Contacts of the helix formed by residues 78 - 92 (chain B) in PDB entry 4IRX
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 ASN 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B ALA* 2.9 17.9 + - - +
76B GLN* 3.9 6.3 - - + +
77B ASN* 1.3 77.8 - - - +
79B SER* 1.3 58.3 + - - +
80B SER* 2.9 24.4 + - - -
81B LYS* 3.0 17.4 + - + +
82B GLN* 3.0 25.5 + - - +
102B THR* 3.9 3.8 - - - +
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Residues in contact with SER 79 (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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77B ASN 4.1 1.2 + - - -
78B ASN* 1.3 70.0 + - - +
80B SER* 1.3 66.0 + - - +
82B GLN* 3.2 3.7 + - - +
83B ILE* 2.9 39.1 + - - +
102B THR* 3.2 25.7 + - - -
103B ASP* 5.2 1.6 - - - -
106B ALA* 4.5 14.2 - - - +
107B LEU* 4.2 11.4 - - - -
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Residues in contact with SER 80 (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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78B ASN* 2.9 10.7 + - - -
79B SER* 1.3 83.0 + - - +
81B LYS* 1.3 63.4 + - - +
83B ILE* 3.7 10.7 - - - +
84B SER* 3.1 23.9 + - - -
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Residues in contact with LYS 81 (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 LEU* 5.4 0.6 - - - +
74B ASP 2.8 25.1 + - - +
75B ALA* 3.8 17.5 - - - +
76B GLN* 3.9 26.4 - - + +
78B ASN* 3.0 24.8 + - + +
80B SER* 1.3 76.0 - - - +
82B GLN* 1.3 59.6 + - - +
84B SER* 3.0 9.9 + - - +
85B ASP* 2.8 57.3 + - - +
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Residues in contact with GLN 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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43B SER* 2.9 33.8 + - - +
44B PHE 3.8 9.7 + - - -
45B ASN 4.0 0.4 - - - +
75B ALA* 3.6 19.2 - - + +
78B ASN 3.0 8.8 + - - +
79B SER* 3.2 8.9 + - - +
81B LYS* 1.3 75.3 - - - +
83B ILE* 1.3 59.0 + - - +
85B ASP* 3.2 6.7 + - - +
86B LEU* 2.9 36.5 + - + +
99B VAL* 3.8 7.8 - - - +
100B ALA 3.0 23.6 + - - -
101B PRO* 3.4 6.3 - - - +
102B THR* 2.8 31.3 + - - +
107B LEU* 3.6 15.4 - - + +
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Residues in contact with ILE 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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79B SER* 2.9 27.3 + - - +
80B SER* 3.7 8.7 - - - +
82B GLN* 1.3 76.4 - - - +
84B SER* 1.3 58.0 + - - +
86B LEU* 3.3 4.1 + - - +
87B GLN* 3.0 50.3 + - - +
106B ALA* 3.9 20.0 - - + +
107B LEU* 3.9 21.8 - - + -
110B ALA* 4.1 18.7 - - + +
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Residues in contact with SER 84 (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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80B SER 3.1 13.8 + - - -
81B LYS* 3.0 20.1 + - - +
83B ILE* 1.3 72.9 - - - +
85B ASP* 1.3 62.8 + - - +
87B GLN* 3.4 16.1 + - - +
88B ALA* 3.0 30.1 + - - +
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Residues in contact with ASP 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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31B LEU* 4.6 3.2 - - - +
43B SER* 5.0 4.6 + - - +
73B LEU* 3.7 38.7 - - + +
74B ASP 4.1 4.5 - - - +
75B ALA* 4.5 0.9 + - - +
81B LYS* 2.8 55.4 + - - +
82B GLN* 3.4 12.5 - - - +
84B SER* 1.3 75.4 + - - +
86B LEU* 1.3 60.0 + - + +
88B ALA* 3.4 6.3 + - - +
89B ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 5.3 3.8 - - + -
43B SER* 3.8 20.4 - - - +
73B LEU* 5.6 0.2 - - + -
82B GLN* 2.9 19.0 + - + +
83B ILE* 3.6 4.9 - - - +
85B ASP* 1.3 75.1 - - + +
87B GLN* 1.3 66.1 + - + +
89B ALA* 3.2 5.7 + - + +
90B ALA 3.1 18.4 + - - -
97B VAL* 3.5 31.2 - - + -
99B VAL* 4.0 19.3 - - + -
107B LEU* 3.9 26.9 - - + -
110B ALA* 4.4 11.7 - - + -
111B ALA* 5.5 2.2 - - + +
114B LEU* 3.7 31.2 - - + +
121B VAL* 6.1 0.4 - - + -
128B ILE* 6.1 1.3 - - + -
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Residues in contact with GLN 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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83B ILE* 3.0 37.5 + - + +
84B SER* 3.7 17.0 - - - +
85B ASP 3.3 0.2 - - - -
86B LEU* 1.3 77.0 - - - +
88B ALA* 1.3 61.0 + - - +
90B ALA* 3.3 7.0 + - - +
91B VAL* 3.0 30.5 + - + +
110B ALA* 5.7 5.7 - - + +
113B ASP* 4.7 17.1 + - - +
114B LEU* 4.7 5.2 - - + -
117B GLN* 5.6 3.0 + - - +
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Residues in contact with ALA 88 (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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31B LEU* 3.6 15.0 - - + -
84B SER 3.0 18.1 + - - +
85B ASP* 3.7 6.5 - - - +
87B GLN* 1.3 73.1 - - - +
89B ALA* 1.3 66.7 + - - +
91B VAL* 3.3 8.6 + - - +
92B GLN* 3.0 37.6 + - - +
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.5 13.6 - - + +
41B VAL* 4.0 35.7 - - + -
85B ASP 3.0 14.5 + - - +
86B LEU* 3.5 12.1 - - - +
88B ALA* 1.3 76.9 - - - +
90B ALA* 1.3 58.6 + - - +
92B GLN* 3.3 3.8 + - - +
93B GLY 3.2 5.5 + - - -
94B ALA* 3.0 31.0 + - + +
97B VAL* 4.6 5.6 - - + -
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Residues in contact with ALA 90 (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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86B LEU 3.1 5.1 + - - -
87B GLN 3.6 7.2 - - - +
88B ALA 3.2 0.2 - - - -
89B ALA* 1.3 73.1 - - - +
91B VAL* 1.3 66.7 + - + +
93B GLY* 3.1 13.5 + - - -
94B ALA* 4.5 3.6 - - - +
114B LEU* 3.6 28.5 - - + -
117B GLN* 3.5 25.8 - - - +
119B VAL* 3.9 20.5 - - + +
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Residues in contact with VAL 91 (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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87B GLN* 3.0 20.1 + - + +
88B ALA* 3.6 10.5 - - - +
90B ALA* 1.3 77.1 - - + +
92B GLN* 1.3 69.7 + - + +
93B GLY* 3.4 1.0 + - - -
117B GLN* 5.4 3.6 - - - +
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Residues in contact with GLN 92 (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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31B LEU* 3.5 42.7 + - + +
32B VAL 4.2 11.2 - - - +
33B PRO* 5.0 4.3 - - + +
34B ARG* 3.3 21.1 + - + +
88B ALA* 3.0 21.9 + - - +
89B ALA* 3.3 4.2 + - - +
90B ALA 3.1 0.2 - - - -
91B VAL* 1.3 85.0 - - + +
93B GLY* 1.3 57.0 + - - +
94B ALA 3.6 0.4 - - - -
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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