Contacts of the helix formed by residues 10 - 25 (chain T) 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 ASN 10 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15421 C 4.8 9.5 + - - +
37Q ARG* 4.8 14.2 + - - +
41Q MET* 3.7 34.3 - - + +
42Q ILE 6.1 0.2 - - - -
43Q GLU* 5.5 2.4 + - - -
45Q ARG* 3.0 19.9 - - - +
7T LYS 5.1 1.3 - - - -
9T VAL* 1.3 79.4 - - - +
11T GLN* 1.3 68.8 + - - +
12T GLN* 2.9 42.4 + - - +
13T GLU* 3.1 10.0 + - + +
14T PHE* 2.8 23.4 + - - +
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Residues in contact with GLN 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15411 G 4.4 3.8 - - - +
15421 C 3.7 35.0 - - - +
6T VAL* 5.5 2.5 - - - +
9T VAL 3.5 3.1 + - - -
10T ASN* 1.3 76.6 + - - +
12T GLN* 1.3 57.5 + - - +
13T GLU 3.4 0.2 - - - -
14T PHE* 3.2 30.5 - - - -
15T VAL* 2.9 56.5 + - + +
18T LEU* 5.3 0.2 - - - +
58T ALA* 4.6 10.9 - - - +
59T SER* 5.6 0.4 - - - +
62T ARG* 3.0 51.2 - - - +
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Residues in contact with GLN 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15401 G 5.5 1.6 - - - +
15411 G 2.9 35.3 + - - +
15421 C 3.9 14.1 + - - +
15921 C 4.7 0.4 + - - -
15931 C 2.7 59.9 + - + +
43Q GLU 5.0 5.0 + - - +
45Q ARG* 3.2 11.9 + - - +
10T ASN* 2.9 25.2 + - - +
11T GLN* 1.3 79.5 - - - +
13T GLU* 1.3 59.9 + - - +
15T VAL* 3.3 18.7 - - - +
16T ARG* 4.0 7.3 + - - +
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Residues in contact with GLU 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Q MET* 6.2 1.3 - - + -
45Q ARG* 5.6 2.0 - - - +
9T VAL* 4.1 18.6 - - + -
10T ASN* 3.1 14.0 + - + +
12T GLN* 1.3 78.3 - - - +
14T PHE* 1.3 63.0 + - - +
15T VAL 3.6 0.2 + - - -
16T ARG* 2.4 53.9 + - - +
17T ALA* 4.0 4.7 + - - +
138T VAL* 4.0 13.1 - - + +
141T ALA* 5.4 6.8 - - - +
142T ASN* 5.3 13.1 - - + +
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Residues in contact with PHE 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6T VAL* 4.5 15.3 - - + +
9T VAL* 4.6 8.5 - - + +
10T ASN 2.8 17.6 + - - +
11T GLN* 3.2 36.3 - - - -
12T GLN 3.3 0.4 - - - -
13T GLU* 1.3 76.8 - - - +
15T VAL* 1.3 59.7 + - - +
17T ALA* 3.5 2.1 + - - +
18T LEU* 2.9 52.3 + - + +
62T ARG* 6.1 0.7 - - + -
131T LEU* 3.7 20.4 - - + -
134T ILE* 3.5 25.1 - - + -
135T ALA* 3.4 33.2 - - + -
138T VAL* 3.6 24.9 - - + -
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Residues in contact with VAL 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15411 G 4.9 14.6 - - - +
11T GLN* 2.9 31.1 + - + +
12T GLN* 3.3 16.6 - - - +
14T PHE* 1.3 75.5 - - - +
16T ARG* 1.3 64.1 + - - +
18T LEU* 4.3 3.6 - - - -
19T ALA* 2.9 35.4 + - + +
55T THR* 4.2 25.1 - - + +
58T ALA* 3.7 25.6 - - + -
59T SER 5.4 0.4 - - - +
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Residues in contact with ARG 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T GLN 4.4 7.4 - - - +
13T GLU* 2.4 48.0 + - - +
14T PHE 3.3 0.4 - - - -
15T VAL* 1.3 86.6 - - + +
17T ALA* 1.3 60.9 + - - +
19T ALA* 4.2 3.3 - - - +
20T ALA* 3.8 14.2 + - - +
141T ALA* 5.9 3.6 - - - +
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Residues in contact with ALA 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T GLU 4.0 4.7 + - - +
14T PHE 3.5 1.8 + - - +
