Contacts of the helix formed by residues 37 - 50 (chain D) in PDB entry 1F80
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 37 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 4.5 9.9 - - + +
11B GLU 5.7 0.9 - - - +
14B ARG* 3.5 38.1 - - + +
15B ILE* 4.1 12.1 - - + -
18B MET* 3.1 41.5 - - + +
25B PHE* 3.7 25.1 - - + -
54B PHE* 3.7 31.0 - - + -
35D ASP* 3.4 2.8 + - - -
36D PN2 1.3 77.7 + - - -
38D ASP* 1.3 60.0 + - - +
40D VAL* 4.2 3.4 - - + +
41D GLU* 3.2 22.5 + - - +
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Residues in contact with ASP 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.0 15.0 + - - -
14D ARG* 4.8 16.1 + - - +
15D LEU* 3.6 29.7 - - + +
33D GLY 4.1 5.4 - - - +
34D ALA* 4.1 4.2 - - + -
35D ASP* 2.7 41.5 + - - +
37D LEU* 1.3 78.0 - - - +
39D VAL* 1.3 57.4 + - - +
41D GLU* 3.4 5.6 + - - +
42D LEU* 3.0 27.8 + - - +
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Residues in contact with VAL 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D PHE* 5.4 0.7 - - + -
29D LYS* 4.4 10.5 - - + -
34D ALA* 4.9 6.3 - - + +
35D ASP 3.1 18.8 + - - +
36D PN2 3.2 96.2 - - + +
38D ASP* 1.3 73.3 - - - +
40D VAL* 1.3 60.8 + - - +
42D LEU* 3.2 9.1 - - + +
43D VAL* 2.8 28.8 + - + +
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 5.3 0.7 - - - -
25B PHE* 3.8 33.2 - - + -
28B ARG* 4.6 19.1 - - - +
29B ILE* 5.1 0.7 - - + -
54B PHE* 5.2 2.9 - - + -
74B PHE* 4.7 11.4 - - + -
36D PN2 3.0 48.5 + - + +
37D LEU* 3.6 11.2 + - + +
39D VAL* 1.3 77.0 - - - +
41D GLU* 1.3 68.7 + - - +
43D VAL* 3.3 7.8 + - - +
44D MET* 2.9 33.3 + - + +
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Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 3.1 21.3 - - - +
21B ARG* 2.7 50.5 + - - +
22B GLN* 4.8 14.0 + - + +
14D ARG* 3.0 37.2 + - - +
37D LEU 3.2 14.0 + - - +
38D ASP* 3.8 5.2 - - - +
39D VAL 3.1 0.4 - - - -
40D VAL* 1.3 84.9 - - - +
42D LEU* 1.3 50.3 - - - +
44D MET* 2.8 26.7 + - + +
45D GLU* 2.9 23.8 + - - +
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ILE* 3.8 32.8 - - + +
11D ILE* 4.2 11.2 - - + -
14D ARG* 4.0 11.6 - - + +
15D LEU* 3.8 34.8 - - + -
28D PHE* 4.0 25.8 - - + -
34D ALA* 5.3 0.2 - - + -
36D PN2 3.8 16.2 - - - -
38D ASP 3.0 11.5 + - - +
39D VAL* 3.2 14.4 - - - +
41D GLU* 1.3 76.2 - - - +
43D VAL* 1.3 62.6 + - - +
45D GLU* 3.2 6.9 + - - +
46D LEU* 3.1 32.2 + - + +
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 4.0 26.2 - - - +
36D PN2 4.2 12.1 - - + -
39D VAL* 2.8 31.8 + - + +
40D VAL* 3.5 11.7 - - - +
41D GLU 3.2 0.2 - - - -
42D LEU* 1.3 76.7 - - - +
44D MET* 1.3 57.3 + - - +
46D LEU* 3.3 11.2 + - - +
47D GLU* 2.9 27.7 + - + +
54D ILE* 3.9 28.7 - - + +
59D ALA* 4.1 20.0 - - + -
62D ILE* 4.8 4.5 - - + -
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Residues in contact with MET 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLN* 3.6 36.6 - - + +
24B ARG* 3.5 32.1 - - + +
25B PHE* 3.7 24.7 - - - -
28B ARG* 3.6 31.4 - - + +
40D VAL* 2.9 19.3 - - + +
41D GLU* 2.8 9.9 + - - +
43D VAL* 1.3 74.0 - - + +
45D GLU* 1.3 68.1 + - - +
47D GLU* 3.5 24.8 + - - +
48D ASP* 3.2 27.6 + - - +
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG* 6.0 1.0 - - - +
22B GLN* 4.0 14.8 + - - +
10D ILE* 3.3 34.3 - - + +
13D ASP* 6.3 1.6 - - + -
14D ARG* 2.6 46.2 + - - +
41D GLU* 2.9 13.5 + - - +
42D LEU* 3.2 10.5 + - - +
44D MET* 1.3 75.6 - - - +
46D LEU* 1.3 51.3 + - - +
48D ASP* 3.1 7.3 + - - +
49D GLU* 2.7 37.8 + - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D VAL* 4.0 20.0 - - + -
10D ILE* 4.1 18.2 - - + -
28D PHE* 5.7 1.3 - - + -
36D PN2 4.6 13.5 - - - -
42D LEU* 3.1 21.9 + - + +
43D VAL* 3.5 9.4 - - - +
45D GLU* 1.3 75.3 - - - +
47D GLU* 1.3 62.8 + - - +
49D GLU* 4.4 0.9 - - - -
50D PHE* 3.1 57.4 + - + +
52D MET* 4.1 3.3 - - - +
54D ILE* 4.4 11.0 - - + -
62D ILE* 4.6 9.2 - - + -
68D ALA* 4.5 19.3 - - + -
72D ILE* 4.2 6.3 - - + -
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 2.5 38.7 + - - +
28B ARG* 3.5 26.3 + - - -
43D VAL* 2.9 21.8 + - - +
44D MET* 3.8 15.9 - - - +
45D GLU 3.4 0.2 - - - -
46D LEU* 1.3 71.6 - - - +
48D ASP* 1.3 58.2 + - - +
51D ASP* 3.2 9.0 + - - -
52D MET* 3.0 44.7 + - - +
53D GLU* 3.7 10.4 - - - +
54D ILE* 3.1 34.6 + - + +
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Residues in contact with ASP 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLN* 2.7 29.5 + - - +
24B ARG* 2.9 24.4 + - - -
44D MET 3.2 9.1 + - - +
45D GLU* 3.1 9.7 + - - +
47D GLU* 1.3 76.6 - - - +
49D GLU* 1.3 57.5 + - - +
50D PHE 3.0 10.2 + - - -
51D ASP* 3.3 10.3 + - - +
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Residues in contact with GLU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ARG* 2.6 47.0 + - + -
10D ILE* 3.4 29.4 - - + +
45D GLU* 2.7 20.0 + - + +
46D LEU 3.2 3.6 + - - +
48D ASP* 1.3 71.8 - - - +
50D PHE* 1.3 73.7 + - + +
51D ASP 3.7 0.2 - - - -
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D THR* 4.0 15.0 - - - -
6D ARG* 3.2 57.9 - - + +
7D VAL* 4.1 2.0 - - + -
10D ILE* 4.8 0.4 - - + -
46D LEU* 3.1 37.7 + - + +
49D GLU* 1.3 92.1 - - + +
51D ASP* 1.3 75.0 + - - +
52D MET* 3.1 29.6 + - + +
72D ILE* 3.3 47.1 - - + -
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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