Contacts of the helix formed by residues 67 - 87 (chain B) in PDB entry 1XK4
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 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B TYR* 3.4 8.7 - - - -
27B HIS* 3.8 13.9 - - + +
28B ALA* 5.4 0.2 - - - -
61B ASN* 5.6 0.6 + - - +
63B ASP* 5.9 0.6 + - - -
65B ALA* 4.0 1.0 - - + +
66B VAL* 1.3 73.9 - - - +
68B PHE* 1.3 64.7 + - - +
69B GLN* 3.0 11.3 + - - +
70B GLU* 2.8 36.6 + - - +
71B PHE* 2.9 21.1 + - - +
68C THR* 5.6 7.6 - - + -
81C MET* 3.4 29.9 - - - +
85C ARG* 3.2 29.6 - - - +
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.4 0.7 - - + -
13B ILE* 3.6 31.6 - - + -
16B TYR* 3.5 52.3 + + + -
27B HIS 4.7 0.8 + - - -
67B ASN* 1.3 75.4 - - - +
69B GLN* 1.3 62.6 + - - +
71B PHE* 3.3 17.1 + + - +
72B LEU* 3.0 43.5 + - + +
87D THR* 3.7 18.4 - - + -
88D TRP* 3.8 15.7 - + + -
91D HIS* 3.6 49.6 - + + +
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 5.9 1.4 - - - +
67B ASN* 3.0 19.4 + - - +
68B PHE* 1.3 78.7 - - - +
70B GLU* 1.3 64.0 + - + +
72B LEU* 3.4 22.0 + - + +
73B ILE* 3.8 8.0 + - - +
81C MET* 3.8 20.9 - - - -
84C ALA* 5.7 3.6 - - - +
85C ARG* 2.7 49.7 + - - +
88D TRP* 3.8 32.1 - - + -
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 3.2 29.4 - - - +
59B ASP* 4.1 0.9 - - - -
60B ILE* 2.8 31.9 + - + +
61B ASN* 3.1 9.2 + - - +
65B ALA 3.2 2.9 - - - +
66B VAL* 3.3 8.6 - - + -
67B ASN* 2.8 46.8 + - - +
69B GLN* 1.3 75.1 - - + +
71B PHE* 1.3 64.8 + - - +
73B ILE* 3.1 27.9 + - - +
2501B CA 2.4 31.1 - - - -
81C MET* 3.7 7.7 - - + +
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 3.9 16.8 - - + -
15B VAL* 4.4 11.7 - - + -
16B TYR* 3.6 42.4 - + + -
29B VAL* 6.3 0.2 - - + -
34B LEU* 5.4 2.7 - - + -
37B LEU* 3.7 27.6 - - + -
58B LEU* 5.0 1.1 - - + -
66B VAL* 3.7 11.7 - - + +
67B ASN 2.9 14.7 + - - +
68B PHE* 3.3 18.8 + + - +
70B GLU* 1.3 75.4 - - - +
72B LEU* 1.3 58.0 + - + +
74B LEU* 2.9 45.0 + - + +
75B VAL* 3.1 32.4 + - + +
8D LEU* 4.4 14.8 - - + -
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.6 2.5 - - + -
68B PHE* 3.0 53.2 + - + +
69B GLN* 3.5 15.5 - - + +
70B GLU 3.2 0.6 - - - -
71B PHE* 1.3 76.5 - - - +
73B ILE* 1.3 55.8 + - - +
75B VAL* 3.6 21.5 - - + +
76B ILE* 2.9 38.5 + - + +
84D ALA* 3.7 35.7 - - + +
87D THR* 4.2 14.8 - - + -
88D TRP* 4.0 14.1 - - + +
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Residues in contact with ILE 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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60A ILE* 3.9 38.6 - - + -
73A ILE* 4.5 12.8 - - + -
57B GLU* 4.9 5.4 - - + +
58B LEU* 3.6 18.6 - - + +
60B ILE* 3.9 34.5 - - + -
69B GLN 3.8 6.5 + - - +
70B GLU* 3.1 20.3 + - - +
72B LEU* 1.3 75.4 - - - +
74B LEU* 1.3 59.5 + - - +
76B ILE* 3.4 3.7 + - + +
77B LYS* 3.0 41.3 + - + +
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Residues in contact with LEU 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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34B LEU* 4.4 4.3 - - + -
