Contacts of the helix formed by residues 52 - 67 (chain F) in PDB entry 4DEM
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 ILE 52 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45F ASP* 4.8 13.7 - - + +
46F GLU* 5.4 0.2 - - - -
49F HIS* 3.1 29.6 + - + +
50F PRO 3.1 1.2 - - - -
51F GLU* 1.3 89.4 - - + +
53F GLY* 1.3 64.5 + - - +
54F ASP 3.3 2.5 - - - -
55F ALA* 3.0 15.3 + - + +
56F ILE* 2.9 42.8 + - + +
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Residues in contact with GLY 53 (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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46F GLU* 4.7 13.7 - - - +
49F HIS 4.1 0.2 + - - -
50F PRO* 2.9 19.1 + - - -
51F GLU 3.3 0.8 - - - -
52F ILE* 1.3 79.0 - - - +
54F ASP* 1.3 60.0 + - - +
56F ILE* 3.4 7.2 + - - +
57F ALA* 3.0 28.1 + - - +
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Residues in contact with ASP 54 (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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51F GLU 4.9 2.3 + - - +
52F ILE 3.3 0.8 - - - -
53F GLY* 1.3 76.4 - - - +
55F ALA* 1.3 58.8 + - - +
57F ALA* 3.4 8.6 + - - +
58F ARG* 3.0 26.3 + - - +
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Residues in contact with ALA 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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52F ILE* 3.0 19.6 + - + +
54F ASP* 1.3 78.5 - - - +
56F ILE* 1.3 62.6 + - + +
58F ARG* 3.2 9.0 + - - +
59F LEU* 3.0 26.5 + - - +
148F LEU* 5.1 6.1 - - + +
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Residues in contact with ILE 56 (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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42F LEU 4.2 13.2 - - - +
43F THR* 3.4 43.2 - - + +
45F ASP* 5.3 4.7 - - + -
46F GLU* 4.4 18.2 - - + +
52F ILE* 2.9 43.1 + - + +
53F GLY 3.8 5.2 - - - +
54F ASP 3.3 0.2 - - - -
55F ALA* 1.3 80.1 - - + +
57F ALA* 1.3 57.0 + - - +
59F LEU* 3.2 15.4 + - + +
60F LYS* 2.9 27.5 + - - +
155F ARG* 5.8 2.9 - - - +
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Residues in contact with ALA 57 (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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53F GLY 3.0 18.4 + - - +
54F ASP* 3.6 8.7 - - - +
56F ILE* 1.3 76.8 - - - +
58F ARG* 1.3 61.3 + - - +
60F LYS* 3.4 9.1 + - - +
61F GLU* 3.1 21.7 + - - +
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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
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54F ASP 3.0 13.7 + - - +
55F ALA* 3.2 11.6 + - - +
57F ALA* 1.3 73.3 - - - +
59F LEU* 1.3 66.0 + - - +
61F GLU* 3.1 24.1 + - - +
62F VAL* 2.9 31.7 + - + +
132F TRP* 4.0 7.0 - - - -
137F GLY 5.0 6.9 + - - -
138F VAL* 4.2 15.3 - - - +
141F ASP* 3.8 25.5 + - - +
145F ASP* 2.8 43.8 + - - +
148F LEU* 5.2 5.8 - - + -
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Residues in contact with LEU 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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42F LEU* 4.0 21.5 - - + +
43F THR* 5.4 1.3 - - + -
55F ALA 3.0 12.7 + - - +
56F ILE* 3.2 21.1 + - + +
58F ARG* 1.3 76.5 - - - +
60F LYS* 1.3 59.0 + - - +
62F VAL* 3.2 7.2 + - + +
63F LEU* 2.8 50.6 + - + +
148F LEU* 4.1 38.8 - - + +
149F LEU* 4.8 5.2 - - + -
152F CYS* 3.7 33.4 - - - -
155F ARG* 6.3 1.3 - - - +
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Residues in contact with LYS 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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39F VAL* 3.7 23.3 - - + +
