Contacts of the helix formed by residues 23 - 50 (chain A) in PDB entry 2MKV
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 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 4.5 12.3 - - + +
20A ASP* 2.4 34.7 + - - +
22A GLU* 1.3 72.7 - - + +
24A VAL* 1.3 49.3 + - - +
25A ARG 2.6 12.7 + - - -
26A ASN* 2.7 7.9 + - - +
27A GLY* 2.4 40.0 + - - -
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Residues in contact with VAL 24 (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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20A ASP 3.7 1.1 + - - +
21A TYR* 2.6 55.7 + - + +
22A GLU* 4.2 2.0 - - - +
23A THR* 1.3 80.7 + - - +
25A ARG* 1.3 74.1 + - + +
27A GLY* 3.8 7.9 + - - +
28A GLY 4.3 5.0 + - - -
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU 3.3 12.3 + - - +
23A THR 2.6 5.7 + - - -
24A VAL* 1.3 89.1 - - + +
26A ASN* 1.3 70.5 + - - +
27A GLY 3.7 0.2 + - - -
28A GLY* 4.4 3.3 + - - -
29A LEU* 5.1 1.7 + - - +
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Residues in contact with ASN 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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23A THR* 2.7 9.6 + - - +
25A ARG* 1.3 85.4 + - - +
27A GLY* 1.3 63.2 + - - +
28A GLY 3.3 1.8 - - - -
29A LEU* 3.4 15.6 + - + +
30A ILE* 3.3 34.9 + - + +
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Residues in contact with GLY 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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23A THR* 2.4 32.4 + - - -
24A VAL* 3.8 4.0 - - - -
25A ARG 3.3 1.0 - - - -
26A ASN* 1.3 69.9 - - - +
28A GLY* 1.3 62.3 + - - +
30A ILE* 3.4 9.4 + - - +
31A PHE* 3.1 24.5 + - - +
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Residues in contact with GLY 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL 4.3 7.5 + - - -
25A ARG 4.4 2.3 + - - -
26A ASN 3.3 0.4 - - - -
27A GLY* 1.3 76.9 - - - +
29A LEU* 1.3 63.4 + - - +
31A PHE* 3.3 6.9 + - - +
32A ALA* 3.0 25.8 + - - +
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Residues in contact with LEU 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 ARG 5.1 1.9 + - - +
26A ASN* 3.4 19.8 + - + +
27A GLY 3.3 0.6 - - - -
28A GLY* 1.3 76.4 - - - +
30A ILE* 1.3 67.3 + - + +
32A ALA* 3.4 7.4 + - + +
33A GLY* 3.3 17.5 + - - -
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Residues in contact with ILE 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 ASN* 3.3 24.2 + - + +
27A GLY* 3.8 8.7 - - - +
29A LEU* 1.3 79.4 - - + +
31A PHE* 1.3 64.6 + - - +
33A GLY* 3.4 3.4 + - - -
34A LEU* 3.3 35.6 + - + +
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Residues in contact with PHE 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 GLY 3.1 17.5 + - - +
28A GLY* 3.6 7.4 - - - +
30A ILE* 1.3 79.1 - - - +
32A ALA* 1.3 67.7 + - + +
34A LEU* 3.1 17.0 + - + +
35A ALA* 2.9 32.8 + - + +
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Residues in contact with ALA 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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28A GLY 3.0 18.3 + - - +
29A LEU* 3.7 9.4 - - + +
31A PHE* 1.3 81.4 - - + +
33A GLY* 1.3 62.8 + - - +
35A ALA* 3.0 18.2 + - - +
36A PHE* 3.0 34.4 + - + -
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Residues in contact with GLY 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 LEU 3.3 10.3 + - - -
30A ILE 3.4 3.3 + - - -
31A PHE 3.3 0.2 - - - -
32A ALA* 1.3 78.0 - - - +
34A LEU* 1.3 62.1 + - - +
36A PHE* 3.4 11.7 + - - +
37A ILE* 3.3 28.7 + - - +
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Residues in contact with LEU 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 ILE* 3.3 29.7 + - + +
31A PHE* 3.1 17.1 + - + +
33A GLY* 1.3 73.0 - - - +
35A ALA* 1.3 65.3 + - - +
37A ILE* 3.3 20.4 + - + +
38A VAL* 3.3 27.4 + - + +
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Residues in contact with ALA 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 PHE* 2.9 27.8 + - + +
32A ALA* 3.0 14.8 + - - +
34A LEU* 1.3 78.4 - - - +
36A PHE* 1.3 65.2 + - + +
38A VAL* 3.3 17.9 + - - +
39A GLY* 3.3 8.7 + - - -
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Residues in contact with PHE 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 ALA* 3.0 40.9 + - + -
33A GLY* 3.7 9.4 - - - +
34A LEU 3.3 0.2 - - - -
35A ALA* 1.3 78.2 - - + +
37A ILE* 1.3 64.2 + - + +
39A GLY* 3.1 12.3 + - - -
40A LEU* 3.3 9.9 + - - +
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Residues in contact with ILE 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 GLY 3.3 15.6 + - - +