37B LEU* 4.0 26.5 - - + -
38B LEU* 4.2 11.2 - - + -
46B ILE* 4.2 5.4 - - + -
54B TRP* 3.8 37.5 - - + -
58B LEU* 3.6 28.0 - - + +
71B PHE* 2.9 25.6 + - + +
73B ILE* 1.3 78.3 - - - +
75B VAL* 1.3 61.0 + - - +
77B LYS* 3.2 0.9 + - - +
78B MET* 2.8 60.6 + - + +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.1 32.8 - - + -
71B PHE* 3.1 46.7 + - + +
72B LEU* 3.6 16.8 - - + +
73B ILE 3.3 0.2 - - - -
74B LEU* 1.3 77.7 - - - +
76B ILE* 1.3 58.9 + - + +
78B MET* 3.5 7.2 + - - +
79B GLY* 3.0 25.3 + - - -
8D LEU* 4.5 11.9 - - + -
12D ILE* 4.4 8.0 - - + +
15D ILE* 5.8 2.7 - - + -
80D ILE* 4.4 6.2 - - + +
84D ALA* 6.3 1.6 - - + -
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 3.8 21.5 - - + +
61A ASN* 3.8 34.5 - - + -
69A GLN* 6.0 1.3 - - - +
72B LEU* 2.9 25.5 + - + +
73B ILE* 3.7 5.4 - - + +
75B VAL* 1.3 77.6 - - + +
77B LYS* 1.3 58.9 + - - +
79B GLY* 3.2 1.4 + - - -
80B VAL* 2.9 30.9 + - + +
80D ILE* 3.9 24.7 - - + +
81D MET* 4.3 17.7 - - + -
84D ALA* 3.7 30.1 - - + -
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Residues in contact with LYS 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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56A LYS 5.2 7.1 + - - -
57A GLU* 5.2 2.4 + - - +
59A ASP 5.2 1.6 - - - -
60A ILE* 3.7 46.2 - - + +
62A THR* 5.7 4.5 - - - -
46B ILE* 4.7 2.9 - - + +
49B LYS* 5.3 1.9 - - - +
54B TRP* 4.0 23.8 - - + -
57B GLU* 2.6 33.4 + - - +
73B ILE* 3.0 24.3 + - + +
74B LEU 3.9 2.7 - - - +
76B ILE* 1.3 75.7 - - - +
78B MET* 1.3 59.1 + - - +
80B VAL* 3.9 5.2 - - - +
81B ALA* 3.0 30.3 + - - +
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Residues in contact with MET 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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41B GLU 4.1 2.0 - - - +
42B SER* 4.0 15.9 - - - -
43B PRO* 3.9 26.0 - - + -
45B TYR* 4.7 1.7 + - - -
46B ILE* 3.8 22.7 - - + -
74B LEU* 2.8 49.3 + - + +
75B VAL* 3.7 2.5 - - - +
77B LYS* 1.3 76.6 - - - +
79B GLY* 1.3 57.1 + - - +
81B ALA* 3.5 1.2 + - - +
82B ALA* 2.8 31.7 + - - +
8D LEU* 3.9 28.3 - - + -
9D GLU* 4.9 3.6 - - + -
12D ILE* 3.7 27.3 - - + +
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Residues in contact with GLY 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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75B VAL 3.0 15.2 + - - -
76B ILE 3.6 3.1 - - - -
78B MET* 1.3 72.6 - - - +
80B VAL* 1.3 65.1 + - - +
82B ALA* 3.3 1.2 + - - +
83B HIS* 2.9 20.6 + - - +
12D ILE* 3.9 19.2 - - - +
16D ILE* 4.2 0.7 - - - +
76D PHE* 3.3 16.8 - - - -
80D ILE* 3.9 13.5 - - - -
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Residues in contact with VAL 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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60A ILE 5.3 0.2 - - - +
61A ASN* 4.0 17.3 - - - +
