Contacts of the helix formed by residues 6 - 28 (chain O) in PDB entry 4LLL
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 SER 6 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M MET* 2.8 35.1 - - - +
108M PHE 5.9 0.7 - - - -
111M MET* 5.3 8.1 - - - +
112M GLU* 4.8 14.0 - - - +
5O TYR* 1.3 76.5 - - - +
7O TYR* 1.3 62.3 + - - +
8O LEU 2.9 7.1 + - - -
9O PHE* 3.5 21.9 + - - -
10O ARG* 3.7 17.8 + - - +
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Residues in contact with TYR 7 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5O TYR* 3.3 3.6 - - - -
6O SER* 1.3 78.7 - - - +
8O LEU* 1.3 69.4 + - - +
10O ARG* 3.8 6.6 + - - +
11O MET* 3.5 48.8 + - + +
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Residues in contact with LEU 8 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131M LEU* 4.3 23.5 - - + +
132M THR* 6.4 1.3 - - + -
135M LEU* 5.1 5.2 - - - +
5O TYR 3.7 12.7 + - - +
6O SER 2.9 1.0 - - - -
7O TYR* 1.3 88.3 - - - +
9O PHE* 1.3 72.9 + - + +
11O MET* 3.4 5.5 - - - +
12O ILE* 3.2 21.1 + - - +
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Residues in contact with PHE 9 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M PHE* 3.6 28.9 - + + +
12M ILE* 3.8 26.7 - - + -
13M SER* 4.6 3.6 - - - -
16M MET* 3.6 36.8 - - + -
131M LEU* 5.7 4.7 - - + -
5O TYR 4.0 17.3 - - - -
6O SER* 3.5 13.4 + - - -
8O LEU* 1.3 83.5 - - + +
10O ARG* 1.3 61.5 + - - +
12O ILE* 3.6 9.0 - - + +
13O SER* 3.1 24.3 + - - -
134O MET* 5.4 21.5 - - + -
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Residues in contact with ARG 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M SER* 4.8 5.6 + - - -
16M MET* 3.5 57.5 + - + +
17M LYS* 4.1 19.1 - - - +
20M ALA* 5.6 5.4 - - - +
108M PHE* 5.7 6.8 - - - -
111M MET* 5.3 5.1 - - - +
6O SER* 3.7 16.2 + - - +
7O TYR* 3.8 5.1 + - - +
8O LEU 3.5 0.6 - - - -
9O PHE* 1.3 78.5 - - - +
11O MET* 1.3 58.1 + - + +
13O SER* 3.2 6.3 + - - -
14O HIS* 2.9 28.6 + - - +
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Residues in contact with MET 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135M LEU* 5.6 10.0 - - + +
7O TYR* 3.5 45.7 + - + +
8O LEU 3.4 12.1 + - - +
10O ARG* 1.3 81.9 - - + +
12O ILE* 1.3 55.7 + - - +
14O HIS* 3.7 19.9 - - + +
15O GLU* 3.5 33.2 - - + +
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Residues in contact with ILE 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M PHE* 3.2 35.1 - - + -
131M LEU 5.6 2.2 - - - +
134M MET* 5.6 5.4 - - + -
135M LEU* 4.9 18.8 - - + +
8O LEU 3.2 14.4 + - - +
9O PHE* 3.6 2.9 - - - -
10O ARG 3.2 0.4 - - - -
11O MET* 1.3 76.0 - - - +
13O SER* 1.3 60.9 + - - +
14O HIS 3.4 0.2 - - - -
15O GLU* 4.2 8.6 - - - +
16O MET* 3.6 18.7 + - - +
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Residues in contact with SER 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M PHE* 4.2 9.4 - - - -
10M ARG* 5.5 4.9 - - - -
13M SER* 3.9 23.1 - - - -
9O PHE 3.1 19.5 + - - -
10O ARG* 3.2 6.5 + - - -
12O ILE* 1.3 76.3 - - - +
14O HIS* 1.3 65.9 + - - +
15O GLU 3.4 0.2 - - - -
16O MET* 3.7 5.7 + - - +
17O LYS* 3.4 20.4 + - - +
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Residues in contact with HIS 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O ARG 2.9 16.0 + - - +
11O MET* 3.7 21.8 - - + +
13O SER* 1.3 76.9 - - - +
15O GLU* 1.3 74.9 + - - +
17O LYS* 3.1 9.9 + - - +
18O GLN* 3.1 53.4 + - + +
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Residues in contact with GLU 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135M LEU* 5.3 3.1 - - - +
138M LEU* 3.4 32.7 - - + +
139M GLN* 2.9 30.3 - - - +
11O MET* 3.5 28.3 + - + +
12O ILE* 4.2 7.8 - - - +
13O SER 3.4 0.2 - - - -
14O HIS* 1.3 83.3 - - + +
16O MET* 1.3 58.6 + - + +
18O GLN* 2.8 30.7 + - - +
19O LYS* 3.1 9.0 + - - +
111O MET* 4.5 3.9 - - + +
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Residues in contact with MET 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M SER* 5.0 13.7 - - - +
9M PHE* 4.0 26.9 - - - -
10M ARG* 5.9 3.4 - - + -
12O ILE 3.6 11.7 - - - +
13O SER* 3.7 8.2 + - - +
14O HIS 3.3 0.6 - - - -
15O GLU* 1.3 77.8 - - + +
17O LYS* 1.3 60.9 + - - +
19O LYS* 3.5 3.1 + - - +
20O ALA* 3.3 21.8 + - - +
108O PHE* 5.3 9.7 - - + -
111O MET* 3.5 45.4 - - + +
