Contacts of the helix formed by residues 32 - 47 (chain A) in PDB entry 2LXW
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 ILE 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.7 26.0 - - + +
29A PRO* 3.7 27.4 - - + -
30A LEU 3.5 0.6 - - - +
31A PRO* 1.3 81.6 - - + +
33A LEU* 1.3 64.5 + - - +
34A ASN 3.2 2.0 - - - -
35A GLN* 3.1 27.7 + - + +
36A HIS* 3.5 6.8 + - - +
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Residues in contact with LEU 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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19A ARG* 3.8 41.5 - - + +
20A ARG 6.2 1.3 - - - -
21A CYS* 6.4 0.9 - - + -
28A LEU* 3.8 37.8 - - + +
29A PRO 5.0 1.1 - - - +
30A LEU* 3.4 27.5 + - + +
31A PRO 3.3 0.6 - - - -
32A ILE* 1.3 76.9 - - - +
34A ASN* 1.3 56.9 + - - +
36A HIS* 3.1 10.1 + - + +
37A GLN* 2.8 52.7 + - + +
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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 LEU* 4.0 6.0 + - - +
31A PRO* 3.2 29.3 + - - +
32A ILE 3.2 0.2 - - - -
33A LEU* 1.3 77.3 - - - +
35A GLN* 1.3 61.4 + - - +
37A GLN* 3.4 8.8 + - - +
38A GLU* 3.1 31.8 + - + +
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Residues in contact with GLN 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 PRO 4.5 0.6 + - - -
32A ILE* 3.1 23.3 + - + +
34A ASN* 1.3 74.8 - - - +
36A HIS* 1.3 64.5 + - - +
38A GLU* 3.6 5.5 + - - +
39A LYS* 3.2 26.4 + - + +
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Residues in contact with HIS 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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21A CYS* 3.2 12.5 - - + -
24A CYS* 3.3 21.1 - - + -
26A ILE* 3.5 21.7 - - + +
28A LEU* 4.0 23.7 - - + +
32A ILE 3.5 2.4 + - - -
33A LEU* 3.1 16.8 + - + +
35A GLN* 1.3 78.4 - - - +
37A GLN* 1.3 60.2 + - - +
39A LYS* 3.2 16.3 + - - +
40A CYS* 2.8 41.7 + - + +
101A ZN 2.0 38.1 - - - -
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Residues in contact with GLN 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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19A ARG* 5.4 3.8 - - - +
33A LEU* 2.8 51.0 + - + +
34A ASN* 3.6 9.4 - - - +
36A HIS* 1.3 75.5 - - - +
38A GLU* 1.3 59.8 + - + +
40A CYS* 4.7 2.7 - - - -
41A ARG* 3.0 35.5 + - - +
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Residues in contact with GLU 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* 3.1 18.7 + - + +
35A GLN* 4.0 5.6 - - - +
36A HIS 3.3 0.2 - - - -
37A GLN* 1.3 77.8 - - + +
39A LYS* 1.3 56.1 + - - +
41A ARG* 3.3 31.5 + - - +
42A TRP* 3.0 29.5 + - - +
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Residues in contact with LYS 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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24A CYS* 5.2 6.3 - - - -
35A GLN* 3.2 21.7 + - + +
36A HIS* 4.0 19.4 - - - +
38A GLU* 1.3 72.4 - - - +
40A CYS* 1.3 60.9 + - - +
42A TRP* 3.2 8.2 + - + +
43A LEU* 3.0 53.3 + - + +
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Residues in contact with CYS 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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21A CYS* 3.3 7.0 - - - -
23A GLN* 5.3 7.2 - - - -
24A CYS* 3.3 7.4 - - - -
36A HIS* 2.8 30.2 + - + +
37A GLN* 4.3 2.5 - - - +
39A LYS* 1.3 73.3 - - - +
41A ARG* 1.3 57.3 + - - +
43A LEU* 3.5 7.1 + - - +
44A ALA* 2.9 32.4 + - - +
101A ZN 2.0 40.4 - - - -
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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 GLN* 3.0 25.3 + - - +
38A GLU* 3.3 41.4 + - - +
40A CYS* 1.3 73.5 - - - +
42A TRP* 1.3 60.4 + - - +
44A ALA* 3.3 5.8 + - - +
45A SER* 2.9 35.6 + - - -
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Residues in contact with TRP 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 GLU 3.0 18.7 + - - +
39A LYS* 3.2 7.6 + - - +
41A ARG* 1.3 75.2 - - - +
43A LEU* 1.3 68.5 + - + +
45A SER* 3.5 5.1 + - - -
46A SER* 2.9 55.6 + - - -
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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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24A CYS* 6.4 1.3 - - - -
39A LYS* 3.0 50.9 + - + +
40A CYS* 3.8 7.2 - - - +
42A TRP* 1.3 86.3 - - + +
44A ALA* 1.3 56.5 + - - +
46A SER* 3.2 6.7 + - - -
47A LYS* 2.9 35.1 + - + +
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Residues in contact with ALA 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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23A GLN* 5.2 11.7 - - - +
40A CYS* 2.9 23.3 + - - +
41A ARG* 3.8 4.7 - - - +
43A LEU* 1.3 72.5 - - - +
45A SER* 1.3 61.6 + - - +
47A LYS* 3.7 20.7 + - - +
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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 ARG* 2.9 22.1 + - - -
42A TRP* 3.7 6.3 - - - -
44A ALA* 1.3 75.6 - - - +
46A SER* 1.3 60.2 + - - +
47A LYS 3.5 0.5 + - - -
48A GLY* 4.2 8.0 + - - -
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TRP* 2.9 48.3 + - - -
43A LEU* 3.6 7.0 - - - -
45A SER* 1.3 74.2 - - - +
47A LYS* 1.3 50.0 + - - +
48A GLY* 2.9 15.4 + - - +
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Residues in contact with LYS 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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23A GLN* 5.8 3.8 - - - +
43A LEU* 2.9 18.2 + - + +
44A ALA* 3.9 17.3 - - - +
45A SER 3.4 0.8 - - - -
46A SER* 1.3 70.8 - - - +
48A GLY* 1.3 55.8 + - - +
49A LYS* 3.9 11.2 + - + +
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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