Contacts of the helix formed by residues 69 - 89 (chain B) in PDB entry 1K9K
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 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.7 4.7 - - - -
27B HIS 4.8 0.4 - - - +
28B THR* 3.8 26.4 - - + -
63B ASN* 5.3 8.5 + - - +
65B ASP* 5.6 1.8 + - - -
67B GLU* 3.9 1.8 - - + -
68B VAL* 1.3 76.7 - - - +
70B PHE* 1.3 60.0 + - - +
71B GLN* 3.3 19.7 + - - +
72B GLU* 2.9 53.7 + - - +
73B TYR* 3.0 25.6 + - - +
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 3.5 33.0 - - + -
82A LEU* 3.7 17.3 - - + -
85A ASN* 3.5 45.1 - - + +
89A LYS* 5.8 1.3 - - - +
13B VAL* 3.8 19.3 - - + -
16B PHE* 3.5 37.6 - + + -
27B HIS 4.4 2.5 + - - +
69B ASN* 1.3 76.3 - - - +
71B GLN* 1.3 59.2 + - + +
73B TYR* 3.1 25.5 + + - +
74B VAL* 2.9 46.6 + - + +
77B LEU* 5.5 0.7 - - + -
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Residues in contact with GLN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 4.1 25.0 - - + +
69B ASN* 3.3 18.7 + - - +
70B PHE* 1.3 77.0 - - + +
72B GLU* 1.3 64.1 + - + +
74B VAL* 3.2 19.4 + - - +
75B THR* 3.2 14.8 + - - -
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.3 31.6 - - - +
61B ASP* 4.1 0.4 - - - -
62B ARG* 3.1 27.8 + - + +
63B ASN* 3.2 11.3 + - - +
67B GLU 2.9 10.0 - - - +
68B VAL* 3.1 13.1 - - + -
69B ASN* 2.9 33.4 + - - +
71B GLN* 1.3 78.4 - - + +
73B TYR* 1.3 62.6 + - - +
75B THR* 3.2 22.3 + - - -
76B PHE 3.3 4.5 + - - -
400B CA 2.5 30.2 - - - -
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Residues in contact with TYR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.6 19.6 - - + +
12B LEU 2.8 29.2 + - - -
15B ILE* 3.7 7.4 - - - +
16B PHE* 3.4 36.3 - + + -
29B LEU* 4.4 7.9 - - + -
34B LEU* 5.6 2.2 - - + -
37B LEU* 4.2 21.5 - - + -
60B LEU* 5.8 0.2 - - - -
68B VAL* 3.8 8.7 - - + +
69B ASN 3.0 13.7 + - - +
70B PHE* 3.1 25.3 + + - +
72B GLU* 1.3 75.2 - - - +
74B VAL* 1.3 64.8 + - - +
76B PHE* 3.0 25.5 + + + +
77B LEU* 3.0 51.5 + - + +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 6.5 0.9 - - + -
78A GLY* 3.8 26.7 - - - +
81A ALA* 4.3 11.0 - - + -
82A LEU* 4.5 9.9 - - + -
70B PHE* 2.9 46.1 + - + +
71B GLN* 3.2 10.3 + - - +
73B TYR* 1.3 76.4 - - - +
75B THR* 1.3 63.9 + - - +
77B LEU* 3.2 14.2 + - + +
78B GLY* 2.9 21.0 + - - -
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Residues in contact with THR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.5 4.9 - - + -
62B ARG* 3.4 39.1 + - - +
71B GLN 3.2 12.0 + - - -
72B GLU* 3.2 14.3 + - - -
73B TYR 3.1 0.4 - - - -
74B VAL* 1.3 77.9 - - - +
76B PHE* 1.3 57.2 + - - +
78B GLY* 3.3 3.7 + - - -
79B ALA* 3.0 28.4 + - + +
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.9 19.7 - - + -
34B LEU* 5.5 4.0 - - + -
37B LEU* 4.7 9.0 - - + -
38B ILE* 4.5 16.6 - - + -
42B LEU* 4.7 9.2 - - + -
56B LEU* 4.1 26.9 - - + -
60B LEU* 3.7 36.5 - - + +
72B GLU 3.3 2.0 + - - +
73B TYR* 3.0 30.0 + + + +
75B THR* 1.3 77.0 - - - +
77B LEU* 1.3 67.4 + - + +
79B ALA* 3.0 11.4 + - + +
80B LEU* 3.0 60.1 + - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.1 8.1 - - + -
9A ILE* 3.7 15.1 - - + +
81A ALA* 5.1 10.3 - - + -
9B ILE* 6.4 0.4 - - + -
12B LEU* 3.9 37.5 - - + -
70B PHE* 5.5 0.9 - - + -
73B TYR* 3.0 63.3 + - + +
74B VAL* 3.2 18.1 + - + +
76B PHE* 1.3 78.4 - - + +
78B GLY* 1.3 63.5 + - - +
80B LEU* 3.2 9.3 + - + +
81B ALA* 3.0 23.1 + - - +
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.8 26.5 - - - +
74B VAL 2.9 14.1 + - - -
75B THR* 3.7 4.3 - - - -
76B PHE 3.2 0.2 - - - -
77B LEU* 1.3 78.1 - - - +
79B ALA* 1.3 60.0 + - - +
81B ALA* 3.4 4.9 + - - +
82B LEU* 3.0 31.2 + - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 6.1 1.3 - - + -
75B THR* 3.0 14.9 + - + +
76B PHE* 3.0 15.9 + - + +
78B GLY* 1.3 76.7 - - - +
80B LEU* 1.3 63.7 + - + +
82B LEU* 3.3 11.2 + - - +
83B ILE* 3.1 34.7 + - + +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.3 11.0 - - + +
6A ASP* 6.2 0.7 - - - -
