Contacts of the helix formed by residues 13 - 28 (chain B) in PDB entry 6A5T
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 THR 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ASP* 5.8 3.1 - - + +
11B THR* 2.8 21.4 + - - +
12B ILE* 1.3 88.8 - - - +
14B THR* 1.3 66.9 + - - +
15B GLU* 3.2 15.6 + - - +
16B ASP* 3.2 25.5 + - - +
17B CYS* 3.7 4.5 + - - -
649B LYS* 5.6 4.3 - - - +
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Residues in contact with THR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B THR* 1.3 73.6 - - - +
15B GLU* 1.3 67.8 + - - +
17B CYS* 2.8 21.7 + - - +
18B TRP* 3.1 34.5 + - + +
705B GLU* 5.2 5.7 + - - -
744B HIS* 4.9 14.0 - - + +
807B GLN* 6.2 0.7 - - + -
1048B THR* 5.8 5.6 - - + +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B THR* 3.2 7.6 + - - +
14B THR* 1.3 81.0 - - + +
16B ASP* 1.3 61.9 + - - +
18B TRP* 2.8 19.4 + - + -
19B THR* 2.8 29.5 + - - +
807B GLN* 5.4 8.7 + - - +
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Residues in contact with ASP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 3.7 16.8 - - + -
13B THR* 3.2 26.6 + - - +
14B THR 3.0 0.8 - - - -
15B GLU* 1.3 76.9 - - - +
17B CYS* 1.3 65.3 + - - +
18B TRP 3.0 1.1 - - - -
19B THR* 3.1 2.8 + - - +
20B VAL* 3.0 27.0 + - - +
649B LYS* 3.2 28.1 - - - +
652B ILE* 3.3 43.3 - - + +
656B GLN* 4.5 4.2 + - - -
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Residues in contact with CYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 4.2 9.6 - - - +
13B THR 3.7 11.1 + - - -
14B THR* 2.8 13.3 + - - +
16B ASP* 1.3 76.2 - - - +
18B TRP* 1.3 62.5 + - + +
20B VAL* 3.3 9.2 + - - +
21B ILE* 3.0 28.6 + - - +
631B PHE* 4.0 20.4 - - - -
704B PRO* 4.4 12.3 - - - -
743B ILE* 3.3 35.5 - - + +
744B HIS* 4.7 7.4 - - + -
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Residues in contact with TRP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR* 3.1 37.3 + - + +
15B GLU* 2.8 23.3 + - + +
17B CYS* 1.3 78.9 - - + +
19B THR* 1.3 59.2 + - - +
21B ILE* 3.6 19.3 + - + -
22B SER* 2.9 29.0 + - - -
744B HIS* 4.2 24.7 + + + +
746B SER* 4.0 15.7 - - - -
747B MET* 4.2 20.9 - - + -
807B GLN* 3.0 66.7 - - + +
808B ALA* 4.4 1.3 - - + -
811B TYR* 3.3 23.6 + + - +
1045B THR* 4.5 3.7 - - + +
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Residues in contact with THR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 2.8 18.0 + - - +
16B ASP* 3.1 6.9 + - - -
18B TRP* 1.3 74.9 - - - +
20B VAL* 1.3 61.6 + - - +
22B SER* 3.0 9.7 + - - -
23B ALA* 2.9 26.3 + - - +
652B ILE* 4.2 22.5 - - + +
655B ILE* 3.6 28.9 - - + -
656B GLN* 4.5 16.7 + - + +
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASP 3.0 14.6 + - - +
17B CYS* 3.7 7.6 - - - +
18B TRP 3.2 0.4 - - - -
19B THR* 1.3 76.8 - - + +
21B ILE* 1.3 64.4 + - - +
22B SER 3.2 0.2 + - - -
23B ALA* 3.2 6.1 + - - +
24B PHE* 3.0 20.8 + - - +
