Contacts of the helix formed by residues 29 - 52 (chain A) in PDB entry 1ZSP
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 LYS 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 2.9 39.0 + - + +
28A SER* 1.3 95.6 - - - +
30A HIS* 1.3 65.6 + - + +
31A HIS 3.5 0.2 - - - -
32A ALA* 3.9 0.6 - - - +
33A ALA* 2.8 35.3 + - - +
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Residues in contact with HIS 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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25A LEU* 3.2 24.4 + - + +
26A HIS* 3.3 25.4 - - + +
29A LYS* 1.3 84.2 - - + +
31A HIS* 1.3 64.3 + - - +
33A ALA* 3.4 5.1 + - - +
34A ALA* 3.2 20.3 + - - +
74A HIS* 5.1 6.0 - - + +
163A HIS* 3.5 54.3 + + + +
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Residues in contact with HIS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.4 13.6 - - + +
5A PRO* 3.6 9.8 - - + +
26A HIS 3.0 16.1 + - - +
27A HIS* 3.5 13.7 - - - +
30A HIS* 1.3 73.0 - - - +
32A ALA* 1.3 64.3 + - - +
34A ALA* 3.0 15.1 + - - +
35A VAL* 3.0 15.6 + - + +
70A GLY 4.4 0.8 + - - -
71A HIS* 3.1 48.4 - + - -
74A HIS* 3.5 21.3 - - + +
75A SER* 3.4 18.4 + - - -
78A TRP* 2.9 31.1 + + + -
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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
----------------------------------------------------------
4A LEU* 3.6 23.5 - - + +
27A HIS 3.3 5.7 + - - +
28A SER 3.1 30.3 - - - +
29A LYS 3.9 0.4 - - - +
30A HIS 3.3 0.4 - - - -
31A HIS* 1.3 77.0 - - - +
33A ALA* 1.3 62.0 + - - +
35A VAL* 3.2 5.8 + - - +
36A ASN* 3.0 33.5 + - - +
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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 LYS 2.8 19.3 + - - +
30A HIS* 3.6 6.1 - - - +
32A ALA* 1.3 73.7 - - - +
34A ALA* 1.3 61.2 + - - +
36A ASN* 3.4 8.9 + - - +
37A ASN* 2.9 41.9 + - - +
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Residues in contact with ALA 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 HIS 3.2 9.4 + - - +
31A HIS* 3.0 11.7 + - - +
33A ALA* 1.3 79.4 - - - +
35A VAL* 1.3 58.1 + - - +
38A LEU* 2.8 32.1 + - - +
66A PHE 5.3 0.2 - - - +
67A ASN* 3.6 35.8 - - - +
70A GLY* 4.2 9.9 - - - -
71A HIS* 4.0 13.2 - - - +
74A HIS* 5.6 1.1 - - + +
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Residues in contact with VAL 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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2A HIS* 3.4 34.3 - - + +
3A SER* 4.0 0.2 - - - -
4A LEU* 3.9 25.1 - - + +
31A HIS* 3.0 22.7 + - + +
32A ALA* 3.2 8.3 + - - +
34A ALA* 1.3 76.8 - - - +
36A ASN* 1.3 67.4 - - - +
38A LEU* 3.2 8.2 + - - +
39A ASN* 3.1 25.8 + - - +
71A HIS* 3.7 31.0 - - + +
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Residues in contact with ASN 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 24.7 + - - +
33A ALA* 3.9 6.7 - - - +
35A VAL* 1.3 82.1 - - - +
37A ASN* 1.3 68.7 + - - +
39A ASN* 3.4 9.0 + - - +
40A VAL* 3.2 27.5 + - + +
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Residues in contact with ASN 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* 2.9 25.5 + - - +
36A ASN* 1.3 80.3 - - - +
38A LEU* 1.3 56.8 + - - +
40A VAL* 3.3 9.1 + - - +
41A THR* 2.9 34.5 + - - +
67A ASN* 3.1 38.5 + - - +
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Residues in contact with LEU 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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2A HIS* 3.6 31.2 - - + -
34A ALA 2.8 21.5 + - - +
35A VAL* 3.5 4.5 - - - +
37A ASN* 1.3 71.1 - - - +
39A ASN* 1.3 60.6 + - - +
41A THR* 3.2 3.6 + - - -
42A GLU* 2.8 40.5 + - + +
64A LEU* 3.8 26.5 - - + -
67A ASN* 3.9 9.3 - - + +
68A GLY* 3.8 19.5 - - - +
71A HIS* 3.8 30.3 - - + -
54B VAL* 4.0 10.8 - - + -
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Residues in contact with ASN 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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1A LYS* 3.4 29.4 + - + +
2A HIS* 2.7 56.6 + - - +
35A VAL* 3.1 23.6 + - - +
36A ASN* 3.4 9.6 + - - +
38A LEU* 1.3 75.0 - - - +
40A VAL* 1.3 62.4 + - + +
42A GLU* 3.6 6.5 + - - +
43A GLU* 3.1 24.4 + - - +
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Residues in contact with VAL 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 ASN* 3.2 15.0 + - + +
37A ASN* 3.5 12.3 - - - +
38A LEU 3.2 0.2 - - - -
39A ASN* 1.3 75.7 - - + +
41A THR* 1.3 67.7 + - - +
43A GLU* 3.3 7.4 + - - +
44A LYS* 3.2 50.1 + - + +
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Residues in contact with THR 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 ASN* 2.9 18.3 + - - +
38A LEU* 3.8 5.2 - - - -
