Contacts of the helix formed by residues 23 - 37 (chain D) in PDB entry 1A9N
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 LYS 23 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D ILE 3.5 2.9 + - - -
22D LYS* 1.3 71.3 - - - +
24D GLU* 1.3 71.9 + - + +
26D LEU* 3.2 9.3 + - + +
27D LYS* 3.0 38.7 + - + +
45D ALA* 3.2 30.5 - - + +
46D LEU* 4.4 5.2 - - - -
47D LYS* 4.0 16.5 - - + +
13R U 2.7 26.9 + - - +
15R C 3.1 33.5 + - - -
16R C 3.2 37.7 + - - +
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Residues in contact with GLU 24 (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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19C VAL* 5.7 0.3 - - - +
22D LYS* 3.3 4.2 - - + +
23D LYS* 1.3 93.5 - - + +
25D GLU* 1.3 59.4 + - - +
27D LYS* 4.2 18.5 - - - +
28D ARG* 3.2 23.4 + - - +
15R C 5.0 4.5 + - - -
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Residues in contact with GLU 25 (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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117C TYR* 3.4 31.1 + - + +
144C VAL* 3.2 17.1 - - - +
149C LYS* 5.9 0.5 - - - +
21D ILE* 3.7 13.5 - - + +
22D LYS* 3.1 43.6 + - + +
24D GLU* 1.3 74.5 - - - +
26D LEU* 1.3 61.7 + - - +
28D ARG* 3.8 5.3 - - + +
29D SER* 2.8 35.9 + - - -
78D TYR* 2.8 29.8 + - - +
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Residues in contact with LEU 26 (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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17D MET* 4.1 31.6 - - + -
18D ASN 5.1 7.2 - - - +
19D ASP* 6.4 0.9 - - - -
21D ILE* 3.9 22.6 - - + +
22D LYS 2.9 12.4 + - - +
23D LYS* 3.2 13.4 + - + +
25D GLU* 1.3 79.3 - - - +
27D LYS* 1.3 57.0 - - - +
29D SER* 3.8 2.9 - - - -
30D LEU* 2.9 40.6 + - + +
45D ALA* 4.5 19.7 - - + -
47D LYS* 5.6 5.8 - - + -
53D GLY* 6.2 1.8 - - - +
54D GLN 4.7 2.7 - - - +
77D PHE* 3.6 29.8 - - + -
78D TYR* 5.3 2.7 - - + -
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Residues in contact with LYS 27 (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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18C ALA 5.0 8.8 + - - +
19C VAL* 4.0 9.6 - - + -
23D LYS* 3.0 25.2 + - + +
24D GLU* 4.2 19.3 - - - +
25D GLU 3.3 0.2 - - - -
26D LEU* 1.3 73.5 - - - +
28D ARG* 1.3 60.7 + - - +
30D LEU* 3.0 5.1 + - - -
31D TYR* 2.7 27.2 + - - +
42D ASP* 5.3 1.6 + - - -
43D ILE* 2.8 52.4 + - + +
45D ALA* 4.3 20.9 - - + +
13R U 2.6 37.4 + - - +
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Residues in contact with ARG 28 (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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19C VAL* 3.9 23.4 - - + +
21C ASP* 5.3 5.4 + - - -
67C LYS* 4.0 6.5 + - - +
68C THR* 3.1 19.5 + - - -
91C THR* 3.9 24.2 - - - +
92C GLU* 2.4 48.2 + - - +
117C TYR* 4.1 29.4 - - + -
24D GLU 3.2 16.4 + - - +
25D GLU* 3.8 5.2 - - - +
27D LYS* 1.3 78.2 - - - +
29D SER* 1.3 63.8 + - - +
31D TYR* 3.1 4.9 + - + +
32D ALA* 3.0 22.6 + - - +
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Residues in contact with SER 29 (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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117C TYR* 4.7 8.5 - - - -
144C VAL* 5.0 1.0 - - - +
147C PHE* 3.3 21.5 - - - -
25D GLU* 2.8 23.9 + - - +
26D LEU 3.9 0.9 - - - -
28D ARG* 1.3 73.9 - - - +
30D LEU* 1.3 57.3 + - - +
32D ALA* 3.4 2.5 + - - -
33D LEU* 2.9 26.2 + - - +
77D PHE* 3.8 10.8 - - - -
78D TYR* 2.6 41.3 + - - -
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Residues in contact with LEU 30 (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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14D ILE* 4.3 2.0 - - + -
17D MET* 4.0 6.7 - - - -
26D LEU* 2.9 38.2 + - + +
27D LYS* 3.3 4.7 - - - +
29D SER* 1.3 72.3 - - - +
31D TYR* 1.3 68.4 + - - +
33D LEU* 3.4 1.1 + - - -
34D PHE* 3.0 55.5 + - + +
43D ILE* 4.0 20.6 - - + -
45D ALA* 5.4 0.4 - - + -
55D ALA* 3.7 29.2 - - + -
