Contacts of the helix formed by residues 21 - 36 (chain A) in PDB entry 2VLA
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 MET 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ALA 3.6 4.2 + - - -
19A LYS 3.2 0.2 - - - -
20A ASN* 1.3 87.0 - - + +
22A LEU* 1.3 64.9 + - - +
23A ASP 3.2 3.1 - - - -
24A ASN* 3.0 37.2 + - + +
25A LEU* 2.8 36.4 + - + +
55A ILE* 4.8 20.2 - - + +
56A LEU* 5.5 7.6 - - - -
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Residues in contact with LEU 22 (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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18A ALA* 2.9 36.2 + - + +
19A LYS* 3.3 15.8 + - + +
20A ASN 3.5 0.6 + - - -
21A MET* 1.3 76.9 - - - +
23A ASP* 1.3 63.1 + - - +
25A LEU* 4.4 1.8 - - - +
26A LEU* 2.9 46.0 + - + +
77A PHE* 4.2 7.2 - - + -
102A GLN* 3.6 19.5 - - - +
106A PHE* 3.8 20.4 - - + -
219A LEU* 3.6 44.0 - - + -
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Residues in contact with ASP 23 (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 MET 3.1 0.8 + - - -
22A LEU* 1.3 81.7 + - - +
24A ASN* 1.3 61.3 + - - +
27A PRO* 3.3 21.6 - - - +
102A GLN* 3.3 27.4 + - - +
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Residues in contact with ASN 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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21A MET* 3.0 33.5 + - + +
23A ASP* 1.3 82.7 - - - +
25A LEU* 1.3 64.9 + - - +
26A LEU 3.4 0.4 - - - -
27A PRO* 3.5 4.4 - - - +
28A ALA* 3.2 22.6 + - - +
55A ILE* 4.7 12.1 - - + +
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Residues in contact with LEU 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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17A LYS 4.0 7.4 - - - +
18A ALA* 3.7 32.5 - - + -
21A MET* 2.8 36.5 + - + +
22A LEU 4.3 0.9 - - - +
24A ASN* 1.3 72.0 - - - +
26A LEU* 1.3 61.6 + - - +
28A ALA* 3.5 2.2 - - + +
29A TYR* 2.8 53.8 + - + +
52A LEU* 3.8 29.4 - - + -
55A ILE* 3.8 18.4 - - + -
56A LEU* 3.9 14.8 - - + -
68A HIS* 4.3 5.8 - - + -
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Residues in contact with LEU 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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22A LEU* 2.9 23.2 + - + +
25A LEU* 1.3 78.8 - - - +
27A PRO* 1.3 69.2 - - + +
29A TYR* 3.4 4.6 + - + +
30A ALA* 3.1 24.1 + - - +
77A PHE* 4.1 17.5 - - + -
79A MET* 4.0 12.3 - - + -
96A TYR* 3.7 29.4 - - + +
102A GLN* 3.9 27.8 - - + +
105A PHE* 3.7 44.0 - - + -
106A PHE* 4.1 5.6 - - + -
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Residues in contact with PRO 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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22A LEU 3.7 1.1 - - - +
23A ASP* 3.3 27.8 - - - +
24A ASN* 3.5 7.9 - - - +
26A LEU* 1.3 95.2 - - + +
28A ALA* 1.3 56.4 + - - +
30A ALA* 3.8 0.6 - - + +
31A ASN* 2.9 46.7 + - - +
96A TYR* 3.4 22.6 - - + +
102A GLN* 5.8 0.4 - - - +
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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
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24A ASN 3.2 16.7 + - - +
25A LEU* 3.2 8.3 + - - +
27A PRO* 1.3 75.2 - - - +
29A TYR* 1.3 66.7 + - - +
31A ASN* 4.1 2.9 - - - +
32A ILE* 2.9 41.5 + - + +
52A LEU* 5.0 4.7 - - + -
