Contacts of the helix formed by residues 72 - 87 (chain B) in PDB entry 2K8M
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 LYS 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASP* 4.2 11.4 - - - +
32B SER* 3.8 18.8 - - - +
66B ASN* 4.5 8.9 - - - +
68B ASP* 2.8 31.8 + - - -
70B GLU* 2.7 33.9 + - - +
71B LEU* 1.3 74.0 - - - +
73B PHE* 1.3 60.1 + - - +
74B ASN* 3.2 2.5 - - + +
75B GLU* 3.0 28.1 + - - +
76B TYR* 2.7 31.9 + - - +
88C ARG* 5.7 2.0 - - - +
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.6 11.0 - - + -
20B PHE* 3.6 35.4 - + - -
31B ASP* 3.6 14.1 + - - +
72B LYS* 1.3 74.7 - - - +
74B ASN* 1.3 60.7 + - + +
76B TYR* 3.5 5.3 + + - +
77B TRP* 3.1 65.6 + + + +
84C ALA 4.6 6.3 - - - -
85C LYS* 5.6 1.8 - - - -
87C ILE* 4.3 19.1 - - + -
88C ARG* 3.8 60.3 - - + +
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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
----------------------------------------------------------
65B VAL* 6.2 0.2 - - - +
72B LYS* 3.2 1.8 - - + +
73B PHE* 1.3 83.1 - - + +
75B GLU* 1.3 92.5 + - - +
77B TRP* 3.3 8.6 + - - +
78B ARG* 3.3 30.7 + - - +
85C LYS* 5.0 18.2 - - - +
89C LYS* 5.6 12.2 - - - -
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.9 27.0 - - - +
64B ASP* 4.2 14.8 - - - +
65B VAL* 3.7 25.0 - - + +
66B ASN* 5.8 1.8 - - - +
70B GLU 5.8 0.2 - - - +
71B LEU* 4.0 15.7 - - + +
72B LYS* 3.0 38.9 + - - +
74B ASN* 1.3 101.9 + - - +
76B TYR* 1.3 62.8 + - - +
78B ARG* 3.2 25.4 - - - +
79B LEU 3.9 1.6 + - - -
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL 5.5 0.4 - - - -
19B THR* 5.4 0.5 - - - +
20B PHE* 3.6 43.0 + + + +
23B PHE* 6.0 0.8 - - + +
33B LEU* 3.6 32.5 - - + -
38B PHE* 3.8 25.1 - + - -
41B LEU* 3.6 32.5 - - + +
71B LEU* 4.3 13.4 - - + +
72B LYS 2.7 22.5 + - - +
73B PHE* 3.8 6.1 - + - +
75B GLU* 1.3 69.1 - - - +
77B TRP* 1.3 71.1 - + - +
78B ARG 3.0 2.2 - - - -
79B LEU* 3.0 29.4 + - + +
80B ILE* 3.8 26.6 + - + +
9C LEU* 5.4 5.5 - - - +
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Residues in contact with TRP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 4.8 15.9 - - + -
16B VAL* 3.8 28.5 - - + -
17B VAL* 4.4 11.4 - - + -
20B PHE* 6.1 1.8 - + + -
73B PHE* 3.1 56.1 + + + +
74B ASN* 3.3 8.5 + - - +
76B TYR* 1.3 81.7 - + - +
78B ARG* 1.3 62.0 + - - +
80B ILE* 3.1 46.3 + - + +
81B GLY* 3.1 12.4 + - - -
77C TRP* 5.7 6.6 - + - -
80C ILE* 5.3 0.6 + - - +
81C GLY* 5.4 6.8 - - - -
84C ALA* 3.4 36.2 - - + +
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B SER 3.7 11.2 + - - -
63B LEU* 2.9 51.9 + - + +
65B VAL* 3.7 19.1 - - - +
74B ASN* 3.3 25.2 + - - +
75B GLU* 3.2 18.4 - - - +
76B TYR 3.0 0.6 - - - -
77B TRP* 1.3 78.2 - - - +
79B LEU* 1.3 59.4 + - - +
81B GLY* 3.3 2.9 + - - +
82B GLU* 3.2 27.2 + - - +
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Residues in contact with LEU 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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38B PHE* 3.7 28.9 - - + +
41B LEU* 4.9 8.1 - - + -
42B VAL* 4.4 20.6 - - + -
50B LEU* 4.8 11.4 - - + -
59B LYS* 5.2 7.2 - - + -
63B LEU* 3.9 28.2 - - + +
75B GLU 3.9 0.8 + - - -
76B TYR* 3.0 23.8 + - + +
78B ARG* 1.3 79.6 - - - +
80B ILE* 1.3 58.4 + - + +
82B GLU* 3.2 7.1 + - + +
