Contacts of the helix formed by residues 16 - 26 (chain B) in PDB entry 1ADI
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 LYS 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B VAL* 4.5 8.1 - - + -
7B LEU* 5.1 3.1 - - - -
8B GLY* 4.6 16.6 - - - +
12B GLY* 5.2 1.0 - - - -
13B ASP* 4.5 10.7 - - - +
14B GLU* 3.7 19.3 + - - +
15B GLY* 1.3 76.0 - - - +
17B GLY* 1.3 68.0 + - - +
18B LYS 2.9 2.8 + - - -
19B ILE* 3.0 21.5 + - - +
20B VAL* 3.2 18.0 + - + +
39B ALA 5.2 8.7 + - - -
222B GLY 3.8 18.8 - - - +
223B ALA* 3.5 29.2 + - - +
224B GLN* 5.0 4.0 - - - +
265B ILE* 3.8 20.8 - - + +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLY* 3.4 3.0 - - - -
16B LYS* 1.3 79.7 - - - +
18B LYS* 1.3 57.0 + - - +
21B ASP* 3.4 31.2 + - - +
41B HIS* 3.4 24.0 - - - -
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Residues in contact with LYS 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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15B GLY 4.3 3.7 + - - +
16B LYS 2.9 2.0 + - - -
17B GLY* 1.3 71.7 - - - +
19B ILE* 1.3 76.0 + - + +
20B VAL 3.1 1.6 - - - -
21B ASP* 3.8 5.0 - - - +
22B LEU* 3.0 31.3 + - + +
414B SER* 3.3 22.0 + - - +
416B GLY 2.4 34.9 + - - +
417B PRO* 3.7 13.9 + - + +
418B ASP 2.9 19.0 + - - -
419B ARG* 4.6 6.8 + - - +
421B GLU 4.1 0.6 + - - -
422B THR* 3.4 29.8 + - + -
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Residues in contact with ILE 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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6B VAL* 5.4 1.1 - - + -
15B GLY 3.0 28.9 - - - +
16B LYS* 3.0 13.5 + - - +
18B LYS* 1.3 85.6 - - + +
20B VAL* 1.3 58.8 + - + +
22B LEU* 3.0 10.2 + - + +
23B LEU* 2.9 55.2 + - + +
263B LEU* 4.0 13.0 - - + -
265B ILE* 3.8 17.7 - - + -
328B CYS* 3.1 34.3 - - - -
330B THR* 4.2 6.5 - - + -
412B ILE* 5.0 8.3 - - + -
414B SER* 4.9 3.4 - - - -
422B THR* 6.3 0.7 - - + -
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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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6B VAL* 4.0 28.9 - - + -
16B LYS* 3.2 22.4 + - + +
17B GLY 3.9 1.8 - - - +
18B LYS 3.1 0.2 - - - -
19B ILE* 1.3 79.7 - - - +
21B ASP* 1.3 57.5 + - - +
23B LEU* 3.9 0.8 - - - -
24B THR* 2.3 40.1 + - - +
41B HIS* 3.5 25.6 - - + +
57B SER* 3.6 9.0 - - - +
219B MET* 4.1 17.4 - - + +
221B GLU* 4.3 26.7 - - + +
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Residues in contact with ASP 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 GLY 3.4 11.2 + - - +
18B LYS* 3.5 6.1 + - - +
20B VAL* 1.3 74.1 - - - +
22B LEU* 1.3 61.5 + - - +
24B THR* 3.6 14.4 - - - -
25B GLU* 3.7 0.9 - - - +
41B HIS* 2.9 24.1 + - - -
42B THR 5.5 0.7 - - - +
43B LEU* 4.9 9.8 - - - +
57B SER* 2.8 30.3 + - - +
60B LEU* 5.5 5.0 - - - +
61B ARG* 5.1 0.5 - - - -
419B ARG* 2.9 42.0 + - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B LYS* 3.0 25.8 + - + +
19B ILE* 3.0 9.4 + - + +
21B ASP* 1.3 77.5 - - - +
23B LEU* 1.3 67.7 + - + +
25B GLU* 3.1 47.2 + - - +
26B ARG* 3.2 26.7 + - - +
412B ILE* 6.2 0.2 - - + -
419B ARG* 3.6 39.7 - - + +
422B THR* 3.9 25.4 - - + +
424B ILE* 5.0 11.0 - - + -
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Residues in contact with LEU 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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4B VAL* 5.0 4.3 - - + -
6B VAL* 4.4 12.3 - - + -
19B ILE* 2.9 48.9 + - + +
22B LEU* 1.3 69.9 - - + +
24B THR* 1.3 61.9 + - - +
25B GLU 2.9 6.8 + - - -
26B ARG* 2.9 27.2 + - - +
27B ALA* 3.2 12.9 + - - +
219B MET* 4.2 15.0 - - - -
263B LEU* 4.2 13.7 - - + -
412B ILE* 5.4 2.7 - - + -
427B ASP* 4.9 2.5 - - - +
428B PRO* 4.0 28.3 - - + -
429B PHE* 3.6 32.3 - - + -
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Residues in contact with THR 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* 2.3 32.9 + - - +
21B ASP* 3.6 14.0 - - - +
23B LEU* 1.3 75.4 - - - +
25B GLU* 1.3 61.5 + - - +
27B ALA* 3.3 27.4 + - - +
30B VAL* 4.6 6.3 - - + +
57B SER* 4.3 4.7 + - - +
58B GLY* 3.7 21.7 - - - +
61B ARG* 3.4 31.0 - - + -
64B VAL* 3.8 6.3 - - + +
219B MET* 3.9 13.4 - - - +
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Residues in contact with GLU 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 ASP 3.7 1.8 - - - +
22B LEU* 3.1 21.2 - - - +
24B THR* 1.3 78.8 - - - +
26B ARG* 1.3 86.1 + - + +
27B ALA 4.9 1.0 - - - +
61B ARG* 4.3 25.5 + - - +
419B ARG* 2.5 37.4 + - - +
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Residues in contact with ARG 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 LEU* 3.2 25.4 + - - +
23B LEU* 2.9 22.5 + - - +
25B GLU* 1.3 109.0 + - + +
27B ALA* 1.3 62.4 + - - +
28B LYS* 3.8 0.7 + - - +
217B PHE* 2.9 42.5 - - + +
424B ILE* 4.1 23.7 - - - +
427B ASP* 4.7 11.4 + - - +
429B PHE* 4.1 11.0 - - + -
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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