57D VAL* 4.7 4.9 - - + -
77D PHE* 3.4 29.8 - - + -
82D MET* 3.9 9.0 - - + -
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Residues in contact with TYR 31 (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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17C ASN* 3.1 26.5 - - + +
18C ALA* 3.9 20.9 - - + -
19C VAL* 4.0 18.4 - - + -
23C GLU* 2.4 38.2 + - - -
46C ALA* 6.1 0.4 - - + -
68C THR* 5.8 5.4 - - + -
70C LEU* 4.2 19.9 - - + +
92C GLU* 5.5 2.7 - - - -
27D LYS 2.7 11.7 + - - +
28D ARG* 3.4 9.0 - - + +
30D LEU* 1.3 78.2 - - - +
32D ALA* 1.3 58.7 + - + +
34D PHE* 3.7 2.4 - - - +
35D SER* 3.0 34.8 + - - -
39D HIS* 4.0 5.6 + - - -
40D VAL* 3.7 42.1 - - + +
43D ILE* 3.6 9.5 - - + +
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Residues in contact with ALA 32 (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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70C LEU* 4.4 6.1 - - + -
72C ASN* 4.6 1.7 + - - +
92C GLU* 3.0 27.8 - - - +
94C ILE* 3.6 34.0 - - + +
147C PHE* 4.1 6.5 - - + -
28D ARG 3.0 11.0 + - - +
29D SER* 3.8 4.9 - - - +
30D LEU 3.3 0.2 - - - -
31D TYR* 1.3 77.0 - - - +
33D LEU* 1.3 61.2 + - - +
35D SER* 2.8 22.4 + - - -
36D GLN 4.3 1.2 + - - -
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Residues in contact with LEU 33 (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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121C LEU* 5.7 0.7 - - + -
147C PHE* 3.5 25.2 - - + -
29D SER 2.9 20.3 + - - +
30D LEU 3.9 2.5 - - - +
32D ALA* 1.3 74.4 - - - +
34D PHE* 1.3 78.8 + - + +
35D SER 3.5 0.5 + - - -
36D GLN* 2.8 39.9 + - - +
37D PHE* 4.4 0.7 - - - -
72D LEU* 3.5 29.8 - - + -
75D PHE* 3.7 28.9 - - + -
77D PHE* 4.3 11.4 - - + -
82D MET* 4.0 22.0 - - + -
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Residues in contact with PHE 34 (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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12D ILE* 4.0 13.9 - - + -
14D ILE* 3.4 33.0 - - + -
30D LEU* 3.0 39.8 + - + +
31D TYR 3.7 0.7 - - - -
33D LEU* 1.3 90.1 - - + +
35D SER* 1.3 62.8 + - - +
36D GLN 3.2 3.4 + - - -
37D PHE* 3.4 13.8 + + - -
38D GLY 3.8 1.7 - - - +
40D VAL* 4.1 11.4 - - + -
57D VAL* 4.2 13.9 - - + -
59D PHE* 3.7 29.4 - + + -
68D ALA* 4.0 21.5 - - + -
72D LEU* 3.4 26.9 - - + -
82D MET* 4.3 5.4 - - + -
84D ILE* 4.3 9.2 - - + -
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Residues in contact with SER 35 (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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27C ARG* 2.4 33.5 + - - -
70C LEU* 3.5 28.8 - - - +
72C ASN* 3.3 14.2 + - - -
31D TYR* 3.0 19.6 + - - -
32D ALA* 2.8 21.8 + - - -
33D LEU 3.3 0.2 - - - -
34D PHE* 1.3 78.4 - - - +
36D GLN* 1.3 59.8 + - - +
37D PHE 3.1 1.6 + - - -
38D GLY 3.3 8.5 - - - +
40D VAL* 4.8 4.3 - - - -
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Residues in contact with GLN 36 (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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27C ARG* 4.4 5.8 + - - +
51C ASP* 4.7 2.4 - - - +
72C ASN* 3.5 31.8 + - + +
73C ASN* 3.6 23.2 + - - +
96C THR* 4.0 23.2 + - + +
122C ARG* 4.4 14.6 + - - -
147C PHE* 6.0 0.4 - - - -
33D LEU* 2.8 39.3 + - - +
35D SER* 1.3 80.1 + - - +
37D PHE* 1.3 90.9 + - + +
72D LEU* 4.5 4.4 - - - +
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Residues in contact with PHE 37 (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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27C ARG* 4.6 1.8 - - - -
34D PHE* 3.4 15.5 + + - +
35D SER 3.1 0.8 - - - -
36D GLN* 1.3 105.1 - - + +
38D GLY* 1.3 58.5 + - - +
59D PHE* 4.5 5.2 - - + -
64D SER* 3.0 31.8 + - - +
67D ASN* 4.0 12.0 - - + +
68D ALA* 4.0 24.5 - - + -
71D GLN* 3.5 44.2 - - + -
72D LEU* 3.4 33.2 - - + -
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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