Contacts of the helix formed by residues 72 - 88 (chain B) in PDB entry 4IP8
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 GLY 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B GLY 3.5 3.3 + - - -
71B HIS* 1.3 78.1 + - - +
73B ALA* 1.3 66.7 + - - -
74B GLU 3.2 2.9 - - - -
75B ASP* 3.3 19.4 + - - +
76B SER* 2.9 25.9 + - - -
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Residues in contact with ALA 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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67B ARG* 5.6 6.7 - - - +
71B HIS 3.8 1.2 + - - -
72B GLY* 1.3 72.5 - - - -
74B GLU* 1.3 63.1 + - + +
76B SER* 3.3 9.9 - - - -
77B LEU* 3.2 27.8 + - + +
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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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72B GLY 3.2 0.8 - - - -
73B ALA* 1.3 77.6 - - + +
75B ASP* 1.3 70.6 + - - +
76B SER 3.1 0.4 - - - -
77B LEU* 3.2 20.8 + - - +
78B ALA* 3.2 21.0 + - - +
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Residues in contact with ASP 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LYS* 4.6 4.6 - - - +
71B HIS* 3.5 26.3 + - + +
72B GLY* 3.3 21.1 + - - +
74B GLU* 1.3 80.0 - - - +
76B SER* 1.3 62.5 + - - +
78B ALA* 3.4 9.0 + - - +
79B ASP* 3.1 25.8 + - - +
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 4.5 13.7 + - - +
67B ARG* 3.8 28.9 + - - +
71B HIS* 3.3 21.2 + - - +
72B GLY 2.9 16.1 + - - -
73B ALA* 3.3 12.0 - - - -
74B GLU 3.1 0.2 - - - -
75B ASP* 1.3 75.3 - - - +
77B LEU* 1.3 67.8 + - - +
79B ASP* 2.9 17.4 + - - +
80B GLN* 3.0 19.9 + - - +
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Residues in contact with LEU 77 (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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73B ALA* 3.2 15.2 + - + +
74B GLU* 3.2 23.1 + - - +
76B SER* 1.3 77.3 - - - +
78B ALA* 1.3 61.4 + - - +
80B GLN* 3.4 28.8 + - - +
81B ALA* 3.2 21.1 + - - +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LYS* 3.8 20.0 - - - +
74B GLU 3.2 11.7 + - - +
75B ASP* 3.6 11.2 - - - +
76B SER 3.1 0.2 - - - -
77B LEU* 1.3 74.6 - - - +
79B ASP* 1.3 65.0 + - - +
81B ALA* 3.3 8.6 + - - +
82B ALA* 3.2 20.3 + - - +
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP* 4.4 1.8 - - - +
34B LYS* 3.2 25.3 + - - +
37B HIS* 3.2 31.2 - - - +
62B ARG* 4.1 12.3 - - - +
63B GLU* 6.5 0.4 - - + -
66B GLN* 3.8 10.4 + - - +
71B HIS* 2.8 33.1 + - - -
75B ASP 3.1 11.4 + - - +
76B SER* 2.9 9.7 + - - +
78B ALA* 1.3 77.7 - - - +
80B GLN* 1.3 58.1 - - + +
82B ALA* 3.1 5.4 + - - +
83B ASN* 2.8 32.2 + - - +
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Residues in contact with GLN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 6.1 0.2 - - - +
63B GLU* 3.1 37.7 - - + +
67B ARG* 5.0 0.2 + - - -
76B SER* 3.0 16.7 + - - +
77B LEU* 3.6 33.5 - - - +
78B ALA 3.3 0.2 - - - -
79B ASP* 1.3 76.1 - - + +
81B ALA* 1.3 58.4 + - - +
83B ASN* 3.2 14.6 + - - +
84B GLU* 2.9 52.3 + - + +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU 3.2 11.0 + - - +
78B ALA* 3.5 11.9 - - - +
79B ASP 3.2 0.4 - - - -
80B GLN* 1.3 78.8 - - - +
82B ALA* 1.3 57.4 + - - +
84B GLU* 3.6 9.7 + - - +
85B TRP* 3.1 28.8 + - - +
95B PHE* 5.0 1.7 - - - -
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Residues in contact with ALA 82 (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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34B LYS* 3.7 38.8 - - + +
37B HIS* 4.1 7.0 - - + -
38B ALA* 3.4 12.6 - - - +
78B ALA 3.2 9.6 + - - +
79B ASP 3.1 8.8 + - - +
81B ALA* 1.3 77.8 - - - +
83B ASN* 1.3 66.6 + - - +
85B TRP* 3.4 7.1 + - - +
86B GLY 3.2 16.5 + - - -
95B PHE* 4.3 12.3 - - + -
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Residues in contact with ASN 83 (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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37B HIS* 3.5 10.2 - - - +
41B ASN* 3.1 24.4 + - - +
59B SER* 3.5 16.5 + - - -
62B ARG* 2.4 45.4 + - - +
63B GLU* 5.8 0.4 + - - +
79B ASP 2.8 16.5 + - - -
80B GLN* 3.3 21.1 - - - +
82B ALA* 1.3 77.8 - - - +
84B GLU* 1.3 57.9 + - + +
87B ARG* 2.9 42.8 + - - +
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLN* 2.9 38.2 + - - +
81B ALA* 4.1 8.1 - - - +
83B ASN* 1.3 74.9 - - + +
85B TRP* 1.3 66.8 + - - +
87B ARG* 3.9 22.1 - - - +
88B SER* 3.0 28.4 + - - -
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Residues in contact with TRP 85 (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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38B ALA* 4.4 2.0 - - + -
81B ALA 3.1 20.2 + - - +
82B ALA 3.4 6.3 - - - +
84B GLU* 1.3 76.3 - - - +
86B GLY* 1.3 61.7 + - - +
88B SER* 3.2 9.0 + - - -
90B LYS* 3.0 77.7 + - + +
91B ASP* 2.8 27.6 + - + -
94B HIS* 3.5 40.4 - + + +
95B PHE* 3.3 35.0 - + + -
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Residues in contact with GLY 86 (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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38B ALA* 3.4 25.4 - - - -
42B TYR* 3.3 22.6 - - - -
45B ALA* 4.6 0.7 - - - +
82B ALA 3.2 7.3 + - - -
83B ASN 3.9 1.6 - - - -
85B TRP* 1.3 79.2 - - - +
87B ARG* 1.3 59.8 + - - +
89B GLY* 2.9 22.0 + - - -
90B LYS 3.8 11.4 - - - -
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Residues in contact with ARG 87 (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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41B ASN* 2.7 39.6 + - + +
45B ALA* 3.3 22.3 - - + +
52B VAL* 4.0 28.0 - - + +
55B ALA* 3.8 13.0 - - + +
56B GLU* 3.3 37.5 - - - +
59B SER* 3.2 25.5 + - - -
60B ASP* 5.5 1.4 + - - -
83B ASN* 2.9 31.2 + - - +
84B GLU* 3.4 20.8 + - - +
86B GLY* 1.3 75.8 - - - +
88B SER* 1.3 58.6 + - - +
89B GLY 3.2 0.4 - - - -
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU 3.0 18.4 + - - -
85B TRP* 3.2 9.4 + - - -
86B GLY 3.1 0.4 + - - -
87B ARG* 1.3 76.2 - - - +
89B GLY* 1.3 58.6 + - - +
90B LYS* 3.7 19.1 + - - +
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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