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Residues in contact with LYS 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O SER 3.4 12.0 + - - +
14O HIS* 3.1 13.1 + - + +
16O MET* 1.3 78.1 - - - +
18O GLN* 1.3 60.5 + - + +
20O ALA* 3.4 4.4 + - - -
21O ASP* 2.8 45.0 + - - +
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Residues in contact with GLN 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O HIS* 3.1 47.6 + - + +
15O GLU* 2.8 17.8 + - - +
17O LYS* 1.3 80.6 + - - +
19O LYS* 1.3 55.3 + - - +
21O ASP* 4.0 8.7 + - - +
22O GLN* 3.1 28.6 + - - +
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Residues in contact with LYS 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O GLU 3.1 6.6 + - - +
16O MET 3.5 1.3 + - - +
17O LYS 3.3 0.4 - - - -
18O GLN* 1.3 75.2 - - - +
20O ALA* 1.3 64.7 + - - +
22O GLN* 3.7 5.3 + - - +
23O LYS* 3.4 27.4 + - - +
107O ILE* 4.2 16.5 - - + +
108O PHE* 6.4 0.4 - - + -
111O MET* 3.5 31.9 - - + -
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Residues in contact with ALA 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O MET 3.3 14.5 + - - +
17O LYS* 3.9 5.6 - - - +
19O LYS* 1.3 78.9 - - - +
21O ASP* 1.3 65.7 + - - +
23O LYS* 3.3 1.8 + - - -
24O LEU* 3.0 32.8 + - + +
104O PHE* 3.8 12.2 - - + -
107O ILE* 5.5 1.1 - - - -
108O PHE* 4.3 26.6 - - + -
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Residues in contact with ASP 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O LYS* 2.8 29.8 + - - +
18O GLN* 4.4 10.0 + - - +
20O ALA* 1.3 78.2 - - - +
22O GLN* 1.3 60.3 + - - +
23O LYS 3.4 0.2 - - - -
24O LEU* 3.6 23.6 - - + +
25O GLU* 3.0 32.4 + - - +
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Residues in contact with GLN 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18O GLN 3.1 20.8 + - - +
19O LYS* 3.9 7.6 - - - +
20O ALA 3.2 0.4 - - - -
21O ASP* 1.3 75.2 - - - +
23O LYS* 1.3 62.0 + - + +
25O GLU* 3.4 10.9 - - - +
26O GLN* 2.9 28.0 + - - +
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Residues in contact with LYS 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19O LYS 3.4 15.0 + - - +
20O ALA 3.3 2.9 + - - +
22O GLN* 1.3 75.8 - - + +
24O LEU* 1.3 66.2 + - - +
26O GLN* 3.0 32.0 + - - +
27O PHE* 3.1 48.0 + - - +
103O ALA* 4.2 17.4 + - - +
104O PHE* 3.4 25.5 - - + +
107O ILE* 3.6 41.5 - - + +
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Residues in contact with LEU 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O ALA* 3.0 22.4 + - + +
21O ASP* 3.6 31.6 - - - +
23O LYS* 1.3 77.4 - - - +
25O GLU* 1.3 51.0 + - - +
27O PHE 3.4 0.3 - - - -
28O ASP* 2.5 36.7 + - - -
29O ILE* 3.2 42.7 + - + +
30O THR* 3.9 9.6 - - - +
31O ASN* 4.5 27.8 - - + +
34O GLY* 5.0 3.1 - - - -
104O PHE* 3.7 17.7 - - + -
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Residues in contact with GLU 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O ASP* 3.0 16.6 + - - +
22O GLN* 3.4 10.6 - - - +
24O LEU* 1.3 79.4 - - - +
26O GLN* 1.3 57.6 + - - +
28O ASP* 3.0 27.2 + - - +
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Residues in contact with GLN 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G A 3.4 46.5 + - - +
19G C 4.4 15.2 + - - -
22O GLN 2.9 16.3 + - - +
23O LYS* 3.0 42.5 + - - +
24O LEU 3.2 0.2 - - - -
25O GLU* 1.3 76.4 - - - +
27O PHE* 1.3 75.2 + - + +
28O ASP* 5.0 1.0 - - - +
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Residues in contact with PHE 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G C 5.8 2.9 - - - -
23O LYS* 3.1 39.3 + - - +
24O LEU 4.1 1.3 - - - +
26O GLN* 1.3 103.8 - - + +
28O ASP* 1.3 72.8 + - - +
29O ILE* 3.3 11.7 + - + +
74O LYS* 5.2 2.6 - - - +
76O LEU* 5.4 2.5 - - + +
99O LYS* 5.1 11.0 - - + -
100O LEU* 3.5 49.4 - - + +
103O ALA* 3.8 21.3 - - + -
104O PHE* 4.7 4.0 - + + -
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Residues in contact with ASP 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O LEU 2.5 16.5 + - - -
25O GLU* 3.0 18.1 + - - +
26O GLN 4.9 1.1 - - - +
27O PHE* 1.3 77.3 - - - +
29O ILE* 1.3 57.1 + - - +
74O LYS* 3.0 35.4 + - - +
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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
------------------------------------------------------------
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