9A ILE* 3.9 23.3 - - + -
42B LEU* 3.9 30.5 - - + -
76B PHE* 3.0 53.7 + - + +
77B LEU* 3.2 12.8 + - + +
79B ALA* 1.3 79.9 - - + +
81B ALA* 1.3 62.2 + - - +
83B ILE* 3.3 17.3 + - + +
84B TYR* 3.1 35.9 + - + -
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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
----------------------------------------------------------
9A ILE* 3.5 23.1 - - + +
12A LEU* 6.3 0.7 - - + -
13A VAL* 3.7 6.6 - - + +
70A PHE* 3.5 21.0 - - + -
74A VAL* 4.3 7.6 - - + -
77A LEU* 5.3 8.7 - - + -
77B LEU 3.0 16.3 + - - +
78B GLY* 3.6 6.5 - - - +
79B ALA 3.3 0.2 - - - -
80B LEU* 1.3 74.8 - - - +
82B LEU* 1.3 66.4 + - - +
84B TYR 3.4 0.9 + - - -
85B ASN* 2.9 25.3 + - - +
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Residues in contact with LEU 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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70A PHE* 3.8 26.2 - - + -
71A GLN* 4.3 26.5 - - + +
74A VAL* 4.3 9.4 - - + -
78B GLY 3.0 22.9 + - - +
79B ALA* 3.7 11.0 - - - +
81B ALA* 1.3 76.7 - - - +
83B ILE* 1.3 59.2 + - + +
85B ASN* 3.3 1.9 + - - +
86B GLU* 2.9 50.0 + - + +
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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 ALA* 3.1 22.4 + - + +
80B LEU* 3.5 20.9 - - + +
82B LEU* 1.3 79.2 - - + +
84B TYR* 1.3 70.8 + - + +
86B GLU* 3.3 8.7 + - - +
87B ALA* 3.2 22.3 + - + +
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Residues in contact with TYR 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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6A ASP* 2.5 51.2 + - + +
9A ILE* 4.0 13.2 - - + -
10A GLY* 5.1 9.0 - - - -
13A VAL* 4.1 17.3 - - + -
43B THR* 4.7 2.4 + - - -
80B LEU* 3.1 32.8 + - + +
81B ALA 3.9 3.1 - - - +
83B ILE* 1.3 84.9 - - + +
85B ASN* 1.3 63.4 + - - +
87B ALA* 3.3 8.8 + - + +
88B LEU* 3.2 31.9 + - + +
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Residues in contact with ASN 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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13A VAL* 4.1 8.6 - - + +
16A PHE* 4.7 1.8 - - - -
17A HIS* 2.6 34.6 + - - -
27A HIS* 5.8 0.2 + - - -
70A PHE* 3.4 47.8 - - + +
71A GLN* 5.0 4.2 - - - +
81B ALA 2.9 17.9 + - - +
82B LEU* 3.7 4.5 + - - +
84B TYR* 1.3 77.2 - - - +
86B GLU* 1.3 64.2 + - - +
88B LEU* 3.3 4.2 + - - +
89B LYS* 3.3 43.4 + - - +
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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
----------------------------------------------------------
82B LEU* 2.9 35.3 + - + +
83B ILE* 3.8 7.5 - - - +
84B TYR 3.3 0.2 - - - -
85B ASN* 1.3 78.1 - - - +
87B ALA* 1.3 66.7 + - - +
89B LYS* 3.3 24.0 + - - +
90B GLY* 3.8 9.9 + - - +
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Residues in contact with ALA 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* 3.2 13.7 + - + +
84B TYR* 3.6 12.3 - - + +
85B ASN 3.3 0.2 - - - -
86B GLU* 1.3 77.6 - - - +
88B LEU* 1.3 65.4 + - + +
90B GLY* 3.1 14.9 + - - -
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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
----------------------------------------------------------
13A VAL* 3.7 30.5 - - + -
14A ALA* 5.5 2.9 - - - +
17A HIS* 3.6 28.4 - - + +
84B TYR* 3.2 14.4 + - + +
85B ASN 3.8 2.9 - - - +
86B GLU 3.3 0.2 - - - -
87B ALA* 1.3 79.5 - - + +
89B LYS* 1.3 60.5 + - - +
90B GLY 3.2 1.6 + - - -
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Residues in contact with LYS 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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17A HIS* 4.5 7.4 - - + -
27A HIS* 3.6 54.2 + - + +
70A PHE* 6.1 0.4 - - - +
71A GLN* 5.1 9.1 - - - +
85B ASN* 3.3 34.7 + - - +
86B GLU* 3.8 16.9 - - - +
87B ALA 3.2 1.4 - - - -
88B LEU* 1.3 76.9 - - - +
90B GLY* 1.3 68.0 + - - +
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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