Contacts of the helix formed by residues 24 - 42 (chain A) in PDB entry 3KMP
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 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS* 4.9 4.8 - - - +
22A GLN 4.1 1.2 + - - +
23A GLY* 1.3 76.1 - - - -
25A GLU* 1.3 67.9 + - - +
26A GLU* 3.9 12.3 - - - +
27A GLU* 3.0 25.9 + - - +
28A LYS* 2.9 24.6 + - - +
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 1.3 75.6 - - - +
26A GLU* 1.3 57.1 + - - +
28A LYS* 3.4 23.4 + - - +
29A TRP* 2.9 31.2 + - - +
32A LYS* 5.5 1.2 + - - -
80A ARG* 4.3 12.3 - - - +
133A GOL 3.7 21.7 + - - +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 3.1 13.4 - - - +
25A GLU* 1.3 81.0 - - - +
27A GLU* 1.3 57.2 + - - +
29A TRP* 3.5 14.3 + - - +
30A ALA* 3.0 28.7 + - + +
80A ARG* 3.0 31.8 + - - +
90A ARG* 5.4 9.4 + - - -
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 3.9 13.7 + - - +
23A GLY* 3.6 21.8 - - - -
24A ASP* 3.0 21.8 + - - +
26A GLU* 1.3 74.1 - - - +
28A LYS* 1.3 66.5 + - - +
30A ALA* 3.3 7.4 + - + +
31A GLU* 3.1 45.5 + - + +
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLN* 3.9 20.5 - - - +
23A GLY* 3.3 27.0 + - - +
24A ASP 2.9 18.7 + - - +
25A GLU* 3.7 22.5 + - - +
27A GLU* 1.3 77.0 - - - +
29A TRP* 1.3 62.1 + - - +
31A GLU* 3.2 25.1 + - - +
32A LYS* 3.2 26.4 + - - +
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Residues in contact with TRP 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLU 2.9 18.1 + - - +
26A GLU* 3.7 14.4 - - - +
28A LYS* 1.3 74.7 - - - +
30A ALA* 1.3 74.5 + - + +
32A LYS* 2.9 12.2 + - + +
33A ALA* 2.9 29.2 + - + -
77A VAL* 2.9 40.9 + - + +
78A SER* 4.4 7.4 - - - -
80A ARG* 3.4 55.9 - - + +
81A LYS 6.0 0.2 - - - -
82A GLY* 5.9 1.1 - - - -
87A ILE* 4.0 40.6 - - + -
90A ARG* 5.9 4.0 - - - -
91A VAL* 5.9 1.8 - - + -
133A GOL 3.7 26.6 + - - +
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU* 3.0 18.8 + - + +
27A GLU* 3.3 9.6 + - + +
29A TRP* 1.3 88.2 - - + +
31A GLU* 1.3 62.8 + - + +
33A ALA* 3.2 6.0 + - - +
34A VAL* 3.0 27.2 + - - +
91A VAL* 4.2 22.8 - - + +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.1 38.0 + - + +
28A LYS* 3.5 17.1 - - - +
29A TRP 3.1 0.8 - - - -
30A ALA* 1.3 75.7 - - + +
32A LYS* 1.3 59.2 + - - +
34A VAL* 3.0 8.0 + - - +
35A ASP* 2.8 29.7 + - - +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLU* 5.5 1.6 + - - -
28A LYS* 3.2 21.2 + - - +
29A TRP* 2.9 12.6 + - - +
31A GLU* 1.3 79.5 - - + +
33A ALA* 1.3 57.5 + - - +
35A ASP* 3.2 8.8 + - - +
36A ALA* 2.8 29.5 + - - +
77A VAL* 3.8 13.7 - - + +
78A SER* 3.7 31.4 + - - -
133A GOL 3.8 19.8 + - - -
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP* 2.9 35.8 + - + +
30A ALA* 3.6 9.0 - - - +
31A GLU 3.2 0.4 - - - -
32A LYS* 1.3 78.1 - - - +
34A VAL* 1.3 60.3 + - - +
36A ALA* 3.5 1.2 + - - +
37A LEU 3.1 9.5 + - - -
77A VAL* 3.7 15.7 - - + +
87A ILE* 4.1 12.6 - - + -
88A TYR* 2.7 34.6 + - + +
