Contacts of the helix formed by residues 81 - 98 (chain B) in PDB entry 3IKG
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 THR 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B HIS* 3.7 2.2 - - - -
65B SER* 4.5 7.6 - - - +
79B THR 4.7 4.7 - - - +
80B ARG* 1.3 78.3 - - - +
82B GLN* 1.3 53.1 + - - +
83B GLU* 3.7 9.2 + - - +
84B GLU* 2.8 43.3 + - - +
85B ALA* 2.8 32.7 + - - +
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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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64B HIS* 3.5 45.8 + - + +
65B SER* 5.3 0.4 + - - -
66B GLN* 6.0 1.5 - - + +
81B THR* 1.3 71.5 - - - +
83B GLU* 1.3 57.0 + - - +
85B ALA* 3.1 3.1 + - - +
86B LEU* 2.7 39.0 + - + +
151B PHE* 4.0 25.9 - - + -
156B ILE* 4.4 10.5 - - + -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B THR* 3.1 9.9 + - - +
82B GLN* 1.3 87.2 + - - +
84B GLU* 1.3 58.9 + - + +
86B LEU* 3.2 18.9 + - - +
87B GLU* 3.0 36.1 + - - +
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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
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79B THR 4.7 0.2 - - - +
80B ARG* 3.2 19.7 - - + +
81B THR* 2.8 50.0 + - - +
83B GLU* 1.3 72.2 - - + +
85B ALA* 1.3 68.1 + - - +
87B GLU* 3.2 20.4 + - - +
88B LEU* 3.0 28.6 + - + +
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Residues in contact with ALA 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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62B VAL* 3.8 18.1 - - + +
63B LYS 3.8 21.3 - - - +
64B HIS* 4.1 6.3 - - + -
80B ARG* 3.8 10.4 - - - +
81B THR 2.8 11.9 + - - +
82B GLN* 3.2 14.6 - - - +
84B GLU* 1.3 76.4 - - - +
86B LEU* 1.3 62.2 + - - +
88B LEU* 3.2 4.9 + - - +
89B ILE* 3.0 27.6 + - - +
156B ILE* 4.4 5.6 - - + -
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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
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82B GLN* 2.7 21.7 + - + +
83B GLU* 3.6 20.4 - - - +
84B GLU 3.2 0.2 - - - -
85B ALA* 1.3 73.1 - - - +
87B GLU* 1.3 53.9 + - - +
89B ILE* 3.3 4.5 + - + +
90B ASN* 2.8 62.7 + - - +
149B PRO* 3.7 30.7 - - + -
151B PHE* 4.1 23.8 - - + -
156B ILE* 4.2 12.3 - - + +
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Residues in contact with GLU 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 GLU* 3.0 20.9 + - - +
84B GLU* 3.3 27.2 - - - +
86B LEU* 1.3 76.5 - - - +
88B LEU* 1.3 61.9 + - + +
90B ASN* 3.6 5.8 + - - +
91B GLY* 3.0 19.1 + - - -
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Residues in contact with LEU 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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62B VAL* 3.9 11.0 - - + -
74B ARG* 6.3 0.2 - - - +
80B ARG* 3.5 36.6 - - + +
84B GLU* 3.0 17.9 + - + +
85B ALA 3.2 5.8 + - - +
87B GLU* 1.3 77.0 - - + +
89B ILE* 1.3 57.1 + - - +
91B GLY* 2.9 3.6 + - - -
92B TYR* 2.8 64.9 + - + +
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Residues in contact with ILE 89 (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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60B LEU* 3.9 11.7 - - + +
62B VAL* 3.6 22.7 - - + -
85B ALA 3.0 15.3 + - - +
86B LEU 3.6 6.3 - - - +
88B LEU* 1.3 77.4 - - - +
90B ASN* 1.3 63.8 + - - +
91B GLY 3.2 0.2 + - - -
92B TYR* 3.2 5.7 + - - +
93B ILE* 2.9 41.2 + - + +
149B PRO* 3.9 23.1 - - + -
156B ILE* 3.5 37.2 - - + +
158B ILE* 3.7 25.4 - - + +
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Residues in contact with ASN 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* 2.8 48.0 + - - +
