Contacts of the helix formed by residues 13 - 29 (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 ALA 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A SER* 1.3 69.2 - - - +
14A PHE* 1.3 59.0 + - - +
15A PHE 2.7 14.3 + - - -
16A LEU* 2.9 29.5 + - - +
17A PHE* 3.5 2.8 + - - +
45A TRP* 4.0 21.1 - - + -
56A TYR* 4.5 4.0 - - + +
57A GLU* 5.2 15.7 - - + +
60A ALA* 5.4 3.4 - - - -
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Residues in contact with PHE 14 (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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12A SER* 4.5 7.8 - - - -
13A ALA* 1.3 79.2 - - + +
15A PHE* 1.3 71.4 + + + +
16A LEU 3.4 0.2 - - - -
17A PHE* 3.2 14.3 - + - +
18A CYS* 2.8 23.5 + - + +
38A ALA* 3.6 26.0 - - + -
41A LEU* 3.3 32.3 - - + -
42A GLY* 3.4 14.8 - - - -
45A TRP* 3.4 50.0 - + + +
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Residues in contact with PHE 15 (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 PRO* 3.3 31.0 - - + -
12A SER* 3.1 27.5 + - - +
13A ALA 2.7 3.8 + - - -
14A PHE* 1.3 83.7 - + + +
16A LEU* 1.3 61.6 + - + +
17A PHE 2.7 4.5 - - - -
18A CYS* 2.7 37.7 + - + +
19A SER* 3.2 15.7 + - - -
22A ARG* 4.6 20.2 - - - -
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Residues in contact with LEU 16 (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 PRO* 3.4 31.0 - - + +
12A SER 3.4 14.4 - - - +
13A ALA* 3.4 9.0 - - - +
15A PHE* 1.3 79.6 - - + +
17A PHE* 1.3 58.5 + - - +
19A SER* 4.4 6.4 + - - -
20A GLU* 4.1 10.6 + - - +
56A TYR* 3.5 43.6 - - + +
59A LYS* 4.7 15.7 - - + -
60A ALA* 4.0 22.7 - - + +
63A LEU* 5.7 6.5 - - + -
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Residues in contact with PHE 17 (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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13A ALA 4.1 0.4 - - - +
14A PHE* 3.2 13.7 - - - +
15A PHE 2.7 0.2 - - - -
16A LEU* 1.3 82.3 - - - +
18A CYS* 1.3 74.1 + - - +
20A GLU* 3.0 4.3 + - - +
21A TYR* 2.8 57.1 + + - -
41A LEU* 3.8 34.5 - - + -
44A MET* 3.9 9.0 - - + -
45A TRP* 3.4 52.5 - + + -
48A THR* 3.7 19.5 - - + -
56A TYR* 3.7 22.9 - + + -
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Residues in contact with CYS 18 (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* 2.8 17.4 + - + +
15A PHE* 2.7 30.1 + - + +
17A PHE* 1.3 69.5 - - - +
19A SER* 1.3 51.8 + - - +
20A GLU 2.6 8.1 + - - -
21A TYR 2.6 2.4 + - - -
22A ARG* 2.4 70.6 + - - -
37A VAL* 4.4 1.3 - - - -
41A LEU* 3.1 38.8 - - + -
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Residues in contact with SER 19 (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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15A PHE* 3.2 18.1 + - - -
16A LEU* 4.4 7.6 - - - -
18A CYS* 1.3 80.3 - - - +
20A GLU* 1.3 57.5 + - - +
22A ARG* 4.0 10.8 - - - +
23A PRO* 3.1 22.6 - - - +
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Residues in contact with GLU 20 (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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16A LEU 4.1 6.4 + - - +
17A PHE 3.0 11.1 + - - +
18A CYS 2.6 5.1 + - - -
19A SER* 1.3 77.4 - - - +
21A TYR* 1.3 82.9 + - + +
22A ARG 3.3 0.4 - - - -
23A PRO* 3.2 14.4 - - - +
24A LYS* 3.6 16.1 - - - +
56A TYR* 3.7 18.4 - - + +
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Residues in contact with TYR 21 (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* 2.8 44.9 + + + +