43F THR* 4.0 15.0 + - + +
56F ILE 2.9 13.7 + - - +
57F ALA* 3.6 11.7 - - - +
58F ARG 3.2 0.2 - - - -
59F LEU* 1.3 77.5 - - - +
61F GLU* 1.3 56.5 + - - +
63F LEU* 3.2 10.6 + - - +
64F GLU* 2.9 62.1 + - - +
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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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57F ALA 3.1 11.4 + - - +
58F ARG* 3.1 27.1 + - - +
60F LYS* 1.3 77.2 - - - +
62F VAL* 1.3 57.4 + - - +
64F GLU* 3.3 6.1 + - - +
65F TYR* 2.9 31.1 + - + +
132F TRP* 3.7 26.1 - - + -
135F LYS* 5.5 3.8 - - - -
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Residues in contact with VAL 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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58F ARG* 2.9 21.5 + - + +
59F LEU* 3.5 13.2 - - + +
61F GLU* 1.3 76.8 - - - +
63F LEU* 1.3 62.5 + - - +
66F ASN* 3.0 42.8 + - - +
115F VAL* 5.6 0.2 - - + -
132F TRP* 3.7 15.9 - - + -
145F ASP* 3.5 46.2 - - + +
148F LEU* 5.5 1.6 - - + -
149F LEU* 3.8 32.5 - - + -
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Residues in contact with LEU 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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35F PHE* 3.7 17.6 - - + -
38F ILE* 5.7 0.4 - - + -
39F VAL* 4.5 16.8 - - + -
42F LEU* 4.1 30.1 - - + -
43F THR* 5.3 1.3 - - + -
59F LEU* 2.8 40.3 + - + +
60F LYS* 3.5 9.2 - - - +
62F VAL* 1.3 78.1 - - - +
64F GLU* 1.3 58.3 + - - +
67F ALA* 3.0 33.8 + - + +
68F ILE 4.1 0.5 + - - -
108F LEU* 3.5 24.5 - - + -
149F LEU* 3.4 26.9 - - + -
152F CYS* 4.9 2.0 - - - -
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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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35F PHE* 4.4 19.2 - - + -
39F VAL* 4.5 9.6 - - + +
60F LYS* 2.9 49.3 + - + +
61F GLU* 4.0 5.3 - - - +
63F LEU* 1.3 79.2 - - + +
65F TYR* 1.3 61.6 + - - +
68F ILE* 3.7 18.8 - - - +
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Residues in contact with TYR 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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61F GLU* 2.9 18.3 + - + +
64F GLU* 1.3 81.2 - - - +
66F ASN* 1.3 71.2 + - - +
67F ALA 3.8 0.2 - - - -
68F ILE 4.1 6.3 - - - +
127F ARG* 5.9 0.9 - - - -
129F GLN* 3.0 61.2 + - + +
130F ILE* 2.6 46.6 + - - +
131F CYS* 5.0 0.2 - - - -
132F TRP* 3.5 43.5 - + + -
135F LYS* 3.6 25.9 + - + +
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Residues in contact with ASN 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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62F VAL* 3.0 34.8 + - - +
65F TYR* 1.3 87.0 - - - +
67F ALA* 1.3 59.1 + - - +
68F ILE 3.4 2.2 - - - -
111F ALA* 3.4 12.6 - - + +
114F LEU* 4.0 13.8 - - + +
115F VAL* 3.4 29.7 - - + +
127F ARG* 2.8 21.1 + - - +
132F TRP* 3.4 41.4 + - - +
149F LEU* 4.3 9.6 - - + -
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Residues in contact with ALA 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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35F PHE* 4.0 16.6 - - + -
63F LEU* 3.0 19.5 + - + +
66F ASN* 1.3 77.8 - - - +
68F ILE* 1.3 61.4 + - - +
72F TYR* 3.6 9.9 - - - -
104F TRP* 3.5 21.8 - - + -
107F GLU* 4.7 9.2 - - - +
108F LEU* 4.2 22.2 - - + -
111F ALA* 4.2 10.1 - - + -
127F ARG* 3.9 6.2 + - - +
149F LEU* 5.3 0.2 - - + -
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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