82D LYS* 3.7 18.3 + - - +
92D GLN* 4.5 2.7 - - + -
93D SER* 4.0 5.8 - - - +
96D ILE* 3.8 24.7 - - + -
325D ILE* 3.8 40.8 - - + -
46E ILE* 3.0 20.0 + - + +
47E ASN* 3.2 10.7 + - - +
49E GLU* 1.3 75.7 - - - +
51E TYR* 1.3 55.9 + - - +
52E LEU 3.0 0.2 - - - -
53E ASP* 2.9 42.7 + - - +
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Residues in contact with TYR 51 (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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47E ASN* 3.3 42.9 + - - -
48E ASP* 3.4 10.3 - - - +
49E GLU 3.0 0.4 + - - -
50E LEU* 1.3 75.1 - - - +
52E LEU* 1.3 62.3 + - + +
53E ASP 3.3 8.0 - - - +
55F ASN* 3.7 36.7 + - + +
57F ARG* 3.4 68.9 + - + +
58F GLN* 5.0 1.9 - - - +
68F ASP* 3.6 13.5 + - - +
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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