Contacts of the helix formed by residues 3 - 21 (chain J) 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 THR 3 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008F FLC 3.3 22.4 - - - +
43H LYS* 3.9 4.5 - - - +
1J MET 4.9 0.9 - - - +
2J LEU* 1.3 77.8 - - - +
4J GLU* 1.3 59.6 + - - +
5J LEU* 3.5 3.0 + - - -
6J GLU* 3.0 25.2 + - - +
7J LYS* 3.0 26.7 + - - +
43L LYS 3.5 25.4 - - - +
44L ASP* 2.6 25.0 + - - +
46L GLN* 3.7 17.5 - - + +
47L ASN* 4.2 0.4 - - - +
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Residues in contact with GLU 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008F FLC 2.8 24.5 + - + +
21H GLN* 2.8 31.3 - - + +
22H TYR* 3.3 34.5 - - + +
25H LYS* 2.7 28.4 + - - -
43H LYS* 2.5 33.7 + - - +
3J THR* 1.3 68.8 - - - +
5J LEU* 1.3 65.6 + - - +
7J LYS* 3.0 14.7 + - - +
8J ALA* 3.0 23.7 + - - +
14L THR* 3.7 6.3 - - + +
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Residues in contact with LEU 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008F FLC 4.7 1.2 + - - +
3J THR* 3.2 2.0 + - - +
4J GLU* 1.3 79.4 - - - +
6J GLU* 1.3 62.1 + - - +
8J ALA* 3.1 2.8 + - + +
9J LEU* 3.0 24.8 + - + +
14L THR* 4.2 6.1 - - + +
15L ILE* 4.0 36.8 - - + +
18L THR* 4.0 21.4 + - + +
40L LEU* 4.1 13.2 - - + -
44L ASP* 3.6 29.8 - - + +
45L LEU* 3.8 30.1 - - + -
79L PHE* 5.0 2.0 - - + -
83L MET* 4.1 20.6 - - - -
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Residues in contact with GLU 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J LEU* 3.4 7.2 - - + +
3J THR* 3.0 27.8 + - - +
5J LEU* 1.3 77.9 - - - +
7J LYS* 1.3 58.6 + - - +
9J LEU* 3.3 6.1 + - - +
10J ASN* 3.0 32.3 + - - -
44L ASP 3.6 7.4 - - - +
45L LEU* 3.2 13.3 - - + -
47L ASN* 2.7 58.6 + - - +
48L PHE* 2.9 46.4 + - + -
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Residues in contact with LYS 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LYS* 4.4 7.0 - - - +
39H GLU* 3.5 24.9 + - - -
42H ARG* 5.5 1.8 - - - +
43H LYS* 2.9 35.9 - - - +
2J LEU* 3.7 24.2 - - + +
3J THR 3.0 15.4 + - - +
4J GLU* 3.0 20.8 + - - +
5J LEU 3.3 0.2 - - - -
6J GLU* 1.3 77.5 - - - +
8J ALA* 1.3 55.2 + - - +
10J ASN* 3.4 7.9 + - - +
11J SER* 2.8 29.5 + - - -
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Residues in contact with ALA 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J GLU 3.0 15.5 + - - +
5J LEU* 3.5 8.7 - - - +
7J LYS* 1.3 73.8 - - - +
9J LEU* 1.3 65.0 + - - +
11J SER* 3.2 3.5 + - - -
12J ILE* 3.1 27.5 + - - +
11L ASN* 3.6 37.2 - - - +
14L THR* 3.9 16.4 - - + +
15L ILE* 4.8 6.1 - - + -
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Residues in contact with LEU 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J LEU* 3.0 16.7 + - + +
6J GLU 3.6 6.1 - - - +
8J ALA* 1.3 75.3 - - - +
10J ASN* 1.3 63.6 + - - +
12J ILE* 3.2 21.5 + - + +
13J ILE* 3.4 6.0 + - - +
15L ILE* 3.7 31.9 - - + -
45L LEU* 4.6 7.2 - - + -
48L PHE* 3.9 26.2 - - + -
83L MET* 4.2 26.2 - - + +
86L LEU* 3.9 26.0 - - + -
87L THR* 3.6 28.1 - - - +
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Residues in contact with ASN 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J LEU* 3.4 30.1 - - - +
6J GLU 3.0 14.7 + - - +
7J LYS* 3.8 6.1 - - - +
9J LEU* 1.3 74.4 - - - +
11J SER* 1.3 62.7 + - - +
13J ILE* 3.1 22.4 + - + +
14J ASP* 3.2 11.7 + - - +
48L PHE* 3.6 11.0 - - - -
90L SER* 2.7 30.7 + - - -
94L MET* 5.0 7.9 - - - +
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Residues in contact with SER 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J LYS 2.8 22.1 + - - -
8J ALA* 3.2 1.5 + - - -
10J ASN* 1.3 70.5 - - - +
12J ILE* 1.3 59.6 + - - +
14J ASP* 3.0 9.4 + - - +
15J VAL* 2.8 29.6 + - - +
7L GLN* 2.8 24.4 + - - +
10L ARG* 5.7 0.2 + - - -
11L ASN* 2.7 37.9 + - - -
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Residues in contact with ILE 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J ALA 3.1 15.4 + - - +
9J LEU* 3.2 17.5 + - + +
11J SER* 1.3 76.6 - - - +
13J ILE* 1.3 60.1 + - - +
15J VAL* 3.4 7.5 + - - +
