Contacts of the helix formed by residues 63 - 76 (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 SER 63 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E MET* 4.7 1.3 - - - -
61E GLU 4.5 0.2 + - - -
62E VAL* 1.3 76.7 - - - +
64E ASP* 1.3 57.7 + - - +
65E VAL* 3.5 19.9 - - - +
66E VAL* 2.7 47.9 + - - +
67E PHE 2.9 9.9 + - - -
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Residues in contact with ASP 64 (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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54E GLU* 4.4 5.5 - - - +
57E MET* 3.4 35.7 - - - +
62E VAL 3.8 1.8 + - - -
63E SER* 1.3 72.4 - - - +
65E VAL* 1.3 65.5 + - + +
66E VAL 2.7 1.9 + - - -
67E PHE 2.8 1.4 + - - -
68E PHE* 2.8 47.2 + - + -
4F PHE* 4.8 12.2 - - - -
5F LEU* 3.7 18.7 - - - +
75F ILE* 4.0 15.3 - - + +
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Residues in contact with VAL 65 (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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63E SER* 3.5 17.0 - - - +
64E ASP* 1.3 74.8 - - + +
66E VAL* 1.3 59.7 + - + +
68E PHE* 4.3 0.9 - - - +
69E GLU* 2.9 48.1 + - - +
72F ILE* 3.4 34.1 - - + +
75F ILE* 4.2 23.1 - - + +
76F LEU* 4.3 24.2 - - + -
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Residues in contact with VAL 66 (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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62E VAL* 3.5 16.2 - - + -
63E SER* 2.7 37.5 + - - +
65E VAL* 1.3 72.8 - - + +
67E PHE* 1.3 65.2 - - - +
68E PHE 3.1 1.6 - - - -
69E GLU* 4.4 10.8 - - + +
70E MET* 2.8 42.4 + - + +
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Residues in contact with PHE 67 (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* 3.9 16.2 - - + -
12E VAL* 3.7 21.1 - - + +
13E ILE* 3.6 30.3 - - + -
16E ILE* 3.8 20.4 - - + -
53E LEU* 3.6 28.7 - - + -
57E MET* 3.5 39.9 - - + -
60E LEU* 4.6 3.8 - - + -
62E VAL* 3.8 7.0 - - + +
63E SER 2.9 7.8 + - - +
64E ASP 2.8 9.8 + - - +
66E VAL* 1.3 71.8 - - - +
68E PHE* 1.3 74.0 + + + +
70E MET* 3.3 6.8 - - - +
71E LEU* 2.8 39.0 + - + +
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Residues in contact with PHE 68 (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* 6.6 0.2 - - + -
53E LEU* 4.6 18.4 - - + -
57E MET* 4.8 3.6 - - + -
64E ASP* 2.8 47.6 + - + +
65E VAL 4.3 0.2 - - - -
67E PHE* 1.3 87.3 - + + +
69E GLU* 1.3 58.5 + - - +
70E MET 3.0 1.6 - - - -
71E LEU* 2.8 10.8 + - + +
72E ILE* 2.6 40.6 + - - +
5F LEU* 3.8 22.4 - - + -
9F VAL* 6.1 0.9 - - + -
68F PHE* 3.8 30.3 - + + -
71F LEU* 3.8 27.1 - - + -
72F ILE* 3.7 21.5 - - + -
75F ILE* 4.0 6.3 - - + -
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Residues in contact with GLU 69 (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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65E VAL* 2.9 42.5 + - - +
66E VAL* 3.8 12.5 - - + +
68E PHE* 1.3 78.3 - - - +
70E MET* 1.3 63.5 + - + +
72E ILE* 3.3 18.7 + - + +
73E LYS* 3.4 25.3 + - - +
72F ILE* 4.1 15.9 - - + +
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Residues in contact with MET 70 (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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12E VAL* 4.5 13.9 - - + +
15E LYS* 4.1 35.4 - - + +
16E ILE* 4.1 27.1 - - + -
19E GLU* 4.8 10.1 - - - +
66E VAL* 2.8 34.2 + - + +
67E PHE* 3.3 7.4 - - - +
69E GLU* 1.3 79.2 - - + +
71E LEU* 1.3 60.8 + - - +
73E LYS* 3.5 33.0 - - + +
74E GLU* 3.7 16.3 + - - +
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Residues in contact with LEU 71 (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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5E LEU* 4.2 7.6 - - + -
8E LYS* 2.6 42.6 - - + +
9E VAL* 4.4 10.1 - - + +
12E VAL* 3.9 15.5 - - + +
67E PHE* 2.8 25.8 + - + +
68E PHE* 2.8 24.3 + - + +
70E MET* 1.3 67.9 - - - +
72E ILE* 1.3 66.2 + - - +
74E GLU* 2.8 16.9 + - + +
75E ILE* 2.8 19.0 + - + +
68F PHE* 3.5 38.4 - - + -
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Residues in contact with ILE 72 (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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68E PHE 2.6 23.1 + - - +
69E GLU* 3.3 12.3 + - + +
71E LEU* 1.3 69.7 - - - +
73E LYS* 1.3 60.7 + - + +
75E ILE* 2.8 29.5 + - - +
76E LEU* 3.3 21.6 - - + +
65F VAL* 3.5 26.5 - - + -
68F PHE* 4.2 17.5 - - + -
69F GLU* 3.8 27.4 - - + +
72F ILE* 3.6 29.6 - - + -
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Residues in contact with LYS 73 (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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69E GLU* 3.4 18.3 + - - +
70E MET* 3.5 28.0 - - + +
71E LEU 3.1 0.4 - - - -
72E ILE* 1.3 78.5 - - + +
74E GLU* 1.3 73.3 + - - +
75E ILE 3.2 1.0 + - - -
76E LEU* 3.3 36.7 + - + +
77E LYS* 4.0 5.1 - - - +
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Residues in contact with GLU 74 (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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8E LYS* 3.2 32.2 + - + +
11E PHE* 3.4 32.1 - - + -
12E VAL* 4.2 15.0 - - + -
15E LYS* 4.1 17.5 + - + -
70E MET* 3.7 18.2 + - + +
71E LEU 2.8 12.5 + - - +
73E LYS* 1.3 82.0 - - - +
75E ILE* 1.3 56.5 + - - +
77E LYS* 3.3 43.6 + - - +
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Residues in contact with ILE 75 (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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4E PHE* 3.2 42.6 - - + -
5E LEU* 5.7 3.1 - - + -
8E LYS* 4.5 7.4 - - + -
71E LEU* 2.8 49.1 - - + +
72E ILE* 2.8 23.1 - - - +
74E GLU* 1.3 76.3 - - - +
76E LEU* 1.3 49.1 + - - +
77E LYS* 2.4 26.0 + - - +
64F ASP* 3.5 14.6 - - - +
65F VAL* 3.8 22.9 - - + -
68F PHE* 4.9 9.0 - - + -
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Residues in contact with LEU 76 (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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72E ILE* 3.3 20.0 - - + +
73E LYS* 3.3 34.0 + - + +
75E ILE* 1.3 70.8 - - - +
77E LYS* 1.3 63.2 + - - +
78E HIS* 3.8 6.0 + - - -
65F VAL* 4.1 23.5 - - + +
69F GLU* 5.7 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