87B GLU* 4.1 5.7 - - - +
89B ILE* 1.3 73.1 - - - +
91B GLY* 1.3 62.2 + - - +
93B ILE* 3.4 11.6 + - - +
94B GLN* 3.2 28.3 + - + +
149B PRO* 3.4 22.7 - - - +
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Residues in contact with GLY 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 GLU 3.0 11.9 + - - -
88B LEU* 2.9 8.7 + - - -
90B ASN* 1.3 74.9 - - - +
92B TYR* 1.3 65.7 + - - +
94B GLN* 3.1 14.3 + - - +
95B LYS* 3.2 18.0 + - - +
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Residues in contact with TYR 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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60B LEU* 3.8 28.7 - - + -
62B VAL* 3.9 19.7 - - + -
74B ARG* 4.7 4.5 + - - -
88B LEU* 2.8 49.6 + - + +
89B ILE* 3.7 6.5 - - - +
91B GLY* 1.3 71.5 - - - +
93B ILE* 1.3 64.7 + - - +
95B LYS* 3.0 22.0 + - + +
96B ILE* 3.1 18.3 + - + +
106B LEU* 4.0 21.9 - - + +
110B PHE* 3.3 49.5 + + + +
158B ILE* 4.0 10.3 - - + -
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Residues in contact with ILE 93 (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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89B ILE* 2.9 31.9 + - + +
90B ASN* 3.6 13.2 - - - +
91B GLY 3.2 0.2 - - - -
92B TYR* 1.3 76.6 - - - +
94B GLN* 1.3 65.9 + - - +
96B ILE* 3.3 9.2 + - - +
97B LYS* 2.9 61.8 + - + +
146B MET* 4.4 7.0 - - + -
147B SER 4.9 1.3 - - - +
148B GLY* 4.4 6.5 - - - -
149B PRO* 3.7 31.4 - - + -
158B ILE* 3.4 25.3 - - + +
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Residues in contact with GLN 94 (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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90B ASN* 3.2 13.6 + - + +
91B GLY* 3.1 9.2 + - - +
92B TYR 3.1 0.6 - - - -
93B ILE* 1.3 83.9 - - - +
95B LYS* 1.3 63.2 + - - +
97B LYS* 3.6 34.4 + - - +
98B SER* 3.1 31.6 + - - -
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Residues in contact with LYS 95 (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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91B GLY 3.2 13.7 + - - +
92B TYR* 3.0 16.9 + - + +
94B GLN* 1.3 77.5 - - - +
96B ILE* 1.3 58.8 + - - +
98B SER* 4.4 1.1 - - - -
99B GLY 3.4 0.5 + - - -
100B GLU* 2.7 79.5 + - - +
101B GLU* 3.1 27.5 + - + +
106B LEU* 4.2 22.2 - - + -
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Residues in contact with ILE 96 (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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60B LEU* 5.6 1.1 - - + -
92B TYR* 3.1 24.6 + - + +
93B ILE* 3.7 6.7 - - - +
95B LYS* 1.3 74.9 - - - +
97B LYS* 1.3 59.0 + - + +
98B SER 3.0 4.7 - - - -
99B GLY* 3.0 19.8 + - - -
101B GLU 3.6 8.3 - - - +
102B ASP* 5.4 0.2 - - - -
103B PHE* 3.8 51.8 - - + +
106B LEU* 4.0 16.4 - - + -
146B MET* 3.8 28.3 - - + -
158B ILE* 4.6 8.3 - - + -
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Residues in contact with LYS 97 (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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93B ILE* 2.9 36.6 + - + +
94B GLN* 3.6 30.9 + - - +
96B ILE* 1.3 76.5 - - + +
98B SER* 1.3 54.1 + - - +
146B MET* 4.2 14.8 - - + -
147B SER 5.9 1.6 - - - -
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Residues in contact with SER 98 (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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94B GLN* 3.1 17.4 + - - -
95B LYS* 4.2 0.7 - - - -
96B ILE 3.0 0.2 - - - -
97B LYS* 1.3 74.0 - - - +
99B GLY* 1.3 60.6 + - - +
100B GLU* 3.1 26.7 + - - +
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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