15T VAL 3.3 0.2 - - - -
16T ARG* 1.3 79.8 - - - +
18T LEU* 1.3 60.1 + - - +
19T ALA 3.2 0.2 - - - -
20T ALA* 2.8 22.6 + - - +
21T PHE* 2.9 35.2 + - + -
138T VAL* 3.6 29.2 - - + -
141T ALA* 6.5 1.1 - - + -
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Residues in contact with LEU 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T GLN* 4.7 0.4 - - - +
14T PHE* 2.9 47.0 + - + +
15T VAL* 4.3 2.7 - - - +
17T ALA* 1.3 76.0 - - - +
19T ALA* 1.3 57.2 + - - +
21T PHE* 4.4 4.9 - - - +
22T LEU* 2.9 59.1 + - + +
58T ALA* 3.6 33.2 - - + +
61T ALA* 4.6 2.2 - - + -
62T ARG* 6.6 0.2 - - + -
131T LEU* 4.2 18.8 - - + -
134T ILE* 3.6 34.7 - - + +
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Residues in contact with ALA 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15T VAL* 2.9 23.5 + - + +
16T ARG* 4.2 4.7 - - - +
18T LEU* 1.3 76.6 - - - +
20T ALA* 1.3 57.9 + - - +
22T LEU* 3.9 0.6 + - - -
23T LYS* 3.2 29.5 + - - +
51T ASN* 5.2 9.4 - - + +
54T TYR* 3.8 29.4 - - + +
55T THR* 4.5 14.1 - - - +
58T ALA* 5.1 0.6 - - - +
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Residues in contact with ALA 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T ARG 3.8 10.0 + - - +
17T ALA* 2.8 14.0 + - - +
19T ALA* 1.3 76.8 - - - +
21T PHE* 1.3 63.7 + - + +
22T LEU 3.2 1.8 - - - -
23T LYS* 2.9 28.9 + - + +
24T LYS* 2.9 14.8 + - - +
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Residues in contact with PHE 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17T ALA* 2.9 50.2 + - + +
18T LEU* 4.1 4.5 - - - +
20T ALA* 1.3 79.5 - - + +
22T LEU* 1.3 62.0 + - - +
23T LYS 3.2 0.2 - - - -
24T LYS* 3.5 39.0 - - + +
25T SER* 3.5 24.3 + - - -
27T LYS* 5.2 1.4 + - - +
134T ILE* 4.4 20.2 - - + -
137T GLN* 3.2 39.9 - - + -
138T VAL* 5.3 0.2 - - + -
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Residues in contact with LEU 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T LEU* 2.9 45.5 + - + +
19T ALA 4.0 1.1 - - - +
20T ALA 3.2 0.2 - - - -
21T PHE* 1.3 78.2 - - - +
23T LYS* 1.3 59.7 + - - +
26T GLY 3.4 1.3 + - - -
27T LYS* 2.8 60.1 + - + +
54T TYR* 3.4 43.3 - - + +
57T ALA* 3.8 20.2 - - + -
58T ALA* 4.2 4.0 - - - +
61T ALA* 6.3 0.7 - - + -
107T LEU* 5.6 2.9 - - + -
112T MET* 4.8 16.6 - - + -
134T ILE* 5.8 2.2 - - + -
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Residues in contact with LYS 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T ALA 3.2 18.6 + - - +
20T ALA* 2.9 15.6 + - - +
22T LEU* 1.3 77.4 - - - +
24T LYS* 1.3 65.3 + - - +
26T GLY* 3.1 11.8 + - - -
51T ASN* 3.4 40.2 + - - +
54T TYR* 3.5 32.8 + - + +
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Residues in contact with LYS 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T ALA 2.9 13.6 + - - +
21T PHE* 3.5 40.6 - - + +
22T LEU 3.4 0.4 - - - -
23T LYS* 1.3 78.8 - - - +
25T SER* 1.3 63.6 + - - +
26T GLY 3.3 0.9 + - - -
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Residues in contact with SER 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T PHE 3.5 11.6 + - - -
24T LYS* 1.3 79.5 - - - +
26T GLY* 1.3 63.1 + - - +
27T LYS* 3.7 35.8 + - - +
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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