Contacts of the helix formed by residues 72 - 86 (chain B) in PDB entry 2IK8
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 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B LEU 3.4 8.5 + - - -
69B LEU* 3.5 2.2 + - - -
71B SER* 1.3 79.2 - - - +
73B LYS* 1.3 61.8 + - - +
74B ASN* 3.6 4.4 + - - +
75B GLY* 2.7 28.8 + - - -
76B VAL* 2.9 26.7 + - - +
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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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71B SER 4.1 1.4 + - - -
72B SER* 1.3 74.2 - - - +
74B ASN* 1.3 70.7 + - - +
76B VAL* 3.3 4.8 + - - +
77B ALA* 3.2 19.2 + - - +
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Residues in contact with ASN 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 SER* 3.4 4.2 + - - +
73B LYS* 1.3 84.1 - - - +
75B GLY* 1.3 64.7 + - - +
77B ALA* 3.2 6.1 + - - +
78B ALA* 3.0 24.8 + - - +
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Residues in contact with GLY 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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69B LEU* 3.4 26.3 - - - +
72B SER* 2.7 24.1 + - - -
74B ASN* 1.3 74.2 - - - +
76B VAL* 1.3 56.0 + - - +
78B ALA* 3.3 5.2 + - - +
79B PHE* 2.9 31.4 + - - +
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.7 7.4 + - - +
70B LEU* 3.7 28.5 - - + +
71B SER 5.0 0.2 - - - -
72B SER 2.9 24.4 + - - +
73B LYS* 3.7 5.2 - - - +
75B GLY* 1.3 75.6 - - - +
77B ALA* 1.3 57.8 + - - +
79B PHE* 3.3 7.7 + - - +
80B HIS* 2.8 29.2 + - + +
92B LEU* 3.7 14.1 - - + +
96B LEU* 3.9 36.8 - - + -
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Residues in contact with ALA 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 LYS 3.2 8.9 + - - +
74B ASN* 3.2 10.2 + - - +
76B VAL* 1.3 79.4 - - - +
78B ALA* 1.3 61.9 + - - +
80B HIS* 3.2 8.9 + - - +
81B ALA* 3.1 22.9 + - - +
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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
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74B ASN 3.0 16.0 + - - +
75B GLY* 3.6 6.3 - - - +
77B ALA* 1.3 73.4 - - - +
79B PHE* 1.3 66.2 + - - +
81B ALA* 3.4 9.0 + - - +
82B PHE* 3.3 16.3 + - - +
171B PHE* 3.6 22.0 - - + -
176B ALA* 5.4 4.1 - - + +
177B TYR* 6.3 0.2 - - - -
180B LEU* 4.6 21.1 - - + -
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Residues in contact with PHE 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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66B PHE* 4.0 22.9 - + - -
69B LEU* 3.9 18.4 - - + -
70B LEU* 4.4 10.1 - - + -
75B GLY 2.9 18.4 + - - +
76B VAL* 3.6 6.1 - - - +
78B ALA* 1.3 73.1 - - - +
80B HIS* 1.3 59.7 + - - +
82B PHE* 3.4 1.8 + + - +
83B LEU* 3.0 68.6 + - + +
92B LEU* 3.8 11.2 - - + -
163B MET* 4.1 23.1 - - + -
167B SER* 4.3 3.1 - - - -
168B TYR* 4.2 14.6 - - - -
171B PHE* 3.7 41.9 - + + -
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Residues in contact with HIS 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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76B VAL* 2.8 15.5 + - + +
77B ALA* 3.3 12.8 - - - +
78B ALA 3.2 0.2 - - - -
79B PHE* 1.3 74.2 - - - +
81B ALA* 1.3 57.6 + - - +
83B LEU* 3.0 6.1 + - - +
84B LYS* 2.8 45.4 + - + +
89B GLU* 3.8 21.7 - - + +
92B LEU* 3.9 22.4 - - + +
93B GLU* 3.3 37.5 + - + +
96B LEU* 5.6 3.6 - - + -
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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
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77B ALA 3.1 9.7 + - - +
78B ALA* 3.5 11.9 - - - +
80B HIS* 1.3 79.1 + - - +
82B PHE* 1.3 61.2 + - - +
84B LYS* 3.4 11.1 - - - +
85B THR* 3.2 24.3 + - - +
176B ALA* 6.1 4.3 - - + -
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Residues in contact with PHE 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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78B ALA 3.3 5.5 + - - +
79B PHE* 3.6 10.1 - + - +
80B HIS 3.1 0.6 - - - -
81B ALA* 1.3 76.0 - - - +
83B LEU* 1.3 62.5 + - + +
84B LYS 3.0 1.6 - - - -
85B THR* 2.3 52.1 + - + -
86B GLU* 3.3 37.1 + - + +
167B SER* 3.5 22.2 - - - -
170B ARG* 3.7 8.7 - - + -
171B PHE* 3.5 44.6 - + + -
174B SER* 3.6 31.0 - - - -
175B PRO* 5.9 0.2 - - + -
176B ALA* 5.2 8.7 - - + +
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Residues in contact with LEU 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 PHE* 3.0 55.1 + - + +
80B HIS* 3.0 4.2 + - - +
82B PHE* 1.3 79.6 - - + +
84B LYS* 1.3 56.4 + - - +
86B GLU* 3.2 4.1 + - - +
87B PHE 3.0 8.7 + - - -
88B SER* 3.0 52.7 + - - +
89B GLU* 3.7 17.5 - - - +
91B ASN* 5.6 0.4 - - - +
92B LEU* 3.6 29.8 - - + +
163B MET* 4.6 5.8 - - + -
167B SER* 3.5 27.1 - - - +
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Residues in contact with LYS 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 HIS* 2.8 32.4 + - + +
81B ALA* 3.4 14.6 - - - +
82B PHE 3.0 0.2 - - - -
83B LEU* 1.3 76.7 - - - +
85B THR* 1.3 63.2 + - + +
87B PHE* 3.2 23.2 + - - -
89B GLU* 4.1 24.9 - - + +
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Residues in contact with THR 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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184A ILE 4.6 1.9 - - - +
81B ALA 3.2 16.2 - - - +
82B PHE* 2.3 46.5 + - + +
84B LYS* 1.3 73.8 - - + +
86B GLU* 1.3 65.4 + - - +
87B PHE* 3.4 16.5 - - - -
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Residues in contact with GLU 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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182A THR 5.0 2.3 - - - +
183A GLY* 3.2 2.9 - - - -
184A ILE 3.0 41.7 + - - +
185A VAL* 4.3 8.2 - - - +
82B PHE* 3.5 30.0 - - + +
83B LEU* 3.2 6.4 + - - +
85B THR* 1.3 88.0 + - - +
87B PHE* 1.3 71.7 + - - +
88B SER* 3.2 9.9 + - - +
167B SER* 3.8 8.3 - - - -
170B ARG* 2.7 46.6 + - - -
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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