83B LEU* 2.8 57.8 + - + +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 5.0 15.3 - - + -
76B TYR* 4.1 27.1 - - + +
77B TRP* 3.1 56.9 + - + +
79B LEU* 1.3 77.8 - - + +
81B GLY* 1.3 61.5 + - - +
83B LEU* 3.4 15.0 - - + +
84B ALA* 3.0 23.9 + - - +
13C ILE* 3.8 26.9 - - + -
77C TRP* 5.3 7.0 - - + -
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Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TRP* 3.1 14.5 + - - -
78B ARG* 3.3 5.1 + - - -
79B LEU 3.2 0.4 - - - -
80B ILE* 1.3 78.5 - - - +
82B GLU* 1.3 65.5 + - - +
84B ALA* 3.4 4.3 + - - +
85B LYS* 3.2 20.7 + - - +
77C TRP* 4.8 16.4 - - - -
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 6.1 2.7 - - + -
63B LEU* 4.9 11.7 - - + -
78B ARG 3.2 12.3 + - - +
79B LEU* 3.2 9.9 + - + +
81B GLY* 1.3 74.4 - - - +
83B LEU* 1.3 56.5 + - + +
85B LYS* 2.7 43.5 + - - +
86B GLU* 2.8 41.2 + - + +
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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
----------------------------------------------------------
41B LEU* 6.1 0.9 - - + -
46B LEU* 3.6 36.3 - - + -
49B LEU* 3.3 30.6 - - + +
50B LEU* 3.6 35.4 - - + -
79B LEU* 2.8 43.6 + - + +
80B ILE* 3.4 17.7 - - + +
82B GLU* 1.3 77.2 - - + +
84B ALA* 1.3 62.3 + - - +
86B GLU* 3.1 13.1 + - - +
87B ILE* 3.3 6.4 + - - +
9C LEU* 5.9 5.6 - - + -
13C ILE* 4.4 6.5 - - + -
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Residues in contact with ALA 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 ILE 3.0 15.5 + - - +
81B GLY 3.7 4.9 - - - +
83B LEU* 1.3 76.4 - - - +
85B LYS* 1.3 57.1 + - - +
87B ILE* 3.1 25.5 - - - +
88B ARG* 4.1 4.0 + - - +
13C ILE* 3.9 21.0 - - + +
73C PHE* 5.6 2.9 - - - -
77C TRP* 3.4 46.1 + - + +
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Residues in contact with LYS 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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81B GLY 3.2 10.8 + - - +
82B GLU* 2.7 49.1 + - - +
83B LEU 3.1 0.4 - - - -
84B ALA* 1.3 76.4 - - - +
86B GLU* 1.3 52.2 + - + +
87B ILE 3.0 4.7 - - - -
88B ARG* 3.1 7.1 + - - +
89B LYS* 2.7 65.0 + - + +
74C ASN* 4.5 19.7 - - - +
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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
----------------------------------------------------------
49B LEU* 4.3 8.2 - - + +
50B LEU* 4.1 25.0 - - + +
82B GLU* 2.8 21.3 + - + +
83B LEU* 3.1 9.8 + - - +
85B LYS* 1.3 76.5 - - + +
87B ILE* 1.3 58.9 + - - +
88B ARG 3.3 0.2 - - - -
89B LYS* 2.6 34.8 + - - +
90B LYS* 2.6 80.3 + - - +
91B LYS* 5.6 0.9 - - - +
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.8 22.2 - - + -
83B LEU 3.3 4.8 + - - +
84B ALA* 3.1 26.7 - - - +
85B LYS 3.0 1.0 - - - -
86B GLU* 1.3 78.6 - - - +
88B ARG* 1.3 61.7 + - + +
90B LYS* 5.5 2.2 - - - -
97B LYS 4.9 8.5 - - - +
98B LYS* 5.5 8.2 - - + +
3C ALA* 4.9 10.5 - - + -
6C LEU* 4.4 29.8 - - + -
10C GLU* 4.9 8.3 - - + +
13C ILE* 5.3 7.9 - - + -
14C GLU* 4.9 12.8 - - + -
17C VAL* 5.7 10.1 - - + -
73C PHE* 6.2 2.5 - - + -
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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
------------------------------------------------------------
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