16J TYR 3.3 16.1 + - - -
68J PHE* 4.8 0.7 - - + -
71J PHE* 3.7 24.5 - - + -
72J LEU* 4.5 2.7 - - + -
75J VAL* 3.9 28.9 - - + -
8L LEU* 4.1 9.9 - - + -
11L ASN* 3.8 20.0 - - + +
12L ILE* 5.2 1.3 - - + +
15L ILE* 3.8 28.3 - - + -
87L THR* 4.1 16.8 - - + +
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Residues in contact with ILE 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J LEU 3.8 6.5 - - - +
10J ASN* 3.1 18.3 + - - +
12J ILE* 1.3 77.2 - - - +
14J ASP* 1.3 62.5 + - - +
16J TYR* 3.2 6.9 + - + +
17J HIS* 3.1 22.7 + - + +
68J PHE* 3.6 25.4 - - + -
87L THR* 3.5 26.5 - - + +
90L SER* 3.9 13.2 - - - +
91L HIS* 3.5 33.7 - - + +
94L MET* 3.5 32.8 - - + -
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Residues in contact with ASP 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J ASN 3.2 7.7 + - - +
11J SER* 3.0 11.8 + - - +
13J ILE* 1.3 80.6 - - - +
15J VAL* 1.3 63.4 + - - +
17J HIS* 3.3 14.2 + - - +
18J LYS* 3.0 30.0 + - - +
7L GLN* 2.8 27.1 + - - +
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Residues in contact with VAL 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J SER 2.8 18.6 + - - +
12J ILE* 3.6 9.6 - - - +
13J ILE 3.2 0.2 - - - -
14J ASP* 1.3 73.2 - - - +
16J TYR* 1.3 66.1 + - - +
18J LYS* 3.2 13.5 + - - +
19J TYR* 3.1 26.7 - - + -
37J LEU* 4.8 1.8 - - + -
41J GLU* 3.9 29.8 - - + +
71J PHE* 4.3 14.4 - - + -
7L GLN* 3.4 33.2 - - + +
8L LEU* 4.0 22.0 - - + +
11L ASN* 4.1 4.9 - - - +
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Residues in contact with TYR 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J ILE 3.3 2.8 + - - -
13J ILE* 3.2 10.3 + - + +
15J VAL* 1.3 79.2 - - - +
17J HIS* 1.3 62.5 + - + +
19J TYR* 3.0 5.9 + - - +
20J SER* 2.9 40.6 + - - -
26J PHE 4.8 0.4 - - - -
27J HIS* 3.2 28.1 + - - -
28J ALA* 3.6 1.9 - - - -
29J VAL* 3.4 23.6 - - + -
37J LEU* 5.0 5.4 - - + -
66J VAL* 2.7 26.9 + - + -
67J ASN* 3.2 13.7 - - - -
68J PHE* 3.5 43.5 - + + -
71J PHE* 3.6 33.1 - + + -
91L HIS* 5.7 3.8 - + - -
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Residues in contact with HIS 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE 5.4 2.6 + - - -
13J ILE* 3.1 16.7 + - + +
14J ASP* 3.5 18.4 - - - +
15J VAL 3.3 0.2 - - - -
16J TYR* 1.3 79.3 - - + +
18J LYS* 1.3 63.6 + - - +
20J SER* 3.6 11.3 + - - -
21J LEU* 3.0 69.6 + - + +
26J PHE* 4.9 6.5 + - + -
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Residues in contact with LYS 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ASP* 3.0 23.5 + - - +
15J VAL* 3.4 17.0 - - - +
16J TYR 3.2 0.6 - - - -
17J HIS* 1.3 74.8 - - - +
19J TYR* 1.3 72.4 + - + +
21J LEU* 4.3 6.8 + - - +
22J ILE* 3.7 14.6 + - - +
40J THR* 5.7 1.2 - - - +
41J GLU* 2.8 31.0 + - - -
7L GLN* 2.7 35.7 + - - +
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Residues in contact with TYR 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J VAL* 3.1 25.8 - - + -
16J TYR 3.0 6.2 + - - +
18J LYS* 1.3 90.8 - - + +
20J SER* 1.3 63.4 + - - +
21J LEU 3.2 1.8 - - - -
22J ILE* 3.3 38.1 + - + +
29J VAL* 3.8 10.1 - - + -
33J ASP* 4.0 19.2 - - + +
36J LYS* 4.0 9.9 - - + -
37J LEU* 3.6 51.1 - - + -
40J THR* 3.1 25.7 - - - +
41J GLU* 3.0 37.1 + - + +
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Residues in contact with SER 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J TYR* 2.9 34.0 + - - -
17J HIS* 3.4 20.1 + - - -
19J TYR* 1.3 77.6 - - - +
21J LEU* 1.3 59.8 + - - +
26J PHE* 2.9 36.7 + - - -
28J ALA 3.4 19.1 - - - -
29J VAL* 3.6 5.1 - - - +
2522J CA 2.2 24.6 - - - -
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Residues in contact with LEU 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 4.3 21.8 - - + +
23B LYS* 3.0 41.2 + - + -
32B ASP* 4.6 0.2 - - - +
17J HIS* 3.0 64.2 + - + +
18J LYS* 4.6 6.1 - - - +
19J TYR 3.2 0.4 - - - -
20J SER* 1.3 78.4 + - - +
22J ILE* 1.3 62.0 + - - +
23J LYS 3.3 1.5 + - - -
26J PHE* 3.8 41.7 - - + -
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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