Contacts of the helix formed by residues 11 - 28 (chain M) in PDB entry 5FLX
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 VAL 11 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12M MET* 1.3 67.6 + - + +
13M ASP* 3.2 24.5 - - - +
14M VAL* 3.4 30.6 - - + +
15M ASN* 3.9 9.9 + - - +
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Residues in contact with MET 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M VAL* 1.3 73.2 - - - +
13M ASP* 1.3 63.1 + - - +
14M VAL 3.1 0.7 + - - -
15M ASN* 3.3 4.3 + - - +
16M THR* 2.9 56.2 + - + +
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Residues in contact with ASP 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M VAL* 3.2 20.9 - - - +
12M MET* 1.3 77.3 - - - +
14M VAL* 1.3 79.3 + - - +
16M THR* 4.5 2.5 - - - -
17M ALA* 2.7 40.3 + - + +
123M VAL* 3.5 30.8 - - + +
127M TYR* 4.9 10.7 - - - +
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Residues in contact with VAL 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M VAL* 3.4 35.2 - - + +
12M MET 3.1 0.6 - - - -
13M ASP* 1.3 90.6 + - - +
15M ASN* 1.3 73.1 + - - +
17M ALA* 4.2 0.5 - - - +
18M LEU* 3.4 19.5 + - + +
127M TYR* 3.4 63.0 - - + +
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Residues in contact with ASN 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M VAL 3.9 6.6 + - - +
12M MET* 3.3 4.9 + - - +
14M VAL* 1.3 91.0 - - - +
16M THR* 1.3 62.8 + - - +
18M LEU* 3.1 3.2 + - - +
19M GLN* 2.9 29.4 + - - +
84M LYS* 5.1 7.7 + - - +
88M TRP* 3.0 39.4 - - + -
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Residues in contact with THR 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M MET* 2.9 43.8 + - + -
13M ASP* 4.5 2.0 - - - -
15M ASN* 1.3 76.3 - - - +
17M ALA* 1.3 59.2 + - - +
19M GLN* 3.2 24.9 + - - +
20M GLU* 2.9 31.5 + - + +
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Residues in contact with ALA 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M ASP* 2.7 29.3 + - + +
14M VAL 4.2 1.3 - - - +
16M THR* 1.3 78.1 - - - +
18M LEU* 1.3 57.6 + - - +
20M GLU* 3.3 6.1 + - - +
21M VAL* 2.9 33.3 + - - +
123M VAL* 5.4 4.7 - - + +
124M ILE* 3.5 29.3 - - + +
127M TYR* 6.2 3.1 - - + -
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Residues in contact with LEU 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M VAL* 3.4 16.8 + - + +
15M ASN* 3.1 6.6 + - - +
17M ALA* 1.3 80.4 - - - +
19M GLN* 1.3 56.3 + - - +
21M VAL* 3.3 7.7 - - + +
22M LEU* 2.9 61.4 + - + +
51M VAL* 5.0 12.3 - - + -
77M ILE* 5.5 8.1 - - + -
79M VAL* 4.5 21.3 - - + -
85M LEU* 5.0 1.6 - - + -
88M TRP* 3.5 42.4 - - + +
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Residues in contact with GLN 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M ASN* 2.9 12.8 + - - +
16M THR* 3.2 37.2 + - - +
18M LEU* 1.3 73.8 - - - +
20M GLU* 1.3 60.7 + - - +
22M LEU* 4.8 1.8 - - - -
23M LYS* 2.8 52.0 + - + +
88M TRP* 3.3 27.8 - - + +
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Residues in contact with GLU 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M THR* 2.9 22.9 + - + +
17M ALA* 3.5 8.3 - - - +
18M LEU 3.2 0.2 - - - -
19M GLN* 1.3 79.2 - - - +
21M VAL* 1.3 58.6 + - + +
23M LYS* 4.8 2.9 - - - +
24M THR* 2.9 49.9 + - - +
118M SER* 5.0 18.2 - - - -
119M GLN* 5.4 10.9 + - + +
