Contacts of the helix formed by residues 4 - 24 (chain D) in PDB entry 4O9U
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 4 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET* 4.1 10.1 - - + -
2D ASP* 3.2 26.4 + - - +
3D LEU* 1.3 77.8 - - + +
5D GLN* 1.3 64.1 + - - +
6D ALA 3.4 0.2 - - - -
7D ALA* 3.7 14.8 + - - +
8D TYR* 3.4 29.2 - - + +
45D ALA* 3.4 28.7 - - - +
48D PHE* 3.3 31.0 - - + +
49D TRP* 4.5 16.2 - - + -
50D PRO* 3.7 19.5 - - + -
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Residues in contact with GLN 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TRP* 3.4 47.8 - - + +
10A TYR* 4.8 3.2 + - - -
1C MET* 3.4 41.2 - - + +
2C GLU 5.0 1.4 + - - +
3C PHE* 3.5 21.6 - - - -
2D ASP* 3.7 11.6 + - + +
4D ILE* 1.3 76.4 - - - +
6D ALA* 1.3 62.3 + - - +
7D ALA 3.2 0.2 - - - -
8D TYR* 3.1 19.8 + - - +
9D PHE* 3.2 13.0 + - - +
228D PRO* 3.4 26.9 - - - +
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Residues in contact with ALA 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TRP* 3.6 28.5 - - + -
2D ASP 4.3 0.7 - - - +
3D LEU* 3.9 28.4 + - + +
4D ILE 3.4 0.6 - - - -
5D GLN* 1.3 75.6 - - - +
7D ALA* 1.3 63.7 + - - +
9D PHE* 3.6 3.6 + - - +
10D VAL* 3.3 27.0 + - - +
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Residues in contact with ALA 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU 3.9 7.8 + - - +
4D ILE 3.7 8.0 + - - +
5D GLN 3.2 0.4 - - - -
6D ALA* 1.3 79.2 - - - +
8D TYR* 1.3 53.2 + - + +
10D VAL* 3.2 6.1 + - - +
11D VAL* 2.7 40.6 + - + +
41D LEU* 3.7 18.9 - - + +
45D ALA* 3.5 31.6 - - + -
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Residues in contact with TYR 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 3.4 20.5 + - - +
1C MET* 5.1 5.2 - - - -
47C VAL* 3.5 11.2 - - + +
4D ILE* 3.4 26.6 + - + +
5D GLN* 3.1 14.4 + - - +
7D ALA* 1.3 80.9 - - + +
9D PHE* 1.3 56.1 + - - +
11D VAL* 3.2 14.6 - - + +
12D ALA* 2.8 27.0 + - - +
42D ALA* 4.5 11.9 - - + -
45D ALA* 5.2 2.9 - - + -
46D THR* 2.9 35.0 - - + +
49D TRP* 3.3 27.6 - + - -
227D ASN* 4.2 11.4 + - - -
228D PRO* 4.3 18.2 - - + -
229D ALA* 3.6 26.2 - - + +
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Residues in contact with PHE 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TRP* 4.5 15.5 - + + -
9A LEU* 3.2 50.5 - - + -
10A TYR* 3.7 36.7 + + + -
13A VAL* 3.2 37.5 - - + -
5D GLN 3.2 10.8 + - - +
6D ALA 4.0 7.0 - - - +
7D ALA 3.2 0.4 - - - -
8D TYR* 1.3 73.4 - - - +
10D VAL* 1.3 72.2 + - + +
12D ALA* 4.1 1.7 - - - +
13D ILE* 3.2 42.9 + - + +
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Residues in contact with VAL 10 (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 ALA 3.3 15.5 + - - +
7D ALA* 3.2 7.5 + - - +
9D PHE* 1.3 84.2 - - + +
11D VAL* 1.3 63.3 + - - +
13D ILE* 3.6 9.6 + - + +
14D LEU* 3.2 40.8 + - + +
41D LEU* 4.0 16.4 - - + -
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Residues in contact with VAL 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL* 5.3 0.2 - - + -
7D ALA 2.7 28.8 + - - +
8D TYR* 3.2 13.9 - - + +