91A VAL* 5.5 1.3 - - + -
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA 3.0 17.0 + - - +
31A GLU* 3.6 8.3 - - - +
33A ALA* 1.3 75.3 - - - +
35A ASP* 1.3 68.2 + - - +
37A LEU* 3.1 4.1 + - + +
38A VAL* 2.9 35.7 + - + +
88A TYR* 4.4 7.0 - - + -
91A VAL* 4.2 15.0 - - + -
92A TRP* 3.8 34.1 - - + -
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Residues in contact with ASP 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU 2.8 13.0 + - - +
32A LYS* 3.4 13.4 - - - +
34A VAL* 1.3 79.3 - - - +
36A ALA* 1.3 62.9 + - - +
38A VAL* 3.2 8.0 + - - +
39A LYS* 3.1 52.9 + - - +
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS 2.8 16.5 + - - +
33A ALA 3.6 6.5 - - - +
35A ASP* 1.3 77.9 + - - +
37A LEU* 1.3 60.3 + - - +
39A LYS* 3.4 20.0 + - - +
40A LYS* 3.4 28.1 + - - +
75A LEU* 6.0 2.2 - - + -
77A VAL* 4.2 17.3 - - + -
88A TYR* 4.6 2.2 - - - +
8C T 3.9 21.3 - - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA 3.1 7.4 + - - +
34A VAL* 3.1 6.3 + - + +
36A ALA* 1.3 74.5 - - - +
38A VAL* 1.3 68.5 + - + +
40A LYS* 3.2 8.6 + - + +
41A LEU* 2.9 47.3 + - + +
51A LEU* 4.1 3.8 - - + -
67A ILE* 3.5 31.9 - - + -
88A TYR* 3.4 40.1 + - + +
92A TRP* 3.9 20.4 - - + -
122A ILE* 3.8 28.0 - - + -
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 2.9 33.4 + - + +
35A ASP* 3.7 8.7 - - - +
37A LEU* 1.3 80.7 - - + +
39A LYS* 1.3 63.0 + - + +
41A LEU* 3.0 11.4 + - + +
42A LYS* 3.0 33.7 + - + +
48A MET* 3.7 37.9 - - + -
51A LEU* 6.4 1.6 - - + -
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASP* 3.1 47.4 + - - +
36A ALA* 3.7 15.0 - - - +
37A LEU 3.2 0.4 - - - -
38A VAL* 1.3 76.6 - - - +
40A LYS* 1.3 62.5 + - + +
42A LYS* 3.9 25.7 + - - +
43A LYS* 3.6 29.2 - - - +
7C C 5.1 14.6 + - - -
8C T 5.1 7.2 + - - +
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Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ALA* 3.4 23.4 + - - +
37A LEU* 3.2 8.7 + - - +
38A VAL 3.1 0.4 - - - -
39A LYS* 1.3 79.9 - - + +
41A LEU* 1.3 61.5 + - + +
43A LYS* 3.4 27.3 + - - +
44A LYS* 4.1 11.1 - - + +
67A ILE* 3.7 38.8 - - + -
68A PRO* 4.7 9.9 - - + -
75A LEU* 4.6 20.8 - - - +
88A TYR* 6.1 0.4 - - - -
8C T 5.8 5.1 + - - -
9C A 4.5 11.3 + - - -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 2.9 46.8 + - + +
38A VAL* 3.0 1.1 + - + +
40A LYS* 1.3 74.9 - - - +
42A LYS* 1.3 66.2 + - - +
43A LYS 3.0 2.5 - - - -
44A LYS* 3.0 28.9 + - + +
47A ALA* 3.7 16.4 - - + +
48A MET* 3.6 28.5 - - + +
51A LEU* 3.9 26.0 - - + -
65A VAL* 3.9 27.8 - - + -
66A THR 4.0 16.8 - - - +
67A ILE* 4.4 2.7 - - + -
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 3.0 38.3 + - + +
39A LYS* 3.9 25.8 - - - +
41A LEU* 1.3 76.4 - - - +
43A LYS* 1.3 59.9 + - + +
44A LYS 3.1 5.1 + - - +
45A LYS* 3.5 18.2 + - - -
48A MET* 4.0 12.5 - - + +
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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