Contacts of the helix formed by residues 32 - 52 (chain A) in PDB entry 1HDL
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 LEU 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A SER* 1.3 70.5 - - - +
33A ASP* 1.3 71.8 + - - +
35A ILE* 3.0 11.6 + - + +
36A MET* 2.7 47.3 + - + +
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Residues in contact with ASP 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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31A SER* 3.4 4.9 - - - -
32A LEU* 1.3 85.4 - - - +
34A GLY* 1.3 57.3 + - - +
36A MET* 3.4 6.2 - - - +
37A PHE* 2.8 32.9 + - - +
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Residues in contact with GLY 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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28A PHE* 3.2 39.9 + - - +
31A SER* 3.3 6.1 + - - -
32A LEU 3.1 0.6 - - - -
33A ASP* 1.3 77.6 - - - +
35A ILE* 1.3 65.7 + - - +
37A PHE* 3.7 4.5 - - - -
38A ILE* 2.8 33.2 + - - +
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Residues in contact with ILE 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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28A PHE 3.8 0.8 + - - -
29A PHE* 3.0 70.4 - - + +
31A SER 2.7 19.9 + - - +
32A LEU* 3.0 12.3 + - + +
34A GLY* 1.3 72.1 - - - +
36A MET* 1.3 57.4 + - + +
38A ILE* 3.8 4.2 - - - +
39A ASN* 2.4 51.4 + - - +
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Residues in contact with MET 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 LEU* 2.7 39.1 + - + +
33A ASP* 3.4 7.0 - - - +
35A ILE* 1.3 74.0 - - + +
37A PHE* 1.3 70.0 + - - +
39A ASN* 2.6 28.6 + - - +
40A LYS* 2.9 11.7 + - - +
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Residues in contact with PHE 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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10A GLU* 4.6 14.8 - - + +
11A PHE* 2.8 51.7 - + + -
14A PHE* 4.3 16.6 - + - -
22A CYS 5.3 5.6 - - - -
24A GLN* 5.8 2.5 - - + -
25A ASP 4.3 5.8 - - - -
26A LYS* 4.2 9.9 - - + -
28A PHE* 3.4 34.8 - + + -
33A ASP 2.8 16.6 + - - +
34A GLY* 3.0 18.4 - - - -
36A MET* 1.3 72.0 - - - +
38A ILE* 1.3 86.5 + - + +
40A LYS* 2.7 7.0 + - - -
41A CYS* 2.5 36.8 + - + -
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Residues in contact with ILE 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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26A LYS* 2.9 53.7 - - + +
29A PHE* 3.2 42.4 - - + +
34A GLY 2.8 14.1 + - - +
35A ILE 3.8 2.7 - - - +
37A PHE* 1.3 106.9 - - + +
39A ASN* 1.3 67.9 + - - +
41A CYS* 3.1 22.2 + - - +
42A ALA* 3.6 8.5 + - - +
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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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29A PHE* 5.7 1.9 - - - -
35A ILE* 2.4 41.7 + - - +
36A MET* 2.6 29.0 + - - +
38A ILE* 1.3 78.7 - - - +
40A LYS* 1.3 55.7 + - - -
41A CYS 3.5 0.2 + - - -
42A ALA* 4.3 2.6 + - - +
43A THR* 3.0 22.7 + - - -
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Residues in contact with LYS 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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3A GLU* 6.0 1.6 - - - -
7A MET* 2.8 31.7 + - - -
8A CYS* 4.1 7.2 - - - +
9A HIS* 3.5 26.6 - - - +
10A GLU* 4.7 3.8 - - + +
11A PHE* 3.7 19.3 - - + -
36A MET 2.9 7.9 + - - +
37A PHE* 2.7 14.0 + - - +
39A ASN* 1.3 73.2 - - - +
41A CYS* 1.3 56.1 + - - +
43A THR* 4.0 9.0 - - + -
44A CYS* 2.5 45.1 + - + +
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Residues in contact with CYS 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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11A PHE* 3.0 24.5 - - + -
22A CYS* 2.0 61.3 - - - -
26A LYS* 4.0 18.8 - - - -
37A PHE* 2.5 11.7 + - + +
38A ILE* 3.1 18.6 + - - +
40A LYS* 1.3 69.5 - - - +
42A ALA* 1.3 72.7 + - - +
43A THR 2.7 2.4 + - - -
44A CYS* 2.9 1.4 + - - +
45A LYS* 2.9 19.8 + - - +
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Residues in contact with ALA 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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22A CYS* 5.4 0.2 - - - -
