Contacts of the helix formed by residues 72 - 88 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C HIS* 1.3 75.8 + - - +
73C ALA* 1.3 59.9 + - - -
74C GLU 3.3 2.9 - - - -
75C ASP* 3.0 18.1 + - - +
76C SER* 2.9 28.6 + - - -
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Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ARG* 4.0 20.2 - - - +
71C HIS 3.5 2.0 + - - -
72C GLY* 1.3 72.5 - - - -
74C GLU* 1.3 61.9 + - + +
76C SER* 3.4 6.9 + - - -
77C LEU* 3.1 30.1 + - + +
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Residues in contact with GLU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLY 3.3 0.6 - - - -
73C ALA* 1.3 78.4 - - + +
75C ASP* 1.3 60.4 + - - +
77C LEU* 3.6 18.5 + - - +
78C ALA* 3.0 27.0 + - - +
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Residues in contact with ASP 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LYS* 5.0 10.5 + - - +
71C HIS* 3.7 23.3 + - + +
72C GLY* 3.0 19.5 + - - +
74C GLU* 1.3 79.7 - - - +
76C SER* 1.3 55.7 + - - +
78C ALA* 3.1 7.3 + - - +
79C ASP* 2.7 40.7 + - - +
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Residues in contact with SER 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLU* 4.4 22.4 - - - +
67C ARG* 3.6 20.1 - - - +
71C HIS* 3.0 26.0 + - - -
72C GLY 2.9 9.8 + - - -
73C ALA* 3.7 9.9 - - - -
75C ASP* 1.3 74.9 - - - +
77C LEU* 1.3 59.2 + - - +
79C ASP* 3.2 7.1 + - - +
80C GLN* 2.9 35.0 + - - +
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ALA* 3.1 21.4 + - + +
74C GLU* 3.8 21.3 - - - +
76C SER* 1.3 76.3 - - - +
78C ALA* 1.3 62.2 + - - +
80C GLN* 3.2 29.6 + - - +
81C ALA* 3.1 21.1 + - - +
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LYS* 3.9 19.8 - - + +
74C GLU 3.0 19.0 + - - +
75C ASP* 3.1 8.5 + - - +
77C LEU* 1.3 76.7 - - - +
79C ASP* 1.3 62.7 + - - +
81C ALA* 3.4 9.1 + - - +
82C ALA* 3.2 20.1 + - - +
95C PHE* 5.3 2.6 - - - -
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASP* 5.4 0.7 - - - +
34C LYS* 3.0 38.4 + - - +
37C HIS* 3.5 28.6 + - - +
62C ARG* 4.1 12.3 - - - +
63C GLU* 6.5 0.7 - - + -
66C GLN* 3.8 7.0 + - - +
71C HIS* 2.9 28.5 + - - -
75C ASP 2.7 14.5 + - - +
76C SER* 3.4 7.4 - - - +
78C ALA* 1.3 75.0 - - - +
80C GLN* 1.3 59.7 + - - +
82C ALA* 3.1 4.1 + - - +
83C ASN* 2.9 34.1 + - - -
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Residues in contact with GLN 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLU* 3.0 33.3 + - + +
76C SER* 2.9 20.6 + - - +
77C LEU* 3.4 31.0 - - - +
79C ASP* 1.3 75.2 - - + +
81C ALA* 1.3 63.4 + - - +
83C ASN* 3.4 13.1 + - - +
84C GLU* 3.0 39.0 + - + +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LEU 3.1 12.7 + - - +
78C ALA* 3.5 12.3 - - - +
79C ASP 3.2 0.4 - - - -
80C GLN* 1.3 77.8 - - - +
82C ALA* 1.3 56.1 + - - +
84C GLU* 3.5 7.4 + - - +
85C TRP* 2.9 31.6 + - - +
95C PHE* 4.7 6.7 - - + -
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LYS* 3.7 33.7 - - + +
37C HIS* 4.1 6.7 - - + -
38C ALA* 3.5 11.0 - - - +
78C ALA 3.2 9.4 + - - +
79C ASP* 3.1 9.7 + - - +
81C ALA* 1.3 76.4 - - - +
83C ASN* 1.3 66.6 + - - +
85C TRP* 3.2 2.4 + - - +
86C GLY 3.0 19.2 + - - -
95C PHE* 3.8 23.7 - - + -
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Residues in contact with ASN 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C HIS* 3.3 10.4 - - - +
41C ASN* 2.8 35.8 + - - +
59C SER* 3.5 11.6 + - - -
62C ARG* 2.3 44.4 + - - +
63C GLU* 6.1 0.4 - - - +
79C ASP 2.9 22.6 + - - -
80C GLN* 3.5 13.0 - - - +
82C ALA* 1.3 76.7 - - - +
84C GLU* 1.3 57.1 - - + +
86C GLY 3.3 0.2 + - - -
87C ARG* 2.8 40.1 + - - +
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Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C GLN* 3.0 27.8 + - - +
81C ALA* 4.0 6.1 - - - +
83C ASN* 1.3 76.6 - - + +
85C TRP* 1.3 64.7 + - - +
87C ARG* 4.0 23.2 + - - +
88C SER* 3.0 27.9 + - - -
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Residues in contact with TRP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ALA* 4.9 0.4 - - + -
81C ALA 2.9 21.4 + - - +
82C ALA 3.4 5.2 - - - +
84C GLU* 1.3 75.7 - - - +
86C GLY* 1.3 62.4 + - - +
88C SER* 2.8 21.0 + - - -
90C LYS* 3.2 68.7 + - + +
91C ASP* 3.0 27.9 + - + -
92C PRO* 4.6 1.8 - - + -
94C HIS* 3.6 39.7 - + + +
95C PHE* 3.6 27.1 - + + -
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Residues in contact with GLY 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ALA* 3.5 24.7 - - - -
42C TYR* 3.3 25.8 - - - +
45C ALA* 4.5 0.5 - - - +
82C ALA 3.0 11.8 + - - -
83C ASN 3.7 1.8 - - - -
85C TRP* 1.3 79.1 - - - +
87C ARG* 1.3 56.3 + - - +
89C GLY* 2.9 20.4 + - - -
90C LYS 4.1 7.4 - - - -
92C PRO* 5.5 0.2 - - - -
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Residues in contact with ARG 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ASN* 3.0 37.4 + - + +
45C ALA* 3.4 20.1 - - + +
52C VAL* 3.9 26.2 - - + +
55C ALA* 4.5 3.4 - - + -
56C GLU* 3.7 45.9 + - - +
59C SER* 3.3 24.0 + - - -
60C ASP* 5.4 1.6 + - - -
83C ASN* 2.8 31.6 + - - +
84C GLU* 4.0 22.9 + - - +
86C GLY* 1.3 72.1 - - - +
88C SER* 1.3 60.6 + - - +
89C GLY 3.1 1.1 + - - -
205C P4C 3.9 5.5 - - - -
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLU 3.0 15.3 + - - -
85C TRP* 2.8 19.4 + - - -
87C ARG* 1.3 77.1 - - - +
89C GLY* 1.3 56.8 + - - +
90C LYS* 3.5 25.3 + - - +
205C P4C 3.9 11.5 + - - -
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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