124M ILE* 5.7 3.8 - - + -
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Residues in contact with VAL 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M ALA 2.9 21.5 + - - +
18M LEU* 3.3 13.9 - - + +
20M GLU* 1.3 78.6 - - - +
22M LEU* 1.3 68.1 + - + +
24M THR* 4.9 2.0 - - - -
25M ALA* 2.6 41.6 + - + +
49M LEU* 5.1 13.0 - - + -
111M VAL* 5.5 6.1 - - + -
114M TYR* 3.5 36.6 - - + +
115M GLY 5.7 1.1 - - - +
118M SER* 5.8 4.3 - - - -
124M ILE* 4.8 17.3 - - + -
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Residues in contact with LEU 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M LEU* 2.9 44.6 + - + +
19M GLN* 4.6 0.9 - - - +
21M VAL* 1.3 87.1 - - + +
23M LYS* 1.3 60.7 + - - +
25M ALA* 4.0 3.8 - - - -
26M LEU* 2.9 27.7 + - - +
31M LEU* 3.5 11.5 - - + +
49M LEU* 5.4 3.1 - - + -
51M VAL* 4.9 8.1 - - + -
85M LEU* 4.9 4.0 - - + -
88M TRP* 3.7 38.1 - - + +
89M VAL* 4.0 11.9 - - + +
109M VAL* 3.9 35.0 - - + -
111M VAL* 5.4 4.9 - - + -
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Residues in contact with LYS 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M GLN* 2.8 41.8 + - - +
20M GLU* 4.2 2.7 - - - +
22M LEU* 1.3 77.3 - - - +
24M THR* 1.3 63.6 + - - +
26M LEU* 3.1 6.2 + - - +
27M ILE* 2.9 37.3 + - + +
88M TRP 4.4 7.7 + - - +
89M VAL 5.8 0.9 - - - -
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Residues in contact with THR 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M GLU* 2.9 36.6 + - - -
21M VAL* 4.5 2.2 - - - -
23M LYS* 1.3 79.2 - - - +
25M ALA* 1.3 60.6 + - - +
27M ILE* 3.5 9.1 + - - +
28M HIS* 3.3 20.3 + - - +
115M GLY* 4.8 8.7 - - - -
117M GLU* 3.4 38.8 - - + +
118M SER* 4.5 15.9 - - - +
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Residues in contact with ALA 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M VAL* 2.6 25.2 + - + +
22M LEU 3.6 4.5 - - - +
23M LYS 3.1 0.2 - - - -
24M THR* 1.3 79.4 - - - +
26M LEU* 1.3 56.5 + - - +
28M HIS* 2.8 26.2 + - - +
30M GLY 4.3 1.0 - - - -
31M LEU* 3.3 24.7 + - + +
111M VAL* 3.7 28.7 - - + -
113M ASP 5.4 1.9 - - - +
114M TYR* 6.3 0.9 - - - -
115M GLY* 5.6 5.8 - - - +
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Residues in contact with LEU 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M LEU 2.9 18.1 + - - +
23M LYS* 3.8 4.0 - - - +
25M ALA* 1.3 73.4 - - - +
27M ILE* 1.3 75.6 + - + +
28M HIS 2.9 10.6 - - - +
31M LEU* 3.4 21.3 - - + +
33M ARG* 4.0 23.3 - - - +
89M VAL* 3.1 44.4 - - + +
90M GLY* 5.3 1.3 - - - -
91M LEU* 5.5 1.6 - - + -
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Residues in contact with ILE 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K HIS* 4.9 16.6 - - + +
23M LYS* 2.9 33.1 + - + +
24M THR* 3.7 11.7 - - - +
26M LEU* 1.3 87.5 - - + +
28M HIS* 1.3 58.1 + - - +
29M ASP 4.0 0.3 + - - -
117M GLU* 4.8 10.8 - - - +
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Residues in contact with HIS 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M THR 3.3 10.5 + - - +
25M ALA* 2.8 23.3 - - - +
26M LEU* 2.9 12.7 - - - +
27M ILE* 1.3 79.2 - - - +
29M ASP* 1.3 65.5 + - + +
30M GLY* 2.9 29.1 + - - +
31M LEU* 3.9 1.9 + - - +
113M ASP* 3.1 33.9 + - - +
117M GLU* 5.9 1.3 + - - +
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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