34A LEU* 3.6 24.9 - - + +
35A ALA 3.3 0.6 - - - -
36A PHE* 1.3 77.6 - - + +
38A VAL* 1.3 65.8 + - + +
40A LEU* 3.1 24.4 + - + +
41A LEU* 3.5 5.2 + - - +
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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 LEU* 3.4 13.9 - - + +
35A ALA* 3.3 10.9 + - - +
36A PHE 3.2 0.4 - - - -
37A ILE* 1.3 79.7 - - + +
39A GLY* 1.3 64.0 + - - +
41A LEU* 3.2 24.1 + - + +
42A ILE* 3.4 16.7 + - + +
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Residues in contact with GLY 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 ALA 3.3 5.9 + - - -
36A PHE* 3.1 9.3 + - - -
38A VAL* 1.3 76.5 - - - +
40A LEU* 1.3 66.5 + - - +
42A ILE* 3.1 30.9 + - - +
43A LEU* 3.5 9.4 + - - +
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Residues in contact with LEU 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 PHE 3.3 8.6 + - - +
37A ILE* 3.1 17.1 + - + +
39A GLY* 1.3 75.5 - - - +
41A LEU* 1.3 64.1 + - - +
43A LEU* 3.0 32.4 + - + +
44A LEU* 3.3 29.0 - - + +
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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 ILE 3.5 4.7 + - - +
38A VAL* 3.2 16.2 + - + +
40A LEU* 1.3 79.2 - - - +
42A ILE* 1.3 63.6 + - + +
44A LEU* 3.1 35.6 + - + +
45A SER* 3.4 9.5 + - - -
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Residues in contact with ILE 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* 3.4 16.6 + - + +
39A GLY* 3.1 23.7 + - - +
41A LEU* 1.3 78.7 - - + +
43A LEU* 1.3 67.3 + - + +
45A SER* 2.9 26.3 + - - -
46A ARG* 3.6 3.3 + - - +
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Residues in contact with LEU 43 (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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39A GLY 3.5 9.4 + - - +
40A LEU* 3.0 29.2 + - + +
42A ILE* 1.3 79.4 - - + +
44A LEU* 1.3 68.1 + - + +
46A ARG* 3.0 26.0 + - + +
47A ARG* 3.5 3.6 + - - +
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Residues in contact with LEU 44 (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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40A LEU* 3.3 31.4 - - + +
41A LEU* 3.1 27.1 + - + +
43A LEU* 1.3 82.1 - - + +
45A SER* 1.3 62.5 + - - +
47A ARG* 2.9 29.3 + - + +
48A PHE* 3.3 17.1 - - + -
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Residues in contact with SER 45 (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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41A LEU 3.4 5.7 + - - -
42A ILE* 2.9 21.6 + - - -
44A LEU* 1.3 78.5 - - - +
46A ARG* 1.3 60.7 + - - +
48A PHE* 3.1 29.6 + - - +
49A ARG* 4.0 4.0 + - - +
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Residues in contact with ARG 46 (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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42A ILE 3.6 3.2 + - - +
43A LEU* 3.0 17.4 + - + +
45A SER* 1.3 80.0 - - - +
47A ARG* 1.3 65.0 + - - +
49A ARG* 2.9 11.4 + - + +
50A SER* 2.8 62.1 + - - +
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Residues in contact with ARG 47 (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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43A LEU 3.5 3.3 + - - +
44A LEU* 2.9 25.9 + - + +
46A ARG* 1.3 85.3 - - - +
48A PHE* 1.3 81.2 - - - +
50A SER* 2.4 33.2 - - - +
51A GLY* 5.9 0.4 - - - -
55A LYS* 4.6 12.1 - - - +
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Residues in contact with PHE 48 (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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44A LEU* 3.3 24.0 - - + -
45A SER* 3.1 17.7 + - - +
46A ARG 3.1 0.6 - - - -
47A ARG* 1.3 99.0 - - + +
49A ARG* 1.3 61.4 + - + +
55A LYS* 2.8 32.7 - - - +
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Residues in contact with ARG 49 (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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45A SER 5.0 3.6 - - - +
46A ARG* 2.9 11.4 + - + +
48A PHE* 1.3 83.0 - - + +
50A SER* 1.3 66.7 + - - +
51A GLY 3.6 0.3 + - - -
54A LYS* 4.9 0.3 - - - -
55A LYS* 3.3 12.4 + - - +
56A ARG* 2.9 56.7 + - + +
58A GLN* 3.6 33.9 + - - +
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 2.8 60.8 + - - +
47A ARG* 2.4 35.3 - - - +
48A PHE 5.1 0.2 - - - -
49A ARG* 1.3 73.2 - - - +
51A GLY* 1.3 57.2 + - - +
55A LYS* 5.0 1.1 - - - +
56A ARG* 5.6 0.7 - - - +
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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