Contacts of the helix formed by residues 65 - 76 (chain A) 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 VAL 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A SER* 2.4 29.3 + - - +
64A ASP* 1.3 90.8 - - - +
66A VAL* 1.3 60.2 + - + +
67A PHE 3.4 0.7 - - - -
68A PHE* 4.1 3.7 - - - +
69A GLU* 3.1 38.4 + - - +
72B ILE* 3.6 30.0 - - + +
75B ILE* 3.9 13.7 - - + -
76B LEU* 4.5 21.5 - - + -
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 3.6 19.5 - - + -
63A SER* 2.7 25.6 + - - +
65A VAL* 1.3 77.9 - - + +
67A PHE* 1.3 71.9 + - - +
69A GLU* 3.0 12.4 + - + +
70A MET* 2.8 37.9 + - + +
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Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.1 14.8 - - + -
12A VAL* 3.4 23.5 - - + +
13A ILE* 3.5 35.7 - - + -
16A ILE* 3.3 28.5 - - + -
53A LEU* 4.1 12.1 - - + -
56A ILE* 5.8 0.4 - - + -
57A MET* 3.5 45.3 - - + -
60A LEU* 4.7 5.2 - - + -
62A VAL* 4.3 7.2 - - + +
63A SER 3.3 7.1 + - - +
64A ASP 4.8 0.2 - - - -
66A VAL* 1.3 84.5 - - - +
68A PHE* 1.3 65.0 + - - +
70A MET* 2.8 16.9 + - - +
71A LEU* 2.8 34.8 + - + +
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.8 9.6 - - + -
57A MET* 3.7 24.0 - - + -
64A ASP* 2.5 30.7 - - + +
65A VAL* 4.0 1.5 + - - +
66A VAL 3.3 0.2 - - - -
67A PHE* 1.3 80.9 - + - +
69A GLU* 1.3 52.8 + - - +
71A LEU* 3.0 21.5 - - + +
72A ILE* 2.7 40.9 + - + +
5B LEU* 3.8 24.7 - - + -
9B VAL* 6.2 0.9 - - + -
68B PHE* 3.4 39.9 - + + +
71B LEU* 3.8 20.2 - - + -
72B ILE* 4.1 18.4 - - + -
75B ILE* 4.7 7.6 - - + -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 3.1 29.7 + - - +
66A VAL* 3.0 13.3 + - + +
67A PHE 2.9 3.2 + - - -
68A PHE* 1.3 70.2 - - - +
70A MET* 1.3 56.9 + - + +
72A ILE* 2.8 30.7 + - + +
73A LYS* 3.1 41.5 + - - +
72B ILE* 4.5 12.2 - - + +
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Residues in contact with MET 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 4.4 11.7 - - + -
15A LYS* 3.5 38.1 - - + -
16A ILE* 3.8 29.8 - - + -
19A GLU* 4.0 13.2 - - - +
62A VAL* 5.9 0.4 - - - -
66A VAL* 2.8 34.2 + - + +
67A PHE 2.8 8.9 + - - +
69A GLU* 1.3 69.9 - - - +
71A LEU* 1.3 55.3 + - - +
73A LYS* 2.9 11.3 + - - +
74A GLU* 2.8 41.6 + - + +
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.6 3.8 - - + -
8A LYS* 4.4 6.7 - - + -
9A VAL* 4.1 36.6 - - + +
12A VAL* 3.9 14.9 - - + +
53A LEU* 6.1 0.4 - - + -
67A PHE* 2.8 28.6 + - + +
68A PHE* 3.0 44.0 - - + +
70A MET* 1.3 76.1 - - - +
72A ILE* 1.3 54.7 + - - -
74A GLU* 3.3 1.8 - - - +
75A ILE* 2.8 52.1 + - + +
68B PHE* 4.1 15.3 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE 2.7 39.6 + - - +
69A GLU* 2.8 17.4 + - + +
71A LEU* 1.3 69.5 - - - +
73A LYS* 1.3 72.7 + - + +
75A ILE* 3.2 9.0 + - - +
76A LEU* 2.8 39.4 + - + +
65B VAL* 3.4 37.0 - - + +
68B PHE* 4.0 22.2 - - + -
69B GLU* 4.6 12.6 - - + +
72B ILE* 3.8 19.7 - - + -
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU* 3.1 46.6 + - - +
70A MET* 2.9 9.8 + - - +
72A ILE* 1.3 81.0 - - + +
74A GLU* 1.3 68.2 + - + +
76A LEU* 3.0 29.9 + - + +
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LYS* 4.4 22.3 + - + +
11A PHE* 3.1 40.1 - - + -
12A VAL* 3.6 20.2 - - + -
15A LYS* 4.5 12.7 + - + -
70A MET* 2.8 17.6 + - + +
71A LEU* 3.3 12.1 - - - +
73A LYS* 1.3 73.8 - - + +
75A ILE* 1.3 55.0 + - + +
76A LEU 2.6 16.1 + - - -
77A LYS* 2.8 18.9 + - - +
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE* 4.2 15.3 - - + -
5A LEU* 4.5 7.0 - - + -
8A LYS* 4.5 20.3 - - + +
71A LEU* 2.8 38.5 + - + +
72A ILE* 3.2 8.5 + - - +
74A GLU* 1.3 70.1 - - - +
76A LEU* 1.3 53.0 + - + +
77A LYS* 2.8 19.5 + - - +
64B ASP* 3.5 36.1 - - + +
65B VAL* 3.9 15.5 - - + +
68B PHE* 3.9 34.3 - - + -
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 2.8 33.2 - - + +
73A LYS* 3.0 23.3 - - + +
74A GLU 2.6 7.9 + - - -
75A ILE* 1.3 71.3 - - + +
77A LYS* 1.3 61.8 + - - +
65B VAL* 3.9 30.1 - - + -
77F LYS 5.5 1.9 - - - +
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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