Contacts of the helix formed by residues 34 - 48 (chain A) in PDB entry 1HMF
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG* 5.7 6.5 - - - +
32A LEU 4.0 1.0 + - - -
33A SER* 1.3 75.2 - - - +
35A GLY* 1.3 61.8 + - - +
37A VAL* 3.8 8.6 - - + +
38A ALA* 3.2 27.0 + - + +
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Residues in contact with GLY 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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33A SER* 2.7 9.9 + - - -
34A ILE* 1.3 78.9 - - - +
36A ASP* 1.3 49.6 + - - -
38A ALA* 5.0 0.2 - - - -
39A LYS* 2.7 54.4 + - - +
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Residues in contact with ASP 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* 3.2 20.3 - - + +
33A SER* 2.7 29.0 + - - +
35A GLY* 1.3 69.3 - - - +
37A VAL* 1.3 60.5 + - - +
39A LYS* 4.2 5.4 - - - -
40A LYS* 2.7 78.2 + - - +
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Residues in contact with VAL 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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18A CYS* 4.4 1.1 - - - -
22A ARG* 3.6 40.2 - - + +
25A ILE* 5.1 1.8 - - + -
26A LYS* 4.7 7.9 - - + -
32A LEU* 3.3 41.3 - - + +
33A SER 2.9 16.9 + - - +
34A ILE* 3.8 8.3 - - + +
36A ASP* 1.3 81.6 - - - +
38A ALA* 1.3 64.5 + - + +
40A LYS* 3.8 1.5 - - - +
41A LEU* 3.0 40.9 + - + +
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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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14A PHE* 3.6 22.7 - - + -
34A ILE* 3.2 18.2 + - + +
35A GLY* 4.0 1.6 - - - +
37A VAL* 1.3 82.7 - - + +
39A LYS* 1.3 59.2 + - + +
41A LEU* 4.3 2.9 - - - -
42A GLY* 2.7 30.5 + - - -
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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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35A GLY* 2.7 44.4 + - - +
36A ASP* 3.8 5.4 - - - +
38A ALA* 1.3 77.1 - - + +
40A LYS* 1.3 56.6 + - + +
42A GLY* 2.7 3.8 + - - +
43A GLU* 2.6 43.1 + - + +
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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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25A ILE* 3.9 34.0 - - + +
29A HIS* 4.7 16.2 + - - -
32A LEU* 4.7 6.0 - - + +
36A ASP* 2.7 54.3 + - - +
37A VAL* 3.8 2.7 - - - +
39A LYS* 1.3 75.2 - - + +
41A LEU* 1.3 57.9 + - - +
43A GLU* 3.1 11.0 + - + +
44A MET* 2.9 39.4 + - + +
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Residues in contact with LEU 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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14A PHE* 3.3 18.4 - - + -
17A PHE* 3.8 10.1 - - + -
18A CYS* 3.1 40.8 - - + +
21A TYR* 3.2 47.3 - - + +
22A ARG* 4.7 1.3 - - + -
25A ILE* 3.7 9.2 - - + -
37A VAL* 3.0 30.2 + - + +
38A ALA* 4.3 3.1 - - - -
39A LYS 3.0 0.4 - - - -
40A LYS* 1.3 74.6 - - - +
42A GLY* 1.3 63.0 + - - +
44A MET* 4.1 4.0 - - + -
45A TRP* 2.8 33.4 + - - +
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Residues in contact with GLY 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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14A PHE* 3.4 13.2 - - - -
38A ALA 2.7 18.1 + - - -
39A LYS* 2.7 6.0 + - - -
41A LEU* 1.3 77.8 - - - +
43A GLU* 1.3 57.8 + - - +
45A TRP* 4.3 1.1 - - - -
46A ASN* 2.8 38.9 + - - +
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Residues in contact with GLU 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 LYS* 2.6 22.1 + - + +
40A LYS* 3.3 15.7 - - + +
41A LEU 3.0 0.2 - - - -
42A GLY* 1.3 73.5 - - - +
44A MET* 1.3 63.0 + - + +
46A ASN* 3.3 7.9 + - - +
47A ASN* 2.5 46.2 + - - +
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Residues in contact with MET 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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17A PHE* 3.9 13.2 - - + -
21A TYR* 4.0 24.0 - - + -
25A ILE* 3.8 34.1 - - + -
40A LYS* 2.9 37.1 + - + +
41A LEU* 4.0 9.2 - - + +
43A GLU* 1.3 77.0 - - + +
45A TRP* 1.3 52.7 + - - +
47A ASN* 2.8 12.2 + - - +
48A THR* 2.5 39.6 + - - +
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Residues in contact with TRP 45 (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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13A ALA* 4.0 10.8 - - + -
14A PHE* 3.4 44.1 - + + +
17A PHE* 3.4 47.5 - + + -
41A LEU 2.8 23.8 + - - +
42A GLY* 4.0 1.6 - - - +
44A MET* 1.3 72.3 - - - +
46A ASN* 1.3 78.7 + - - +
48A THR* 2.7 24.3 + - + -
53A LYS* 3.2 49.3 - - + +
56A TYR* 3.9 30.5 - + + -
57A GLU* 5.6 0.9 - - + -
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Residues in contact with ASN 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 GLY* 2.8 26.0 + - - +
43A GLU* 3.4 11.2 - - - +
45A TRP* 1.3 94.6 - - - +
47A ASN* 1.3 64.4 + - - +
48A THR 4.1 0.2 - - - +
53A LYS* 4.1 10.7 + - - +
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Residues in contact with ASN 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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43A GLU* 2.5 40.5 + - - +
44A MET* 2.8 13.4 + - - +
46A ASN* 1.3 81.6 - - - +
48A THR* 1.3 65.4 + - - +
49A ALA* 3.0 4.5 + - - -
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Residues in contact with THR 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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17A PHE* 3.7 18.5 - - + -
21A TYR* 5.7 0.7 + - - -
44A MET* 2.5 21.9 + - - +
45A TRP* 2.7 23.7 + - + -
46A ASN 4.1 0.5 - - - +
47A ASN* 1.3 69.5 - - - +
49A ALA* 1.3 70.9 + - - +
50A ALA 3.4 0.2 + - - -
52A ASP* 3.1 40.2 - - + +
53A LYS* 2.7 36.9 + - + -
56A TYR* 5.6 1.6 - - + -
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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