Contacts of the helix formed by residues 57 - 78 (chain B) in PDB entry 1K2D
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 ASP 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 4.6 1.4 - - - +
76A ARG* 2.4 45.6 + - - -
37B TYR* 4.0 10.9 - - - -
38B LEU* 3.9 20.3 - - + +
54B GLY* 2.8 10.6 + - - +
55B ARG 2.8 5.8 + - - -
56B PRO* 1.3 74.6 - - - +
58B ALA* 1.3 71.3 + - - +
59B GLU 3.6 1.1 - - - -
60B TYR* 3.0 16.8 + - - +
61B TYR* 3.2 18.0 + - + +
7P SER* 3.0 27.9 - - - -
8P GLN* 4.0 6.1 + - - +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.3 12.0 - - + +
47B TYR* 4.6 4.5 - - - +
48B ARG* 5.5 3.4 - - - -
49B ALA* 5.1 11.9 - - + +
54B GLY 3.2 9.5 + - - +
55B ARG* 3.3 14.1 + - - +
57B ASP* 1.3 80.9 - - - +
59B GLU* 1.3 66.0 + - + +
61B TYR* 3.0 11.8 + - - +
62B ASN* 3.4 19.4 + - - +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG 5.0 0.4 + - - -
58B ALA* 1.3 78.8 - - - +
60B TYR* 1.3 62.6 + - - +
62B ASN* 3.5 10.0 + - - +
63B LYS* 3.1 58.7 + - + +
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Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PRO 4.9 0.9 - - - +
57B ASP* 3.0 15.7 + - - +
58B ALA 2.9 0.4 + - - -
59B GLU* 1.3 82.2 - - - +
61B TYR* 1.3 75.7 + + - +
63B LYS* 3.4 5.2 + - + +
64B GLN* 2.9 66.3 + - + +
67B TYR* 3.5 14.8 + - - -
6P PRO* 4.2 2.9 + - - +
7P SER 3.3 31.3 + - - -
8P GLN* 3.5 39.5 - - + +
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASN* 4.3 2.8 + - - -
30B TYR* 3.5 27.8 - + - -
37B TYR* 5.6 1.4 + - - -
38B LEU* 3.2 33.1 - - + +
47B TYR* 3.6 37.6 - + + -
57B ASP* 3.2 10.0 + - - -
58B ALA 3.0 7.8 + - - +
60B TYR* 1.3 84.5 - + - +
62B ASN* 1.3 65.8 + - - +
67B TYR* 3.0 55.3 + + + -
68B LEU 3.7 4.2 + - - -
5P ARG* 2.5 25.6 + - + -
7P SER* 3.3 33.4 + - - -
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Residues in contact with ASN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 3.3 24.7 + - - +
47B TYR* 3.2 40.8 + - - +
58B ALA* 3.4 16.4 + - - +
59B GLU* 3.8 10.3 - - + +
60B TYR 3.4 0.4 - - - -
61B TYR* 1.3 77.8 - - - +
63B LYS* 1.3 61.7 + - + +
68B LEU* 3.1 46.7 + - + +
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 3.1 54.5 + - + +
60B TYR* 3.8 5.4 - - + +
62B ASN* 1.3 80.4 - - + +
64B GLN* 1.3 70.7 + - - +
68B LEU 5.2 0.2 - - - -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR* 2.9 48.8 + - + +
63B LYS* 1.3 89.1 + - - +
67B TYR* 1.3 91.9 + - + +
68B LEU 4.1 0.2 - - - -
70B ARG* 5.0 2.9 + - - +
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Residues in contact with TYR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 4.5 3.4 - - - -
60B TYR* 3.5 7.5 - - - -
61B TYR* 3.0 52.0 + + + -
64B GLN* 1.3 98.4 - - + +
68B LEU* 1.3 61.3 + - - +
69B GLU* 3.3 2.9 - - - +
70B ARG* 3.2 16.2 + - + -
71B THR* 2.9 29.1 + - - -
5P ARG* 3.5 46.9 - - + +
6P PRO* 2.5 39.1 + - + -
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Residues in contact with LEU 68 (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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40B PHE* 3.3 29.6 - - + -
45B GLY 3.8 5.8 - - - +
46B GLU* 4.6 7.2 - - + +
47B TYR* 4.5 3.8 - - + -
61B TYR 3.7 3.5 + - - -
62B ASN* 3.1 52.1 + - + +
64B GLN 4.1 0.2 - - - -
67B TYR* 1.3 74.0 - - - +
69B GLU* 1.3 66.5 + - - +
71B THR* 4.3 3.4 - - - -
72B ARG* 3.0 56.4 + - + +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 3.3 0.8 - - - -
68B LEU* 1.3 79.7 - - - +
70B ARG* 1.3 96.0 + - + +
72B ARG* 4.4 10.4 - - - +
73B ALA* 3.3 21.0 + - - +
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN 5.0 2.0 - - - +
67B TYR* 3.2 22.9 + - + +
68B LEU 3.1 0.2 - - - -
69B GLU* 1.3 109.3 + - + +
71B THR* 1.3 63.8 + - - +
73B ALA* 3.2 18.4 - - - +
74B GLU* 3.2 15.9 - - - +
3P GLN* 4.1 7.9 - - - +