40A VAL* 1.3 80.3 - - - +
42A GLU* 1.3 56.9 + - - +
44A LYS* 3.2 11.1 + - - +
45A TYR* 2.9 26.4 + - + +
60A LEU* 4.0 21.0 - - + +
63A ALA* 3.8 19.5 + - + +
64A LEU* 3.8 41.5 - - + +
67A ASN* 4.5 1.7 + - - -
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Residues in contact with GLU 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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1A LYS 4.6 7.8 + - - -
2A HIS* 2.8 41.6 + - - -
38A LEU* 2.8 25.6 + - + +
39A ASN* 3.9 5.3 - - - +
41A THR* 1.3 73.5 - - - +
43A GLU* 1.3 67.6 + - - +
45A TYR* 3.2 8.0 + - - +
46A GLN* 3.0 22.2 + - - +
64A LEU* 4.1 3.1 - - + -
49B LEU* 3.8 25.3 - - + +
52B GLY* 4.4 5.9 - - - -
54B VAL* 3.9 6.6 - - - +
57B GLN* 2.9 29.0 - - - +
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Residues in contact with GLU 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 ASN 3.1 19.8 + - - +
40A VAL* 3.7 6.2 - - - +
42A GLU* 1.3 76.2 - - - +
44A LYS* 1.3 70.2 + - - +
46A GLN* 3.2 17.4 + - + +
47A GLU* 2.9 41.3 + - - +
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Residues in contact with LYS 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 VAL* 3.2 37.7 + - + +
41A THR* 3.2 9.1 + - - +
43A GLU* 1.3 84.0 - - - +
45A TYR* 1.3 60.5 + - - +
47A GLU* 3.3 10.4 + - - +
48A ALA* 3.0 26.5 + - - +
60A LEU* 3.9 27.0 - - + +
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Residues in contact with TYR 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 THR* 2.9 16.7 + - + +
42A GLU* 3.2 8.9 + - - +
44A LYS* 1.3 75.1 - - - +
46A GLN* 1.3 60.5 + - - +
48A ALA* 4.2 1.1 - - - -
49A LEU* 2.9 34.3 + - + +
57A GLN* 2.7 64.8 + - + +
60A LEU* 3.7 21.3 - - + +
61A GLN* 5.1 8.4 + - + -
64A LEU* 5.3 6.7 - - + -
45B TYR* 3.3 60.5 - + + +
49B LEU* 4.5 4.5 - - + -
57B GLN* 5.5 0.7 - - - +
61B GLN* 6.2 0.7 - - + -
64B LEU* 3.5 15.8 - - - +
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Residues in contact with GLN 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 GLU 3.0 12.2 + - - +
43A GLU* 3.4 14.6 - - + +
44A LYS 3.2 0.2 - - - -
45A TYR* 1.3 79.3 - - - +
47A GLU* 1.3 62.0 - - + +
49A LEU* 4.4 0.7 - - - +
50A ALA* 3.1 23.2 + - + +
46B GLN* 3.0 42.3 + - - -
49B LEU* 3.6 19.4 - - + +
50B ALA* 5.5 2.4 - - - +
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Residues in contact with GLU 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 GLU* 2.9 40.4 + - - +
44A LYS* 3.6 11.1 - - - +
45A TYR 3.2 0.2 - - - -
46A GLN* 1.3 77.5 - - + +
48A ALA* 1.3 64.1 + - - +
50A ALA* 3.4 5.2 + - - +
51A LYS* 3.0 51.9 + - - +
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Residues in contact with ALA 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 LYS 3.0 17.0 + - - +
45A TYR* 3.7 7.2 - - - +
46A GLN 3.4 0.2 - - - -
47A GLU* 1.3 77.6 - - - +
49A LEU* 1.3 56.8 + - - +
51A LYS* 3.1 4.5 + - - -
52A GLY 2.9 23.4 + - - -
53A ASP* 2.9 18.5 + - - +
56A ALA* 3.9 24.0 - - + -
57A GLN* 3.8 22.0 - - + +
60A LEU* 4.4 2.9 - - + -
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Residues in contact with LEU 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 TYR* 2.9 22.2 + - + +
46A GLN* 3.9 4.7 - - - +
48A ALA* 1.3 77.0 - - - +
50A ALA* 1.3 61.7 + - - +
52A GLY* 3.0 14.0 + - - -
57A GLN* 3.7 16.7 + - - +
42B GLU* 3.7 46.3 - - + +
45B TYR* 4.3 12.6 - - + -
46B GLN* 3.3 57.2 - - + +
49B LEU* 4.9 2.9 - - + -
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Residues in contact with ALA 50 (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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46A GLN* 3.1 25.0 + - + +
47A GLU* 3.8 6.1 - - - +
49A LEU* 1.3 77.1 - - - +
51A LYS* 1.3 61.3 + - + +
46B GLN* 5.3 3.1 - - - +
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Residues in contact with LYS 51 (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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47A GLU* 3.0 44.8 + - - +
48A ALA* 3.6 6.3 - - - +
49A LEU 3.1 0.8 - - - -
50A ALA* 1.3 80.3 - - + +
52A GLY* 1.3 61.2 + - - +
53A ASP* 3.5 12.5 + - + +
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Residues in contact with GLY 52 (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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48A ALA 2.9 4.2 + - - -
49A LEU 3.0 12.8 + - - -
51A LYS* 1.3 79.8 - - - +
53A ASP* 1.3 59.4 + - - +
54A VAL* 3.1 8.5 + - - +
57A GLN* 4.5 2.0 - - - -
2B HIS* 3.3 31.4 + - - -
42B GLU* 4.5 4.7 - - - -
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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
------------------------------------------------------------
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