26A LYS* 5.6 6.7 - - - +
38A ILE 3.6 7.8 + - - +
39A ASN* 4.7 3.6 - - - +
41A CYS* 1.3 84.5 - - - +
43A THR* 1.3 62.2 + - - +
45A LYS* 3.5 22.5 - - - +
46A MET* 3.7 7.4 + - - +
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Residues in contact with THR 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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7A MET* 5.6 7.4 - - + -
39A ASN 3.0 19.2 + - - -
40A LYS* 3.6 10.3 - - + -
41A CYS 2.7 1.0 + - - -
42A ALA* 1.3 77.3 - - - +
44A CYS* 1.3 63.8 + - - +
45A LYS 2.9 4.3 - - - -
46A MET* 2.6 42.7 - - + +
47A ILE* 3.1 11.4 - - + +
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Residues in contact with CYS 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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7A MET 6.0 0.2 - - - -
8A CYS* 2.0 52.0 - - - -
11A PHE* 3.1 33.2 - - + -
20A LEU* 3.7 10.5 - - - -
40A LYS* 2.5 31.5 + - + +
41A CYS 3.6 2.7 - - - +
43A THR* 1.3 74.6 - - - +
45A LYS* 1.3 57.1 + - - +
47A ILE* 3.1 10.2 - - - +
48A LEU* 2.7 28.6 - - - +
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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
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20A LEU* 3.4 25.7 - - + +
22A CYS* 4.5 13.5 - - + -
23A PRO* 6.0 6.3 - - + -
41A CYS 2.9 10.7 + - - +
42A ALA* 3.5 17.9 - - - +
43A THR 2.8 1.4 + - - -
44A CYS* 1.3 78.2 - - - +
46A MET* 1.3 63.1 + - + +
47A ILE 3.1 0.9 + - - -
48A LEU* 3.1 15.2 + - - +
49A GLU* 3.5 31.2 + - + +
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Residues in contact with MET 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 3.7 4.4 + - - +
43A THR* 2.6 40.2 + - - +
45A LYS* 1.3 81.5 - - + +
47A ILE* 1.3 78.2 + - + +
49A GLU* 3.2 30.9 + - - +
50A LYS* 3.2 54.4 + - + +
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Residues in contact with ILE 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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7A MET* 4.1 37.9 - - + +
8A CYS* 3.9 14.6 - - + +
43A THR* 3.1 23.1 - - + +
44A CYS* 3.1 22.2 - - - +
46A MET* 1.3 96.5 - - + +
48A LEU* 1.3 65.0 + - + +
50A LYS* 3.3 17.7 - - - +
51A GLU* 4.0 8.2 - - - +
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Residues in contact with LEU 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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8A CYS* 4.0 11.0 - - + -
15A MET* 6.0 7.9 - - + -
18A GLY* 5.3 11.2 - - - +
20A LEU* 3.3 30.3 - - + -
44A CYS 2.7 24.0 - - - +
45A LYS 3.1 6.7 + - - +
47A ILE* 1.3 80.3 - - + +
49A GLU* 1.3 67.1 + - + +
50A LYS 3.0 2.2 - - - -
51A GLU* 2.9 45.4 + - - +
52A ALA* 3.7 2.9 + - - +
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Residues in contact with GLU 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 LYS* 3.5 40.2 + - + +
46A MET* 3.4 23.4 - - - +
48A LEU* 1.3 77.3 - - + +
50A LYS* 1.3 66.3 + - + +
52A ALA* 3.2 23.3 + - - +
53A LYS* 3.8 12.3 + - - +
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Residues in contact with LYS 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 MET* 3.2 45.1 + - + +
47A ILE* 3.3 12.1 - - + +
48A LEU 2.9 0.2 + - - -
49A GLU* 1.3 83.3 + - - +
51A GLU* 1.3 63.4 + - + +
53A LYS* 3.1 47.3 + - + +
54A SER* 3.6 8.0 + - - -
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Residues in contact with GLU 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 ILE* 4.0 8.7 - - - +
48A LEU* 2.9 43.4 + - - +
50A LYS* 1.3 77.9 - - + +
52A ALA* 1.3 61.4 + - - +
54A SER* 3.3 22.9 + - - -
55A GLN* 3.7 12.8 + - - +
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Residues in contact with ALA 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 LEU 3.7 1.6 + - - +
49A GLU* 3.2 19.5 + - - +
50A LYS 3.1 0.4 - - - -
51A GLU* 1.3 79.7 - - - +
53A LYS* 1.3 61.9 + - + +
54A SER 3.3 0.2 - - - -
55A GLN 3.2 22.2 - - - +
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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
------------------------------------------------------------
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