Contacts of the helix formed by residues 25 - 46 (chain A) in PDB entry 2VGL
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 SER 25 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A CYS* 3.2 6.7 + - - +
24A LYS* 1.3 81.7 - - - +
26A LYS* 1.3 66.7 + - - +
27A GLU* 3.0 12.0 + - - +
28A ALA* 2.7 33.3 + - - +
29A GLU* 2.9 23.1 + - - +
99M GLU* 5.0 0.7 - - - -
103M ASN* 3.4 24.2 - - - -
138M ILE* 4.7 11.6 - - - +
139M LYS 5.9 1.1 - - - -
140M SER* 5.9 1.3 - - - -
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 1.3 72.9 - - - +
27A GLU* 1.3 57.1 + - - +
29A GLU* 3.7 19.3 - - - +
30A ILE* 3.1 49.3 + - + +
70A HIS* 5.2 8.1 - - - -
99M GLU* 4.0 27.4 + - + +
103M ASN* 4.3 5.3 + - - +
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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
----------------------------------------------------------
25A SER* 2.9 9.6 + - - +
26A LYS* 1.3 76.5 - - - +
28A ALA* 1.3 65.8 + - - +
29A GLU 3.2 0.3 + - - -
30A ILE* 3.3 9.7 + - + +
31A LYS* 3.0 34.7 + - + +
99M GLU* 3.7 12.5 + - - +
139M LYS 4.4 2.4 - - - +
140M SER* 3.3 32.6 - - - -
141M GLN 3.4 22.5 + - - -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A CYS* 3.7 23.5 - - + -
24A LYS* 4.3 5.4 - - + +
25A SER* 2.7 27.6 + - - +
27A GLU* 1.3 71.7 - - - +
29A GLU* 1.3 60.8 + - - +
31A LYS* 3.2 12.6 + - - +
32A ARG* 3.0 19.6 + - - +
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Residues in contact with GLU 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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20A ILE* 4.2 20.9 - - + +
23A CYS* 3.6 18.3 - - + -
25A SER 2.9 16.3 + - - +
26A LYS* 3.7 21.6 - - - +
28A ALA* 1.3 73.4 - - - +
30A ILE* 1.3 67.2 + - - +
32A ARG* 3.1 5.1 + - - +
33A ILE* 3.0 36.2 + - + +
68A LEU* 3.9 31.2 - - - +
70A HIS* 4.7 6.5 - - - -
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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 LYS* 3.1 40.9 + - + +
27A GLU* 3.6 7.6 - - + +
29A GLU* 1.3 81.1 - - + +
31A LYS* 1.3 63.6 + - + +
33A ILE* 3.5 7.8 + - - +
34A ASN* 3.2 41.1 + - - +
70A HIS* 4.2 22.4 - - + +
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Residues in contact with LYS 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* 3.0 26.1 + - + +
28A ALA* 3.5 12.5 - - - +
29A GLU 3.1 0.2 - - - -
30A ILE* 1.3 79.5 - - + +
32A ARG* 1.3 62.8 + - - +
34A ASN* 3.4 6.3 + - - +
35A LYS* 3.1 23.3 + - - +
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Residues in contact with ARG 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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15A VAL* 4.3 7.3 - - - +
16A PHE* 3.1 28.7 - - + +
19A ASP* 2.9 41.8 + - + +
20A ILE* 4.8 6.7 - - + +
23A CYS* 4.4 10.3 - - - -
28A ALA 3.0 12.9 + - - +
29A GLU* 3.1 6.9 + - - +
31A LYS* 1.3 77.4 - - - +
33A ILE* 1.3 60.3 + - - +
35A LYS* 3.4 36.0 - - - +
36A GLU* 2.9 64.9 + - - +
61A LYS* 5.3 0.4 - - - +
1609A IHP 5.2 3.4 + - - -
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Residues in contact with ILE 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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16A PHE* 4.1 21.8 - - + -
20A ILE* 4.6 5.8 - - + -
29A GLU* 3.0 30.8 + - + +
30A ILE* 3.8 7.4 - - - +
32A ARG* 1.3 76.7 - - - +
34A ASN* 1.3 66.7 + - - +
36A GLU* 2.9 5.9 + - - +
37A LEU* 2.9 33.4 + - + +
65A ILE* 4.0 25.6 - - + -
68A LEU* 4.1 14.8 - - + -
70A HIS* 3.3 43.5 - - + +
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Residues in contact with ASN 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* 3.2 34.1 + - - +
31A LYS* 3.4 5.6 + - - +
33A ILE* 1.3 79.6 - - - +
35A LYS* 1.3 67.6 + - - +
37A LEU* 3.2 15.7 + - - +
38A ALA* 2.9 25.7 + - - +
70A HIS* 6.1 0.7 - - - -
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Residues in contact with LYS 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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19A ASP* 5.7 0.2 + - - -
31A LYS 3.1 13.7 + - - +
32A ARG* 3.4 41.2 - - - +
34A ASN* 1.3 76.4 - - - +
36A GLU* 1.4 57.0 + - - +
