Contacts of the helix formed by residues 42 - 58 (chain F) in PDB entry 3ECS
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 42 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41F THR* 1.3 84.7 - - + +
43F GLN* 1.3 95.8 + - + +
44F GLY* 2.8 20.5 + - - +
45F LEU* 2.9 47.8 + - + +
46F ARG* 3.2 14.7 + - - +
88F LYS* 5.9 4.3 - - + -
89F CYS* 5.8 0.2 - - - -
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Residues in contact with GLN 43 (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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41F THR 3.8 2.4 + - - -
42F ILE* 1.3 86.5 - - + +
44F GLY* 1.3 62.7 + - - +
46F ARG* 3.9 13.4 - - - +
47F ALA* 3.7 17.5 + - - +
88F LYS* 3.6 51.5 + - + +
89F CYS* 5.5 1.4 - - - +
91F LYS* 5.8 4.7 - - + -
93F MSE 4.7 11.7 - - - +
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Residues in contact with GLY 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ILE* 2.8 15.0 + - - +
43F GLN* 1.3 81.6 - - - +
45F LEU* 1.3 54.3 + - - -
47F ALA* 3.0 9.7 + - - +
48F ASN* 2.5 42.7 + - - -
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Residues in contact with LEU 45 (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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40F GLU* 2.5 42.3 - - + +
41F THR* 5.1 1.8 - - + +
42F ILE* 2.9 31.1 + - + +
44F GLY* 1.3 72.1 - - - +
46F ARG* 1.3 55.1 + - - +
48F ASN* 3.3 22.1 - - + +
49F LEU* 2.7 34.0 + - + +
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Residues in contact with ARG 46 (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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33F PHE* 5.5 1.0 - - - -
34F LEU* 5.7 4.0 - - + -
37F ASP* 2.9 48.2 + - - +
38F LYS* 3.6 30.9 + - - +
40F GLU* 3.6 13.8 + - - +
41F THR* 3.3 31.7 + - - +
42F ILE 3.2 11.0 + - - +
43F GLN* 3.9 12.2 - - - +
44F GLY 3.2 0.2 - - - -
45F LEU* 1.3 76.4 - - - +
47F ALA* 1.3 58.6 + - - +
49F LEU* 3.8 0.9 - - - +
50F THR* 2.8 34.0 + - - -
89F CYS* 2.9 34.5 + - - +
91F LYS* 3.7 24.5 - - + +
93F MSE 3.8 24.7 - - + -
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Residues in contact with ALA 47 (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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43F GLN 3.7 10.6 + - - +
44F GLY* 3.0 10.2 + - - +
46F ARG* 1.3 79.7 - - - +
48F ASN* 1.3 57.1 + - - +
50F THR* 2.7 26.3 - - - +
51F SER* 3.0 11.4 + - - -
73F LEU* 4.1 13.7 - - + +
76F ILE* 6.1 1.3 - - + +
77F SER 6.1 4.0 - - - +
93F MSE 4.9 10.0 - - - +
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Residues in contact with ASN 48 (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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44F GLY* 2.5 38.9 + - - +
45F LEU* 3.3 23.4 - - + +
47F ALA* 1.3 76.9 - - - +
49F LEU* 1.3 63.2 + - - +
50F THR 3.0 4.5 - - - -
51F SER* 3.0 19.8 + - - -
52F ALA* 3.4 8.1 + - - +
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Residues in contact with LEU 49 (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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1F MSE 6.0 0.7 - - - +
33F PHE* 4.0 19.1 - - + -
37F ASP* 3.8 9.2 - - - +
40F GLU* 2.8 40.2 - - - +
45F LEU* 2.7 17.0 + - + +
46F ARG 4.1 0.9 - - - +
48F ASN* 1.3 74.8 - - - +
50F THR* 1.3 59.5 + - - +
52F ALA* 3.3 30.2 + - + +
53F ILE* 3.4 12.2 - - + +
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Residues in contact with THR 50 (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 LEU* 5.0 6.4 + - - +
33F PHE* 4.4 6.9 - - - -
34F LEU* 5.5 7.8 - - - +
46F ARG 2.8 13.8 + - - -
47F ALA* 2.7 33.9 - - - +
48F ASN 3.0 0.2 - - - -
49F LEU* 1.3 77.0 - - - +