10D VAL* 1.3 74.1 - - - +
12D ALA* 1.3 60.0 + - - +
14D LEU* 3.6 3.1 + - - +
15D PHE* 3.1 59.3 + - + -
38D GLY* 3.5 19.1 - - - +
41D LEU* 3.7 17.7 - - + -
42D ALA* 3.7 25.6 - - + +
229D ALA* 4.3 12.6 - - + -
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Residues in contact with ALA 12 (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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10A TYR* 3.8 23.6 - - + +
8D TYR 2.8 18.7 + - - +
9D PHE 3.6 1.8 + - - +
10D VAL 3.4 0.2 - - - -
11D VAL* 1.3 71.5 - - + +
13D ILE* 1.3 61.9 + - + +
15D PHE* 3.1 16.2 + - + +
16D ILE* 2.9 35.0 + - + +
229D ALA* 5.6 2.9 - - - -
232D VAL* 3.9 23.1 - - + -
233D ALA 5.6 0.2 - - - +
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Residues in contact with ILE 13 (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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13A VAL* 3.7 25.4 - - + -
17A PHE* 4.0 14.4 - - + -
9D PHE* 3.2 49.5 + - + +
10D VAL* 4.0 9.4 - - + +
11D VAL 3.5 0.2 - - - -
12D ALA* 1.3 76.4 - - + +
14D LEU* 1.3 57.3 + - + +
16D ILE* 3.2 8.4 + - + +
17D VAL* 2.8 55.4 + - + +
34D TRP* 6.3 1.6 - - + -
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 3.2 30.3 + - + +
11D VAL 3.7 4.7 - - - +
13D ILE* 1.3 79.3 - - + +
15D PHE* 1.3 58.2 + - - +
17D VAL* 4.7 2.7 - - - +
18D GLY* 3.1 25.2 + - - +
34D TRP* 3.2 56.3 - - + +
35D ALA* 3.9 0.5 + - - -
37D TRP* 4.1 13.9 - - + -
38D GLY* 3.7 26.9 - - - +
41D LEU* 4.3 11.2 - - + -
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Residues in contact with PHE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PHE* 5.9 0.2 - + - -
41C ILE* 4.2 24.9 - - + +
44C VAL* 3.3 30.7 - - + -
11D VAL* 3.1 27.8 - - + -
12D ALA* 3.1 15.2 + - + +
14D LEU* 1.3 79.8 - - - +
16D ILE* 1.3 58.0 + - - +
18D GLY* 3.9 0.2 - - - -
19D LEU* 2.9 30.5 + - - +
35D ALA* 3.8 19.1 - - + +
38D GLY* 3.2 39.5 - - - -
39D MET* 4.0 4.9 - - + -
229D ALA* 5.2 3.1 - - + -
232D VAL* 6.6 0.2 - - + -
233D ALA* 3.8 24.2 - - + -
236D LEU* 4.2 16.2 - - + +
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Residues in contact with ILE 16 (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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13A VAL* 5.8 4.0 - - + -
14A LEU* 3.7 28.9 - - + -
17A PHE* 4.8 14.6 - - + -
15C THR* 4.8 0.9 - - - +
18C LEU* 3.6 32.5 - - + -
22C LEU* 3.5 10.6 - - + +
12D ALA* 2.9 27.8 + - + +
13D ILE* 3.8 8.1 - - + +
15D PHE* 1.3 72.7 - - + +
17D VAL* 1.3 55.5 + - + +
19D LEU* 3.1 8.2 - - - +
20D LYS* 2.7 34.3 + - + +
232D VAL* 4.3 10.3 - - + -
236D LEU* 3.8 25.4 - - + -
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Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 3.4 38.8 - - + -
13D ILE* 2.8 31.3 + - + +
14D LEU 4.6 0.2 - - - +
16D ILE* 1.3 68.9 - - + +
18D GLY* 1.3 55.9 + - - +
20D LYS* 3.4 10.1 - - + +
21D ARG* 2.7 54.2 + - + +
34D TRP* 3.9 31.2 - - + -
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Residues in contact with GLY 18 (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 LEU 3.1 21.0 + - - -
15D PHE 3.9 0.7 - - - -