631B PHE* 4.4 17.3 - - + -
647B ILE* 4.0 16.2 - - + -
652B ILE* 3.7 18.6 - - + -
655B ILE* 5.6 2.5 - - + -
678B TRP* 3.7 23.9 - - + -
681B LEU* 4.0 10.3 - - + -
687B ILE* 4.0 14.6 - - + -
743B ILE* 4.8 6.1 - - + -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B CYS 3.0 16.2 + - - +
18B TRP* 4.0 25.4 - - + +
19B THR 3.4 0.2 - - - -
20B VAL* 1.3 74.7 - - - +
22B SER* 1.3 63.0 + - - +
24B PHE* 3.5 8.0 - - + +
25B PHE* 3.0 38.0 + - + -
535B LEU* 5.1 8.7 - - + -
743B ILE* 4.3 24.0 - - + -
744B HIS* 5.4 1.8 - - + -
747B MET* 3.4 39.0 - - + -
811B TYR* 3.6 25.4 - - + -
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B TRP 2.9 14.9 + - - -
19B THR* 3.0 15.2 + - - -
21B ILE* 1.3 77.8 - - - +
23B ALA* 1.3 64.2 + - - +
25B PHE* 3.2 2.8 + - - +
26B GLU* 2.8 25.7 + - - +
811B TYR* 2.1 38.3 + - - -
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B THR 2.9 7.2 + - - +
20B VAL* 3.8 7.9 - - - +
22B SER* 1.3 76.2 - - - +
24B PHE* 1.3 63.3 + - - +
26B GLU* 3.0 10.1 + - - +
27B GLU* 3.0 19.6 + - - +
655B ILE* 3.8 29.8 - - + +
677B GLY* 4.8 4.7 - - - -
678B TRP* 3.5 29.2 + - + +
681B LEU* 5.1 2.2 - - + -
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Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL 3.0 10.9 + - - +
21B ILE* 3.5 11.9 - - + +
22B SER 3.1 0.2 - - - -
23B ALA* 1.3 76.5 - - - +
25B PHE* 1.3 80.4 + + - +
26B GLU 2.9 1.2 + - - -
27B GLU* 3.0 11.4 + - - +
28B LYS* 3.1 51.9 + - + -
29B GLY 5.5 1.3 - - - -
534B LEU 4.7 3.6 - - - -
535B LEU* 3.3 41.1 - - + -
536B SER 5.5 3.8 - - - -
629B PRO* 5.1 5.8 - - + -
678B TRP* 3.1 62.5 - + + -
689B TYR* 5.5 0.2 - + - -
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.0 34.0 + - + +
22B SER 3.6 0.4 - - - +
24B PHE* 1.3 90.5 - + - +
26B GLU* 1.3 60.1 + - - +
27B GLU 3.4 0.2 - - - -
29B GLY* 3.6 29.5 + - - +
30B LEU* 3.7 29.4 - - + -
534B LEU* 3.6 45.1 - - + -
535B LEU* 5.3 1.1 - - + -
747B MET* 5.1 3.8 - - + -
808B ALA* 6.0 0.4 - - + -
811B TYR* 3.2 53.2 - + + +
812B LEU* 5.6 0.7 - - + -
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B SER* 2.8 18.2 + - - +
23B ALA* 3.3 14.1 - - - +
24B PHE 2.9 0.4 + - - -
25B PHE* 1.3 81.3 - - - +
27B GLU* 1.3 60.5 + - - +
29B GLY 4.9 0.2 - - - -
811B TYR* 6.1 1.0 - - - -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA 3.0 5.2 + - - +
26B GLU* 1.3 81.3 - - - +
28B LYS* 1.3 70.4 + - + +
29B GLY 3.6 0.2 + - - -
677B GLY* 5.2 1.8 - - - -
678B TRP* 2.9 24.8 - - + +
679B SER* 2.4 58.1 + - - -
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 3.1 49.2 + - + +
27B GLU* 1.3 89.8 - - + +
29B GLY* 1.3 71.5 + - - +
32B SER* 3.4 36.5 - - - +
536B SER 6.0 1.1 - - - +
537B GLY* 4.8 12.3 - - - -
627B TYR* 4.6 8.7 + - - -
678B TRP* 4.2 12.3 - - + +
679B SER* 5.6 2.0 - - - -
689B TYR* 3.9 22.6 + - - -
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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