Contacts of the helix formed by residues 30 - 42 (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 TYR 30 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23J LYS* 3.5 36.6 - - + -
24J GLY* 3.9 6.9 - - - -
25J ASN* 2.9 24.0 + - - +
28J ALA* 3.7 13.9 - - + -
29J VAL* 1.3 76.2 - - - +
31J ARG* 1.3 68.9 + - - +
32J ASP* 3.3 11.0 - - - +
33J ASP* 3.1 25.2 + - - +
34J LEU* 2.9 19.4 + - - +
55J PHE* 3.8 2.2 - - - -
64J GLY 3.7 18.6 - - - +
65J ALA* 4.1 5.6 - - + -
2007J CL 4.4 11.0 - - + -
2522J CA 3.6 8.1 - - - -
68K THR 2.6 30.7 + - - -
69K ASN* 4.7 3.5 - - - -
70K ALA* 5.4 0.3 - - - +
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Residues in contact with ARG 31 (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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30J TYR* 1.3 76.5 - - - +
32J ASP* 1.3 63.6 + - - +
34J LEU* 3.2 4.3 + - - +
35J LYS* 3.1 21.7 + - - +
51J ALA* 5.2 3.5 - - + +
52J ASP* 3.3 47.0 + - - +
55J PHE* 3.5 57.4 - - + +
56J LYS* 5.3 1.2 - - - +
64J GLY 4.6 1.2 + - - +
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Residues in contact with ASP 32 (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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23J LYS* 2.9 38.9 + - - -
30J TYR* 3.7 9.0 - - - +
31J ARG* 1.3 74.0 - - - +
33J ASP* 1.3 66.8 + - - -
35J LYS* 3.2 11.9 + - + +
36J LYS* 3.2 32.6 + - - +
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Residues in contact with ASP 33 (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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19J TYR* 4.0 24.8 - - + +
22J ILE* 3.6 23.0 - - + +
23J LYS* 2.8 28.8 + - - +
28J ALA 4.7 0.7 - - - +
29J VAL* 3.7 13.9 - - + -
30J TYR* 3.1 39.5 + - - +
32J ASP* 1.3 78.3 + - - +
34J LEU* 1.3 57.7 + - - +
36J LYS* 3.2 11.5 + - - +
37J LEU* 2.9 27.4 + - - +
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Residues in contact with LEU 34 (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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29J VAL* 3.5 16.3 - - + +
30J TYR 2.9 14.3 + - - +
31J ARG 3.2 9.4 + - - +
33J ASP* 1.3 77.7 - - - +
35J LYS* 1.3 62.2 + - - +
37J LEU* 3.1 17.8 + - + +
38J LEU* 2.9 37.9 + - + +
51J ALA 4.2 5.8 - - - +
54J TRP* 4.2 5.4 - - + -
55J PHE* 3.6 47.6 - - + +
58J LEU* 4.1 24.0 - - + -
66J VAL* 4.4 8.5 - - + -
71J PHE* 5.7 1.8 - - + -
74J LEU* 4.8 4.3 - - + -
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Residues in contact with LYS 35 (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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31J ARG 3.1 13.1 + - - +
32J ASP* 3.2 13.9 + - + +
34J LEU* 1.3 75.4 - - - +
36J LYS* 1.3 59.4 + - + +
38J LEU* 3.3 2.2 + - - +
39J GLU* 2.9 59.0 + - + +
51J ALA* 3.8 29.3 - - + +
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Residues in contact with LYS 36 (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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19J TYR* 4.0 12.8 - - + -
22J ILE* 4.5 18.4 - - + -
32J ASP* 3.2 18.3 + - - +
33J ASP* 3.5 9.9 - - - +
35J LYS* 1.3 76.5 - - + +
37J LEU* 1.3 66.1 + - - +
39J GLU* 3.3 8.5 + - - +
40J THR* 2.9 32.2 + - - +
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Residues in contact with LEU 37 (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* 4.7 4.0 - - + +
16J TYR* 5.0 5.6 - - + -
19J TYR* 3.6 46.8 - - + -
29J VAL* 5.1 5.4 - - + -
33J ASP 2.9 14.1 + - - +
34J LEU* 3.1 19.3 + - + +
36J LYS* 1.3 74.9 - - - +
38J LEU* 1.3 59.9 + - + +
41J GLU* 2.7 51.3 + - + +
42J SER* 5.9 0.9 - - - -
71J PHE* 3.9 27.8 - - + -
74J LEU* 3.9 27.4 - - + -
8L LEU* 4.8 3.6 - - + -
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Residues in contact with LEU 38 (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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34J LEU* 2.9 31.9 + - + +
35J LYS* 3.8 2.7 - - - +
37J LEU* 1.3 74.9 - - + +
39J GLU* 1.3 67.3 + - + +
42J SER* 2.8 40.0 + - - +
46J ILE* 4.2 4.5 - - + +
47J ARG* 3.2 16.9 - - + -
50J GLY 4.9 0.2 - - - -
51J ALA* 3.7 32.3 - - + +
54J TRP* 3.9 30.7 - - + -
74J LEU* 3.9 37.7 - - + -
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Residues in contact with GLU 39 (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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35J LYS* 2.9 58.6 + - + +
36J LYS* 3.8 8.8 - - - +
38J LEU* 1.3 78.6 - - + +
40J THR* 1.3 60.4 + - - +
42J SER 4.5 1.4 - - - +
47J ARG* 3.6 25.6 + - - +
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Residues in contact with THR 40 (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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18J LYS* 5.7 0.7 - - - +
19J TYR* 3.1 24.0 + - - +
36J LYS* 2.9 19.8 + - - +
39J GLU* 1.3 82.1 - - - +
41J GLU* 1.3 63.5 + - - +
42J SER 3.8 0.2 - - - -
6L SER* 3.5 15.0 - - - -
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Residues in contact with GLU 41 (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* 3.9 15.5 - - + -
18J LYS* 2.8 31.5 + - - -
19J TYR* 3.0 29.7 + - + +
37J LEU* 2.7 27.8 + - + +
40J THR* 1.3 81.0 - - - +
42J SER* 1.3 55.7 + - - +
78J MET* 4.2 2.1 - - - +
6L SER* 2.7 29.6 + - - -
7L GLN* 3.5 3.9 + - - +
8L LEU* 3.2 45.3 + - + +
9L GLU* 3.5 9.7 - - - +
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Residues in contact with SER 42 (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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37J LEU* 5.9 0.4 - - - -
38J LEU* 2.8 30.2 + - - +
39J GLU 4.5 1.7 - - - +
40J THR 5.2 0.2 - - - -
41J GLU* 1.3 80.3 - - - +
43J PRO* 1.3 68.7 - - - +
46J ILE* 3.6 24.6 - - - +
47J ARG* 2.9 37.1 + - - +
78J MET* 3.9 14.1 - - - -
9L GLU* 3.4 5.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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