Contacts of the helix formed by residues 63 - 76 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B GLU 4.1 2.4 + - - -
62B VAL* 1.3 74.4 - - - +
64B ASP* 1.3 73.2 + - - +
65B VAL* 4.4 7.7 - - - +
66B VAL* 3.0 37.2 + - - +
67B PHE 3.1 8.5 + - - -
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Residues in contact with ASP 64 (chain B).
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* 3.8 25.5 - - - -
5A LEU* 5.2 6.1 - - + +
75A ILE* 3.5 24.7 - - + +
57B MET* 3.3 33.2 - - + +
62B VAL 3.4 3.2 + - - -
63B SER* 1.3 71.8 - - - +
65B VAL* 1.3 87.1 + - - +
67B PHE* 2.9 14.2 + - - +
68B PHE* 3.1 17.4 + - + -
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Residues in contact with VAL 65 (chain B).
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* 3.4 36.7 - - + +
75A ILE* 3.9 11.6 - - + +
76A LEU* 3.9 25.4 - - + -
63B SER* 3.1 7.6 + - - +
64B ASP* 1.3 94.8 + - - +
66B VAL* 1.3 53.3 + - + +
68B PHE* 3.1 4.7 + - - +
69B GLU* 2.8 52.3 + - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 4.3 16.6 - - + -
63B SER* 3.0 27.2 + - - +
65B VAL* 1.3 78.9 - - + +
67B PHE* 1.3 58.7 + - - +
69B GLU* 3.0 9.6 + - - +
70B MET* 2.8 45.0 + - + +
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Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 4.0 23.8 - - + -
12B VAL* 3.6 29.9 - - + +
13B ILE* 4.2 16.8 - - + -
16B ILE* 4.3 13.2 - - + -
53B LEU* 3.9 32.5 - - + -
56B ILE* 5.8 0.2 - - + -
57B MET* 3.5 24.9 - - + -
60B LEU* 5.1 6.3 - - + -
62B VAL* 3.6 17.0 - - + -
63B SER 3.1 4.4 + - - +
64B ASP 2.9 14.3 + - - +
66B VAL* 1.3 73.8 - - - +
68B PHE* 1.3 69.3 + + - +
70B MET* 3.7 5.0 - - - +
71B LEU* 2.8 44.8 + - + +
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.9 23.3 - - + -
9A VAL* 6.2 0.2 - - + -
68A PHE* 3.4 37.7 - + + -
71A LEU* 4.1 16.6 - - + -
72A ILE* 4.0 16.8 - - + -
75A ILE* 3.9 29.6 - - + -
50B ILE* 6.2 2.2 - - + -
53B LEU* 4.9 10.5 - - + -
57B MET* 4.2 16.2 - - + -
64B ASP 3.1 16.9 + - - -
65B VAL* 3.1 7.1 + - - +
67B PHE* 1.3 84.9 - + - +
69B GLU* 1.3 61.7 + - - +
71B LEU* 3.3 16.1 - - + +
72B ILE* 2.8 37.9 + - - +
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Residues in contact with GLU 69 (chain B).
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* 4.6 15.3 - - + +
65B VAL* 2.8 37.4 + - + +
66B VAL* 3.4 9.0 - - - +
68B PHE* 1.3 80.8 - - - +
70B MET* 1.3 63.2 + - - +
72B ILE* 3.1 19.5 + - + +
73B LYS* 3.3 30.9 + - - +
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Residues in contact with MET 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.6 23.1 - - + -
15B LYS* 3.1 46.7 - - + +
16B ILE* 4.0 23.1 - - + -
19B GLU* 4.5 10.8 - - - +
66B VAL* 2.8 29.0 + - + +
67B PHE* 3.7 4.5 - - - +
69B GLU* 1.3 71.0 - - - +
71B LEU* 1.3 66.5 + - - +
73B LYS* 3.3 12.5 + - - +
74B GLU* 3.2 21.8 + - + +
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Residues in contact with LEU 71 (chain B).
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* 3.8 27.6 - - + -
5B LEU* 5.3 4.0 - - + -
8B LYS* 3.8 30.7 - - + +
9B VAL* 4.7 10.8 - - + +
12B VAL* 3.9 14.8 - - + +
67B PHE* 2.8 30.7 + - + +
68B PHE* 3.3 34.1 - - + +
70B MET* 1.3 75.9 - - - +
72B ILE* 1.3 67.2 + - - +
74B GLU* 2.8 16.2 + - + +
75B ILE* 3.3 21.8 + - + +
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 3.6 28.9 - - + +
68A PHE* 4.1 21.3 - - + -
69A GLU* 4.5 15.0 - - + +
72A ILE* 3.8 26.9 - - + -
68B PHE 2.8 27.9 + - - +
69B GLU* 3.3 12.3 - - + +
71B LEU* 1.3 70.3 - - - +
73B LYS* 1.3 59.4 - - + +
75B ILE* 2.8 46.4 + - + +
76B LEU* 3.3 17.8 + - + +
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU* 3.3 25.6 + - - +
70B MET* 3.6 10.5 - - - +
71B LEU 3.2 0.6 - - - -
72B ILE* 1.3 84.6 - - + +
74B GLU* 1.3 60.7 + - - +
76B LEU* 3.3 26.9 + - + +
77B LYS* 3.7 6.6 + - - +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS* 3.3 38.2 + - + +
11B PHE* 3.3 37.2 - - + +
12B VAL* 4.5 16.2 - - + +
15B LYS* 5.0 19.2 + - + +
70B MET* 3.2 12.1 + - + +
71B LEU 2.8 12.7 + - - +
73B LYS* 1.3 75.6 - - + +
75B ILE* 1.3 61.3 + - - +
77B LYS* 4.2 12.0 + - - +
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ASP* 3.6 48.7 - - - +
65A VAL* 3.9 15.0 - - + -
68A PHE* 4.7 5.4 - - + -
4B PHE* 3.6 28.1 - - + -
5B LEU* 6.2 1.3 - - + -
8B LYS* 4.3 12.0 + - + +
71B LEU* 3.3 18.8 - - + +
72B ILE* 2.9 30.7 - - + +
74B GLU* 1.3 77.5 - - - +
76B LEU* 1.3 61.9 + - + +
77B LYS 2.9 20.3 - - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 4.5 25.4 - - + -
72B ILE* 3.6 27.6 - - + +
73B LYS* 3.3 18.3 + - + +
75B ILE* 1.3 77.2 - - + +
77B LYS* 1.3 61.7 + - - +
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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