38A ALA* 3.2 6.9 + - - +
39A ASN* 3.0 27.4 + - + +
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Residues in contact with GLU 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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16A PHE* 3.1 31.2 - - + -
32A ARG* 2.9 39.2 + - - +
33A ILE 2.9 10.6 + - - +
35A LYS* 1.4 74.0 - - - +
37A LEU* 1.3 59.6 + - - +
39A ASN* 3.2 12.9 + - - +
40A ILE* 2.9 40.2 + - + +
61A LYS* 3.1 37.2 + - + +
65A ILE* 4.3 7.4 - - + -
1609A IHP 3.6 10.7 + - - -
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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 ILE* 2.9 23.1 + - + +
34A ASN* 3.7 22.2 - - - +
36A GLU* 1.3 77.0 - - - +
38A ALA* 1.3 64.1 + - - +
40A ILE* 3.3 2.5 + - - -
41A ARG* 3.0 26.6 + - - +
62A LEU* 3.5 29.8 - - + -
65A ILE* 4.2 11.0 - - + -
70A HIS* 6.0 1.8 - - + -
71A ASP 4.4 15.7 - - - +
72A ILE* 3.8 15.0 - - + -
74A PHE* 4.0 17.8 - - + -
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Residues in contact with ALA 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 ASN 2.9 12.9 + - - +
35A LYS* 3.3 11.9 - - - +
37A LEU* 1.3 77.0 - - - +
39A ASN* 1.3 64.3 + - - +
41A ARG* 3.2 4.9 + - - +
42A SER* 3.0 26.1 + - - -
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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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35A LYS* 3.0 13.8 + - + +
36A GLU* 3.5 22.0 + - - +
38A ALA* 1.3 77.2 - - - +
40A ILE* 1.3 60.4 + - - +
42A SER* 3.4 6.8 + - - -
43A LYS* 2.9 64.0 + - - +
58A TYR* 3.9 5.7 + - - -
1609A IHP 3.4 24.4 + - - -
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Residues in contact with ILE 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 GLU* 2.9 39.7 + - + +
37A LEU 4.0 2.9 - - - +
38A ALA 3.2 0.2 - - - -
39A ASN* 1.3 77.2 - - - +
41A ARG* 1.3 58.3 + - - +
43A LYS* 3.3 3.7 + - - -
44A PHE* 2.9 64.8 + - + -
58A TYR* 3.6 26.5 - - + +
61A LYS* 3.9 22.0 - - + -
62A LEU* 3.8 26.5 - - + -
65A ILE* 5.0 1.6 - - + -
74A PHE* 3.9 10.3 - - + -
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Residues in contact with ARG 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 3.0 17.4 + - - +
38A ALA* 3.8 4.9 - - - +
40A ILE* 1.3 75.0 - - - +
42A SER* 1.3 60.7 + - - +
44A PHE* 3.8 2.4 - - - +
45A LYS* 2.8 75.5 + - + +
74A PHE* 4.0 32.0 - - + +
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Residues in contact with SER 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 ALA 3.0 16.9 + - - -
39A ASN* 3.4 11.5 - - - -
41A ARG* 1.3 76.5 - - - +
43A LYS* 1.3 56.8 + - - +
45A LYS* 2.9 6.1 + - - +
46A GLY* 2.4 38.7 + - - -
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Residues in contact with LYS 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* 2.9 39.8 + - - +
40A ILE 4.0 2.7 - - - +
41A ARG 3.3 0.2 - - - -
42A SER* 1.3 82.1 - - - +
44A PHE* 1.3 61.6 + - - +
46A GLY* 3.5 11.0 + - - +
48A LYS 4.5 4.0 - - - +
50A LEU* 3.2 36.1 - - + +
58A TYR* 3.2 43.1 + - + +
1609A IHP 2.6 45.5 + - - -
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Residues in contact with PHE 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 ILE* 2.9 40.0 + - + +
41A ARG* 3.9 4.9 - - + +
43A LYS* 1.3 81.3 - - + +
45A LYS* 1.3 60.7 + - + +
46A GLY 3.5 2.4 + - - +
50A LEU* 3.7 25.4 - - + -
55A LYS* 5.0 2.2 - - - -
58A TYR* 3.5 30.7 - + + -
59A VAL* 4.2 11.7 - - + -
62A LEU* 4.0 4.5 - - + -
74A PHE* 4.2 13.2 - + + -
75A GLY* 3.9 13.2 - - - -
78A GLU* 3.0 57.2 - - + +
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 2.8 68.6 + - + +
42A SER* 3.6 4.0 - - - +
44A PHE* 1.3 71.7 - - + +
46A GLY* 1.3 69.0 + - - +
47A ASP* 4.9 1.4 - - - +
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Residues in contact with GLY 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 SER 2.4 23.9 + - - -
43A LYS* 3.5 7.8 + - - +
44A PHE 3.2 6.1 - - - +
45A LYS* 1.3 79.5 - - - +
47A ASP* 1.3 69.3 + - - -
48A LYS 3.8 5.1 - - - +
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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