17D VAL* 1.3 74.9 - - - +
19D LEU* 1.3 50.7 + - - +
21D ARG* 3.0 5.7 + - - +
22D MET* 2.6 46.0 + - - +
31D GLY* 3.8 9.6 - - - -
34D TRP* 3.8 17.2 - - - +
35D ALA* 4.7 5.2 - - - -
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLY* 4.2 7.6 - - - -
22C LEU* 3.7 18.4 - - + -
23C ILE* 3.6 28.5 - - + -
34C LEU* 5.0 11.7 - - + +
38C SER* 5.8 5.8 - - - +
41C ILE* 4.5 18.2 - - + +
15D PHE 2.9 16.1 + - - +
16D ILE 3.1 9.4 - - - +
18D GLY* 1.3 74.0 - - - +
20D LYS* 1.3 56.2 + - - +
22D MET* 3.0 10.1 + - + +
23D ALA* 2.9 31.1 + - - +
35D ALA* 5.8 0.2 - - - +
236D LEU* 3.7 39.5 - - + +
240D ALA* 4.6 8.3 - - + -
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Residues in contact with LYS 20 (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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17A PHE* 5.5 11.4 - - + -
20A TYR* 3.3 35.9 + - - -
21A GLU* 3.7 22.7 + - - +
24A THR* 6.2 0.7 - - - -
22C LEU* 3.6 26.3 - - + +
16D ILE* 2.7 17.0 + - + +
17D VAL* 3.4 14.1 - - + +
19D LEU* 1.3 73.1 - - - +
21D ARG* 1.3 74.9 + - + +
23D ALA* 3.3 5.7 + - - +
24D HIS* 3.1 40.0 + - + +
27D THR* 6.0 0.7 - - + -
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Residues in contact with ARG 21 (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 VAL* 2.7 37.5 + - + +
18D GLY* 3.3 3.4 - - - +
20D LYS* 1.3 85.2 - - + +
22D MET* 1.3 59.1 + - - +
24D HIS 3.3 6.5 - - - +
27D THR* 2.8 54.0 + - + +
28D ALA* 2.9 26.9 + - - -
30D SER* 4.5 12.1 + - - -
31D GLY* 4.3 6.5 - - - -
34D TRP* 4.3 27.9 - - - +
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Residues in contact with MET 22 (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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30C LEU* 3.2 19.4 - - + +
33C PRO 3.9 23.1 - - - +
34C LEU* 3.4 29.7 - - + +
37C GLY* 4.1 21.5 - - - -
38C SER 5.6 0.2 - - - -
41C ILE* 5.2 7.9 - - - -
83C THR* 4.5 1.1 - - - +
87C LEU* 4.7 6.3 - - + -
18D GLY 2.6 24.8 + - - +
19D LEU* 3.0 12.3 + - + +
21D ARG* 1.3 75.1 - - - +
23D ALA* 1.3 64.4 + - - +
24D HIS 3.2 0.7 - - - -
28D ALA* 3.7 13.3 - - + +
31D GLY* 3.8 20.4 - - - +
32D ILE* 4.3 22.4 - - + +
35D ALA* 5.6 4.9 - - - -
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Residues in contact with ALA 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU 3.1 33.9 - - - +
23C ILE* 4.2 5.2 - - + -
26C VAL* 3.2 34.1 - - + +
27C PRO* 3.3 6.9 - - - +
30C LEU* 3.3 10.7 - - - +
34C LEU* 4.1 5.2 - - - -
19D LEU 2.9 11.1 + - - +
20D LYS 3.3 11.8 + - - +
22D MET* 1.3 77.8 - - - +
24D HIS* 1.3 60.7 + - + +
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Residues in contact with HIS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.8 21.7 + - - -
22C LEU 3.9 12.3 + - - -
25C ARG* 3.1 42.9 + - + +
30C LEU* 3.6 2.2 - - - -
20D LYS* 3.1 41.1 + - + +
21D ARG 3.3 4.0 + - - +
22D MET 3.2 0.2 - - - -
23D ALA* 1.3 79.5 - - + +
25D PRO* 1.4 69.1 - - + +
26D THR* 3.6 4.7 + - - +
27D THR* 3.7 15.6 + - + +
28D ALA* 3.1 27.4 + - - +
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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