62A THR* 3.7 20.2 - - + +
76B ILE* 2.9 24.2 + - + +
77B LYS* 3.9 6.5 - - - +
79B GLY* 1.3 75.1 - - - +
81B ALA* 1.3 63.6 + - - +
83B HIS* 3.4 4.0 + - - +
84B LYS* 3.0 29.1 + - + +
76D PHE* 4.1 8.3 - - + -
77D GLU* 3.9 24.6 - - + +
80D ILE* 4.0 21.5 - - + -
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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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45B TYR* 3.7 25.4 - - + -
46B ILE* 4.3 8.7 - - + -
77B LYS 3.0 18.1 + - - +
78B MET 3.8 2.5 - - - +
80B VAL* 1.3 77.7 - - - +
82B ALA* 1.3 63.4 - - - +
84B LYS* 3.3 11.3 + - - +
85B LYS* 3.1 27.1 + - - +
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Residues in contact with ALA 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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45B TYR* 3.4 18.5 + - - +
78B MET 2.8 22.9 + - - +
81B ALA* 1.3 73.6 - - - +
83B HIS* 1.3 59.0 + - - +
85B LYS* 3.2 5.2 + - - +
86B SER* 2.9 30.0 + - - -
12D ILE* 3.9 12.3 - - + -
16D ILE* 3.6 18.9 - - + +
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Residues in contact with HIS 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 GLY 2.9 17.6 + - - +
80B VAL 3.7 4.1 + - - +
82B ALA* 1.3 76.7 - - - +
84B LYS* 1.3 66.1 + - - +
86B SER* 3.2 20.4 + - - -
87B HIS* 3.3 22.4 + + - -
16D ILE* 3.4 24.3 - - + +
19D PHE* 4.4 5.0 - + - -
30D ASP* 2.7 43.4 + - - -
76D PHE* 3.5 51.6 - + + +
77D GLU* 4.9 10.4 + - - -
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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 VAL* 3.0 21.1 + - + +
81B ALA* 3.4 13.2 - - - +
83B HIS* 1.3 83.3 + - - +
85B LYS* 1.3 63.1 + - + +
87B HIS* 3.3 19.2 + - + +
88B GLU* 3.4 23.2 - - - +
77D GLU* 5.2 8.3 - - - +
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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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45B TYR* 3.9 53.9 - - + +
48B LYS* 5.9 0.8 - - - +
81B ALA* 3.1 16.0 + - - +
82B ALA* 3.2 7.4 + - - +
84B LYS* 1.3 75.0 - - + +
86B SER* 1.3 63.5 + - - +
87B HIS 3.0 6.8 + - - -
88B GLU* 3.2 48.1 + - - +
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Residues in contact with SER 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 ALA 2.9 14.4 + - - -
83B HIS* 3.2 13.2 + - - -
85B LYS* 1.3 74.7 - - - +
87B HIS* 1.3 60.8 + - - +
88B GLU 3.8 0.6 - - - +
13D GLU* 5.1 6.5 - - - -
16D ILE* 3.7 26.9 - - - +
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Residues in contact with HIS 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 HIS* 3.3 27.0 + + - -
84B LYS* 3.4 11.6 + - + +
85B LYS 3.0 0.4 - - - -
86B SER* 1.3 81.2 + - - +
88B GLU* 1.3 61.4 + - - +
30D ASP* 3.1 36.4 + - + +
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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
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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