Contacts of the helix formed by residues 49 - 60 (chain E) in PDB entry 4IVZ
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 THR 49 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48E LEU* 1.3 78.6 - - - +
50E ILE* 1.3 55.7 - - - +
51E LYS* 3.5 2.8 + - - +
52E SER* 3.0 18.0 + - - -
53E LEU* 2.8 34.3 + - - +
47F ASN* 3.3 28.9 + - - +
48F LEU 3.3 8.5 - - - +
49F THR* 4.1 8.3 - - + -
50F ILE* 5.2 1.8 - - - -
12G A 3.6 18.6 - - - +
12H A 3.5 9.4 - - - +
13H G 2.3 36.2 + - - +
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Residues in contact with ILE 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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49E THR* 1.3 70.1 - - - +
51E LYS* 1.3 54.1 + - - +
53E LEU* 3.3 12.7 + - + +
54E GLU* 2.7 34.3 + - + +
68E PHE* 6.6 0.2 - - + -
5F LEU* 3.2 31.2 - - + -
6F LEU* 3.2 34.8 - - + -
9F VAL* 4.7 12.8 - - + -
48F LEU* 3.1 26.0 + - + +
49F THR 4.6 1.8 - - - +
50F ILE* 3.7 25.8 - - + -
53F LEU* 4.5 16.4 - - + -
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Residues in contact with LYS 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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49E THR* 3.2 6.9 - - - +
50E ILE* 1.3 74.7 - - - +
52E SER* 1.3 52.1 + - - +
54E GLU* 2.9 11.7 + - - +
55E LEU* 2.8 41.6 + - + +
3F SER* 4.6 21.8 - - - +
6F LEU* 4.1 19.8 - - + +
47F ASN* 3.1 31.8 + - - +
12G A 4.8 9.5 + - - +
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Residues in contact with SER 52 (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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33E LEU* 3.8 18.7 - - - +
37E PHE* 4.0 5.5 - - - -
48E LEU* 4.0 9.2 - - - -
49E THR* 3.0 15.3 + - - -
51E LYS* 1.3 73.0 - - - +
53E LEU* 1.3 70.0 + - - +
54E GLU 3.2 0.2 + - - -
55E LEU* 3.3 9.7 + - - +
56E ILE* 2.8 26.7 + - - +
13H G 2.8 42.5 + - - -
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Residues in contact with LEU 53 (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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9E VAL* 4.6 7.0 - - + -
13E ILE* 4.5 12.1 - - + -
48E LEU* 3.7 17.4 - - + +
49E THR 2.8 17.7 + - - +
50E ILE* 3.3 18.6 + - + +
52E SER* 1.3 71.7 - - - +
54E GLU* 1.4 55.0 + - - +
56E ILE* 2.4 28.9 + - + +
57E MET* 2.9 36.4 + - + +
67E PHE* 3.6 37.2 - - + -
68E PHE* 4.6 16.4 - - + -
5F LEU* 4.3 13.2 - - + -
50F ILE* 5.4 7.0 - - + -
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Residues in contact with GLU 54 (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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50E ILE* 2.7 22.3 + - + +
51E LYS* 2.9 8.2 + - - +
53E LEU* 1.4 67.7 - - - +
55E LEU* 1.3 73.5 + - - +
57E MET* 3.5 17.0 - - + +
58E LYS* 3.1 31.8 + - - +
64E ASP* 4.4 5.3 - - - +
3F SER* 3.9 16.2 + - - -
4F PHE* 3.8 13.8 + - - +
5F LEU* 3.3 46.7 + - + +
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Residues in contact with LEU 55 (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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30E LYS 4.8 0.7 - - - +
31E SER* 3.2 30.9 + - - +
32E ASN* 4.5 9.4 - - + +
33E LEU* 4.0 23.8 - - + -
51E LYS* 2.8 20.3 + - + +
52E SER* 3.3 9.4 - - - +
54E GLU* 1.3 78.8 - - - +
56E ILE* 1.3 54.7 + - - +
58E LYS* 2.4 41.0 + - + +
59E GLY 2.8 8.7 + - - -
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Residues in contact with ILE 56 (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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13E ILE* 4.2 21.1 - - + -
27E LEU* 3.8 20.0 - - + +
31E SER* 3.6 18.6 - - - +
33E LEU* 3.8 15.5 - - + -
38E ILE* 4.0 17.0 - - + -
41E ILE* 4.2 8.5 - - + -
48E LEU* 3.5 27.8 - - + -
52E SER* 2.8 19.0 + - - +
53E LEU* 2.4 20.4 + - + +
55E LEU* 1.3 68.7 - - - +
57E MET* 1.3 53.6 + - - +
59E GLY* 2.7 21.5 + - - -
60E LEU* 2.8 27.9 + - + +
67E PHE* 5.7 0.2 - - + -
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Residues in contact with MET 57 (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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53E LEU* 2.9 32.6 + - + -
54E GLU* 3.5 27.6 - - + +
56E ILE* 1.3 71.6 - - - +
58E LYS* 1.3 65.9 + - - +
60E LEU* 3.7 2.9 + - - -
61E GLU* 3.3 1.7 + - - -
62E VAL* 3.1 42.4 + - + +
64E ASP* 3.4 38.1 - - + +
67E PHE* 3.5 51.1 - - + -
68E PHE* 4.8 2.7 - - + -
5F LEU* 4.0 6.7 - - + -
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Residues in contact with LYS 58 (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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30E LYS 5.1 6.1 - - - +
54E GLU* 3.1 28.3 + - - +
55E LEU* 2.4 36.7 + - + +
57E MET* 1.3 68.2 - - - +
59E GLY* 1.3 55.2 + - - +
61E GLU* 3.0 28.9 + - - +
62E VAL 5.2 0.2 - - - -
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Residues in contact with GLY 59 (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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22E MET* 4.4 1.0 - - - +
27E LEU* 3.7 12.1 - - - +
30E LYS* 3.3 55.3 + - - -
31E SER* 4.5 1.3 - - - -
55E LEU 2.8 6.4 + - - -
56E ILE 2.7 9.1 + - - -
58E LYS* 1.3 74.6 - - - +
60E LEU* 1.3 55.7 + - - -
61E GLU* 2.9 12.6 + - - +
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Residues in contact with LEU 60 (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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13E ILE* 4.3 15.5 - - + +
16E ILE* 3.9 29.8 - - + +
17E ARG* 3.6 35.2 - - + +
20E LYS* 2.5 39.2 + - + +
22E MET* 4.5 9.8 - - - +
27E LEU* 3.4 24.3 - - + +
30E LYS* 6.0 0.2 - - - -
56E ILE* 2.8 29.7 + - + +
57E MET* 4.1 1.1 - - - +
59E GLY* 1.3 69.6 - - - -
61E GLU* 1.3 57.8 + - - +
62E VAL* 3.8 18.4 - - + -
67E PHE* 4.6 6.5 - - + -
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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