18A CYS 2.6 7.7 + - - -
20A GLU* 1.3 94.9 - - + +
22A ARG* 1.3 50.8 + - - -
23A PRO* 3.5 1.6 - - - -
24A LYS* 4.1 16.8 - - + -
25A ILE* 2.6 38.1 - - - +
41A LEU* 3.3 20.2 - - + -
44A MET* 4.0 24.5 - - + -
48A THR* 5.8 0.7 - - - -
52A ASP* 5.5 2.6 + - - -
56A TYR* 4.4 3.4 - - - -
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Residues in contact with ARG 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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15A PHE* 4.6 17.3 - - - -
18A CYS* 2.4 51.7 + - - +
19A SER* 4.0 6.5 - - - +
21A TYR* 1.3 73.2 - - - +
23A PRO* 1.3 67.7 - - + +
24A LYS 3.4 0.2 - - - -
25A ILE* 4.0 4.9 - - - +
26A LYS* 2.8 39.2 + - + +
34A ILE* 5.7 6.1 - - - +
37A VAL* 3.6 32.7 - - + +
41A LEU* 4.5 1.3 - - - -
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Residues in contact with PRO 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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19A SER 3.1 22.7 - - - +
20A GLU 3.2 11.9 - - - +
22A ARG* 1.3 94.5 - - + +
24A LYS* 1.3 65.6 + - + +
26A LYS* 4.3 2.7 - - + -
27A GLY* 2.5 34.0 + - - +
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Residues in contact with LYS 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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20A GLU* 3.6 28.5 - - - +
21A TYR* 4.1 20.2 - - + +
23A PRO* 1.3 85.9 - - + +
25A ILE* 1.3 65.5 + - + +
27A GLY* 3.7 0.5 - - - -
28A GLU* 3.2 22.9 + - - +
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Residues in contact with ILE 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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21A TYR 2.6 28.3 - - - +
22A ARG* 4.0 4.3 - - - +
24A LYS* 1.3 73.4 - - + +
26A LYS* 1.3 53.8 + - - +
27A GLY 2.8 5.2 + - - -
28A GLU* 2.8 5.7 + - - -
29A HIS* 2.7 47.0 + - + +
32A LEU* 4.3 12.8 - - + -
37A VAL* 4.5 4.0 - - + +
40A LYS* 3.9 32.1 - - + +
41A LEU* 3.7 21.8 - - + -
44A MET* 3.8 22.7 - - + -
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Residues in contact with LYS 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 ARG* 2.8 29.0 + - + +
23A PRO* 4.3 2.9 - - + -
25A ILE* 1.3 80.0 - - - +
27A GLY* 1.3 57.6 + - - +
29A HIS 2.7 36.0 - - - +
30A PRO* 2.9 12.3 - - + +
31A GLY* 3.2 18.3 - - - +
32A LEU* 3.5 41.1 - - + +
37A VAL* 4.7 6.5 - - + -
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Residues in contact with GLY 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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23A PRO* 2.5 28.8 + - - +
24A LYS 3.7 0.9 - - - -
25A ILE 2.8 1.2 + - - -
26A LYS* 1.3 76.5 - - - +
28A GLU* 1.3 59.1 + - - +
29A HIS 3.1 3.8 + - - -
30A PRO* 3.3 13.9 - - - +
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Residues in contact with GLU 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 LYS 3.2 11.7 + - - +
25A ILE* 2.8 8.1 + - - +
27A GLY* 1.3 75.7 - - - +
29A HIS* 1.3 75.4 + - + +
30A PRO* 3.4 6.6 - - - +
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Residues in contact with HIS 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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25A ILE* 2.7 24.1 + - + +
26A LYS* 2.7 18.7 - - - +
27A GLY 2.9 0.8 - - - -
28A GLU* 1.3 106.8 + - + +
30A PRO* 1.3 55.3 - - - +
31A GLY* 2.6 18.5 + - - -
32A LEU* 3.5 29.5 + - + +
40A LYS* 4.7 16.6 + - - -
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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