5P ARG* 3.8 16.2 - - - +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 3.6 16.3 - - + +
28B THR* 5.3 2.7 - - + +
40B PHE* 3.3 50.3 - - + -
47B TYR* 3.1 20.7 + - - +
67B TYR 2.9 16.4 + - - -
68B LEU* 3.2 2.4 + - - -
70B ARG* 1.3 72.9 - - - +
72B ARG* 1.3 68.4 + - - +
73B ALA 3.0 1.1 - - - -
74B GLU* 3.0 18.6 + - - +
5P ARG* 3.2 22.5 + - - +
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.9 13.0 - - + -
45B GLY* 2.7 38.4 + - - -
46B GLU* 5.3 1.2 - - - +
68B LEU* 3.0 48.6 + - + +
69B GLU* 4.4 7.7 - - - +
71B THR* 1.3 76.3 - - - +
73B ALA* 1.3 62.9 + - - +
75B LEU* 3.2 23.1 + - - +
76B ASP* 4.4 0.9 + - - +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU 3.3 15.2 + - - +
70B ARG* 3.2 17.7 + - - +
72B ARG* 1.3 81.3 - - - +
74B GLU* 1.3 59.2 + - + +
76B ASP* 3.1 9.0 + - - +
77B THR* 3.1 28.6 + - + +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 3.0 32.3 + - + -
70B ARG 3.2 13.9 - - - +
71B THR* 3.0 2.2 + - - +
73B ALA* 1.3 71.7 - - + +
75B LEU* 1.3 53.7 + - - +
76B ASP 2.7 11.7 + - - -
77B THR* 3.0 12.3 - - - +
78B VAL* 2.6 49.2 + - + +
79B CYS 3.2 0.7 + - - -
1P ALA 3.8 4.9 - - - +
3P GLN* 3.2 40.9 + - - +
5P ARG* 2.7 28.0 + - - -
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Residues in contact with LEU 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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24B ILE* 4.1 24.6 - - + +
26B TYR* 3.4 41.1 - - + +
40B PHE* 5.8 1.6 - - + -
42B SER* 2.8 31.9 - - - +
72B ARG* 3.2 17.9 + - - +
74B GLU* 1.3 75.4 - - - +
76B ASP* 1.3 70.8 + - + +
79B CYS* 3.5 7.5 - - - +
80B ARG* 3.3 24.9 + - - +
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Residues in contact with ASP 76 (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 ARG 5.5 1.1 - - - +
73B ALA* 3.1 8.3 + - - +
74B GLU 2.7 1.6 + - - -
75B LEU* 1.3 93.4 - - - +
77B THR* 1.3 61.2 + - + +
78B VAL 3.3 2.0 - - - -
80B ARG* 2.7 52.7 + - - +
81B TYR* 3.2 25.1 + - - +
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA* 3.1 14.5 + - + +
74B GLU* 3.0 28.8 + - - +
76B ASP* 1.3 79.7 - - + +
78B VAL* 1.3 60.8 - - - +
81B TYR* 3.6 21.4 - - - +
0P GLY* 4.8 5.9 - - - -
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Residues in contact with VAL 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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9A TYR* 4.1 9.2 - - + -
15B CYS* 4.5 2.9 - - - -
26B TYR* 5.2 0.7 - - + +
74B GLU* 2.6 41.9 + - + +
77B THR* 1.3 78.5 - - - +
79B CYS* 1.3 74.3 + - - +
81B TYR 4.1 0.2 - - - -
82B ASN* 2.7 45.8 + - - +
0P GLY* 3.5 12.6 - - - +
1P ALA 3.4 22.0 - - - +
2P SER* 3.5 21.5 - - - +
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Residues in contact with CYS 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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9A TYR* 4.6 2.0 - - - -
15B CYS* 2.0 56.5 - - + -
17B PHE* 4.2 8.0 - - + -
24B ILE* 4.2 12.1 - - + -
26B TYR* 3.8 36.1 - - - -
74B GLU 3.2 2.8 + - - -
75B LEU 3.5 10.8 - - - +
78B VAL* 1.3 85.7 - - - +
80B ARG* 1.3 65.4 + - - +
82B ASN* 2.9 7.4 + - - +
83B TYR* 3.0 13.0 + - - +
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Residues in contact with ARG 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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21B THR* 4.1 23.6 + - + -
22B GLN 4.9 4.4 + - - -
24B ILE* 3.6 32.8 - - + +
75B LEU* 3.3 20.2 + - - +
76B ASP* 2.7 46.4 + - - +
79B CYS* 1.3 78.3 - - - +
81B TYR* 1.3 62.5 + - - +
83B TYR* 3.7 1.3 - - - +
84B GLU* 3.0 46.4 + - - +
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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
------------------------------------------------------------
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