Contacts of the helix formed by residues 41 - 56 (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 LYS 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A CYS 3.8 1.0 + - - -
40A ASP* 1.3 71.9 - - - +
42A ALA* 1.3 64.5 + - - +
44A PHE* 3.0 17.8 + - - +
45A VAL* 3.1 20.7 + - + +
82A GLU* 5.4 5.4 - - - +
85A GLU* 4.0 11.1 + - - +
87A ILE* 4.1 19.0 - - + +
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Residues in contact with ALA 42 (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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40A ASP* 3.3 9.3 + - - +
41A LYS* 1.3 80.3 - - - +
43A SER* 1.3 62.2 + - - +
45A VAL* 3.5 7.3 + - - +
46A LYS* 3.5 19.4 + - - +
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Residues in contact with SER 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 CYS* 4.5 8.7 - - - -
40A ASP* 2.3 44.5 + - - -
42A ALA* 1.3 74.3 - - - +
44A PHE* 1.3 57.9 + - - +
46A LYS* 3.4 4.2 + - - +
47A ASP* 2.9 47.0 + - - -
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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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33A ILE* 4.4 5.8 - - + -
36A ILE* 3.5 25.8 - - + -
37A CYS* 3.6 28.7 - - - -
39A CYS* 3.8 10.3 - - - -
40A ASP 2.9 14.1 + - - +
41A LYS* 3.3 10.5 - - - +
43A SER* 1.3 77.4 - - - +
45A VAL* 1.3 60.6 + - + +
48A PHE* 2.8 53.0 + + - +
69A ARG* 3.7 24.2 - - - -
80A PHE* 3.7 46.2 - + - -
87A ILE* 3.9 19.1 - - + -
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Residues in contact with VAL 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 LYS* 3.1 14.5 + - + +
42A ALA* 3.8 8.1 - - - +
43A SER 3.3 0.2 - - - -
44A PHE* 1.3 78.2 - - + +
46A LYS* 1.3 66.0 + - - +
48A PHE* 4.0 0.2 - - - +
49A ASN* 3.2 29.4 + - - +
62A LYS* 5.5 7.2 - - - +
66A ASP* 4.3 7.0 - - - +
69A ARG* 3.6 43.3 - - - +
104L A 5.9 0.4 - - - +
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Residues in contact with LYS 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 ALA 3.5 9.0 + - - +
43A SER* 3.4 8.4 + - - +
44A PHE 3.3 0.2 - - - -
45A VAL* 1.3 82.3 - - + +
47A ASP* 1.3 65.4 + - - +
49A ASN* 3.9 3.5 - - - +
50A ASN* 3.0 52.9 + - - +
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Residues in contact with ASP 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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36A ILE* 3.9 30.3 - - + +
39A CYS* 5.5 1.7 - - - +
43A SER* 2.9 31.0 + - - +
46A LYS* 1.3 82.9 - - - +
48A PHE* 1.3 66.2 + - - +
50A ASN* 3.5 7.2 + - - +
51A ARG* 3.2 28.7 + - + +
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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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29A TYR* 4.1 26.0 - + - -
32A ILE* 3.7 30.9 - - + +
33A ILE* 4.3 12.8 - - + -
36A ILE* 3.6 4.8 - - + +
44A PHE* 2.8 38.7 + + + +
47A ASP* 1.3 77.2 - - - +
49A ASN* 1.3 66.3 + - - +
51A ARG* 3.2 4.3 + - - +
52A LEU* 2.9 51.9 + - + +
65A LEU 4.4 0.2 - - - -
69A ARG* 3.5 44.2 - - + -
73A ALA* 4.1 14.4 - - + -
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Residues in contact with ASN 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 VAL* 3.2 20.8 + - - +
46A LYS* 3.9 3.8 - - - +
48A PHE* 1.3 86.2 - - - +
50A ASN* 1.3 65.6 + - - +
52A LEU* 4.5 3.6 - - - +
53A ILE* 3.1 28.4 + - - +
62A LYS* 4.3 12.5 - - - +
65A LEU* 3.7 35.0 - - + +
66A ASP* 2.9 24.9 + - - -
69A ARG* 2.9 18.9 + - - +
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Residues in contact with ASN 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 LYS* 3.0 41.1 + - - +
47A ASP* 3.9 8.7 + - - +
48A PHE 3.3 0.2 - - - -
49A ASN* 1.3 79.5 - - - +
51A ARG* 1.3 62.8 + - + +
53A ILE* 3.4 19.6 - - - +
54A GLU* 3.9 9.4 - - - +
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Residues in contact with ARG 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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31A ASN* 3.8 8.7 - - - +
32A ILE* 3.5 49.7 - - + +
35A ASP* 3.0 39.6 + - - +
36A ILE* 4.5 10.0 - - + +
47A ASP* 3.2 18.3 + - + +
48A PHE 3.7 0.7 - - - +
50A ASN* 1.3 76.4 - - + +
52A LEU* 1.3 66.2 + - - +
53A ILE 3.2 0.2 - - - -
54A GLU* 3.2 21.9 + - - +
55A ILE* 4.0 6.4 + - - +
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Residues in contact with LEU 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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25A LEU* 3.8 29.2 - - + -
28A ALA* 5.0 1.3 - - + -
29A TYR* 4.0 13.0 - - + -
32A ILE* 3.8 11.4 - - + +
48A PHE* 2.9 37.7 + - + +
49A ASN* 4.1 2.9 - - - +
51A ARG* 1.3 76.4 - - - +
53A ILE* 1.3 58.0 + - - +
55A ILE* 2.8 28.9 + - + +
56A LEU* 3.1 23.4 + - + +
65A LEU* 4.0 11.9 - - + +
68A HIS* 3.5 37.7 - - + +
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Residues in contact with ILE 53 (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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49A ASN 3.1 13.1 + - - +
50A ASN* 3.4 21.8 - - - +
52A LEU* 1.3 78.6 - - - +
54A GLU* 1.3 69.7 + - - +
56A LEU* 3.9 2.0 - - - +
57A GLY* 2.9 46.7 + - - +
58A GLU* 4.1 15.7 + - - +
60A THR* 4.0 17.0 - - - +
65A LEU* 3.8 28.7 - - + +
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Residues in contact with GLU 54 (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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50A ASN 3.9 11.0 - - - +
51A ARG* 3.2 14.6 + - - +
52A LEU 3.1 0.8 + - - -
53A ILE* 1.3 86.9 - - - +
55A ILE* 1.3 68.1 + - + +
57A GLY* 4.5 2.6 + - - -
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Residues in contact with ILE 55 (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* 4.8 15.1 - - + +
24A ASN* 4.7 18.6 - - + +
25A LEU* 3.8 26.7 - - + -
28A ALA* 3.9 25.4 - - + -
32A ILE* 5.6 0.7 - - + -
51A ARG 4.3 7.9 - - - +
52A LEU* 2.8 17.3 + - + +
54A GLU* 1.3 85.6 - - + +
56A LEU* 1.3 64.1 + - + +
57A GLY 3.4 0.2 - - - -
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Residues in contact with LEU 56 (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* 5.5 8.1 - - - -
25A LEU* 3.9 26.5 - - + -
52A LEU* 3.1 34.2 + - + +
53A ILE* 4.6 1.8 - - - +
55A ILE* 1.3 78.8 - - + +
57A GLY* 1.3 57.6 + - - +
59A GLU* 4.2 6.9 - - - +
60A THR* 3.5 26.0 + - + +
65A LEU* 4.1 10.3 - - + -
68A HIS* 3.5 39.9 - - + +
205M C 4.5 7.9 - - - +
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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