55A ILE* 3.9 30.7 - - + -
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Residues in contact with TYR 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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18A ALA* 3.8 18.9 - - + +
25A LEU* 2.8 34.2 + - + +
26A LEU* 3.8 6.3 - - - +
28A ALA* 1.3 71.7 - - - +
30A ALA* 1.3 64.1 + - - +
32A ILE* 3.8 4.7 - - + +
33A ILE* 3.0 31.1 + - - +
48A PHE* 4.1 20.0 - + - -
52A LEU* 4.0 24.5 - - + -
68A HIS* 2.8 38.6 + - + -
72A ILE* 3.7 31.7 - - + +
73A ALA* 4.4 10.1 - - + -
77A PHE* 4.2 6.7 - + - -
79A MET* 3.7 28.7 - - - -
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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 LEU 3.1 14.3 + - - +
27A PRO* 3.8 2.9 - - + +
29A TYR* 1.3 80.9 - - - +
31A ASN* 1.3 59.6 + - - +
33A ILE* 3.4 2.3 + - - +
34A ASP* 2.9 30.3 + - - +
79A MET* 3.8 14.4 - - + -
93A THR* 4.1 11.5 - - + +
96A TYR* 3.7 27.1 - - + -
97A ILE* 3.8 14.6 - - + +
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Residues in contact with ASN 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 PRO* 2.9 31.4 + - - +
28A ALA* 4.1 3.3 - - - +
30A ALA* 1.3 74.8 - - - +
32A ILE* 1.3 67.9 + - - +
34A ASP* 4.4 5.1 - - - +
35A ASP* 3.0 35.6 + - - +
51A ARG* 3.8 12.3 - - - +
97A ILE* 3.6 17.8 - - - +
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Residues in contact with ILE 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 ALA* 2.9 35.4 + - + +
29A TYR* 3.8 5.2 - - - +
31A ASN* 1.3 78.0 - - - +
33A ILE* 1.3 64.1 + - - +
35A ASP* 3.7 0.2 - - - +
36A ILE* 3.0 36.4 + - + +
48A PHE* 3.7 43.3 - - + +
51A ARG* 3.5 52.5 - - + +
52A LEU* 3.8 24.2 - - + +
55A ILE* 5.6 1.1 - - + -
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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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29A TYR 3.0 23.2 + - - +
30A ALA* 3.8 3.4 - - - +
32A ILE* 1.3 75.6 - - - +
34A ASP* 1.3 63.5 + - - +
36A ILE* 4.4 2.5 - - - -
37A CYS* 3.0 43.3 + - - +
44A PHE* 4.4 10.8 - - + -
48A PHE* 4.3 13.9 - - + -
73A ALA* 4.4 10.1 - - + -
79A MET* 3.6 36.1 - - + +
80A PHE* 3.8 19.5 - - + -
89A PRO* 3.7 31.2 - - + -
93A THR* 4.5 2.9 - - + +
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Residues in contact with ASP 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 2.9 18.2 + - - +
31A ASN* 3.9 5.4 - - - +
33A ILE* 1.3 77.4 - - - +
35A ASP* 1.3 69.3 + - - +
37A CYS 3.4 13.0 - - - +
89A PRO* 4.4 15.9 - - - +
93A THR* 5.2 2.4 - - + +
94A ASN* 4.8 6.1 - - - +
97A ILE* 4.0 36.1 - - + +
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Residues in contact with ASP 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ASN* 3.0 24.7 + - - +
32A ILE 3.7 1.1 - - - +
34A ASP* 1.3 88.3 - - - +
36A ILE* 1.3 62.0 + - + +
37A CYS 3.7 2.8 + - - +
51A ARG* 3.0 38.2 + - - +
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Residues in contact with ILE 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 ILE* 3.0 26.3 + - + +
35A ASP* 1.3 82.9 - - + +
37A CYS* 1.3 63.9 + - - +
38A PRO 3.5 2.9 - - - +
39A CYS* 3.2 24.9 - - - +
44A PHE* 3.5 38.8 - - + +
47A ASP* 3.9 25.8 - - + +
48A PHE* 3.6 29.4 - - - +
51A ARG* 4.5 11.4 - - + +
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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