51F SER* 1.3 60.8 + - - +
53F ILE* 2.6 42.1 - - - +
54F GLU* 2.8 15.6 + - - +
72F PHE* 5.1 7.3 - - - -
73F LEU* 3.4 26.5 - - + +
93F MSE 6.6 0.2 - - - -
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Residues in contact with SER 51 (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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47F ALA 3.0 17.0 + - - -
48F ASN* 3.0 9.2 + - - -
50F THR* 1.3 77.2 - - - +
52F ALA* 1.3 65.9 + - - +
53F ILE 3.1 1.4 + - - -
54F GLU* 3.2 26.6 + - - +
55F THR* 3.5 9.5 + - - -
73F LEU* 4.6 9.9 - - - +
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Residues in contact with ALA 52 (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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48F ASN 3.4 3.9 + - - +
49F LEU* 3.3 30.9 + - + +
50F THR 3.3 0.2 - - - -
51F SER* 1.3 80.2 - - - +
53F ILE* 1.3 59.1 + - + +
55F THR* 3.7 9.5 - - - -
56F LEU* 3.0 28.2 + - + +
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Residues in contact with ILE 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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6F LEU* 3.3 20.0 - - + -
30F LEU* 3.2 31.9 - - + +
33F PHE* 3.3 63.0 - - + -
49F LEU* 3.4 5.2 - - + +
50F THR* 2.6 34.8 - - - +
52F ALA* 1.3 75.7 - - + +
54F GLU* 1.3 66.4 + - - +
55F THR 3.0 2.0 - - - -
56F LEU* 2.8 14.3 + - + +
57F CYS* 2.7 25.0 + - - +
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Residues in contact with GLU 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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30F LEU* 3.1 31.8 - - - +
50F THR* 2.8 23.8 + - - +
51F SER* 3.3 22.0 - - - +
53F ILE* 1.3 77.5 - - - +
55F THR* 1.3 53.2 + - - +
57F CYS* 3.1 9.3 + - - +
58F GLY* 2.7 31.9 + - - -
65F VAL* 5.1 2.9 - - - +
69F GLY* 3.1 39.9 - - - +
70F GLU* 4.8 0.4 - - - -
72F PHE* 5.2 0.2 - - - -
73F LEU* 5.1 8.9 - - + +
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Residues in contact with THR 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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51F SER 3.5 10.4 + - - -
52F ALA* 3.7 10.1 + - - -
53F ILE 3.0 0.4 - - - -
54F GLU* 1.3 75.8 - - - +
56F LEU* 1.3 62.0 + - + +
58F GLY* 2.6 28.1 + - - +
59F VAL 3.7 0.2 + - - -
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Residues in contact with LEU 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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3F ASP* 2.8 36.1 - - + +
6F LEU* 3.3 21.5 - - + -
7F ILE* 5.1 17.0 - - + +
52F ALA* 3.0 14.6 - - + +
53F ILE* 2.8 31.1 + - + +
55F THR* 1.3 79.3 - - + +
57F CYS* 1.3 63.0 + - - +
59F VAL* 3.0 23.5 + - - +
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Residues in contact with CYS 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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6F LEU* 5.5 11.9 - - - -
7F ILE* 6.2 0.9 - - - -
10F PHE* 4.7 19.2 - - + -
26F ALA* 4.6 11.0 - - + -
29F THR* 3.8 23.1 - - - -
30F LEU* 4.5 12.1 - - + -
53F ILE 2.7 15.9 + - - +
54F GLU* 3.4 10.1 - - - +
56F LEU* 1.3 68.3 - - - +
58F GLY* 1.3 53.9 + - - +
59F VAL* 2.4 27.8 + - - +
60F ASP* 3.0 19.1 + - - +
65F VAL* 4.1 17.3 - - + +
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Residues in contact with GLY 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 GLU 2.7 11.6 + - - -
55F THR* 2.6 23.8 + - - -
57F CYS* 1.3 68.0 - - - +
59F VAL* 1.3 49.2 + - - -
60F ASP 2.6 26.0 + - - +
61F SER* 3.7 5.4 + - - -
65F VAL* 4.8 5.6 - - - -
66F SER* 6.0 1.8 - - - -
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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