Contacts of the helix formed by residues 16 - 32 (chain B) in PDB entry 3IO6
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 GLY 16 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 5.3 2.2 - - - -
15B LYS* 1.3 71.0 - - - +
17B TYR* 1.3 57.6 + - - -
18B ASN 3.3 2.9 - - - -
19B GLY* 3.0 4.5 + - - -
20B LEU* 2.9 26.7 + - - +
293B VAL* 3.8 19.6 - - - +
296B ASP* 3.3 24.5 - - - -
297B LYS* 4.0 16.0 + - - +
299B LEU* 5.1 0.6 - - - +
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Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 3.6 26.4 - - + +
12B ASN 5.2 0.2 - - - +
13B GLY* 3.7 20.6 - - - -
15B LYS 2.8 21.2 + - - +
16B GLY* 1.3 71.8 - - - +
18B ASN* 1.3 86.5 + - - +
20B LEU* 3.3 9.6 + - - +
21B ALA* 2.8 28.5 + - + +
37B VAL* 4.1 15.7 - - + +
39B HIS* 3.3 50.5 + + + -
296B ASP* 3.8 2.0 + - - -
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Residues in contact with ASN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY 3.3 0.6 - - - -
17B TYR* 1.3 109.7 + - - +
19B GLY* 1.3 64.1 + - - +
21B ALA* 3.5 11.3 + - - +
22B GLU* 3.3 28.1 + - - +
296B ASP* 3.5 19.9 + - - +
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Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY 3.0 8.7 + - - -
18B ASN* 1.3 79.6 - - - +
20B LEU* 1.3 60.1 + - - +
22B GLU* 3.3 21.7 + - - +
23B VAL* 3.5 12.5 + - - +
292B ALA* 3.4 26.3 - - - +
293B VAL* 4.0 7.2 - - - -
296B ASP* 3.6 12.7 + - - +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.8 21.3 - - + -
11B ILE* 4.0 19.3 - - + -
16B GLY 2.9 12.8 + - - +
17B TYR* 3.4 8.5 - - - +
18B ASN 3.3 0.2 - - - -
19B GLY* 1.3 75.4 - - - +
21B ALA* 1.3 52.8 + - - +
23B VAL* 3.2 7.9 + - - +
24B GLY* 2.8 28.8 + - - -
37B VAL* 3.8 28.8 - - + +
61B PHE* 4.1 10.1 - - + -
279B PHE* 4.2 14.8 - - + -
284B LEU* 3.7 38.8 - - + -
293B VAL* 4.2 10.4 - - + +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TYR* 2.8 17.9 + - + +
18B ASN* 3.6 17.5 - - - +
19B GLY 3.3 0.2 - - - -
20B LEU* 1.3 75.0 - - - +
22B GLU* 1.3 61.7 + - - +
24B GLY* 2.9 2.6 + - - +
25B LYS* 2.8 34.4 + - + +
35B VAL 5.9 0.9 - - - +
37B VAL* 4.1 18.1 - - + +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASN 3.3 15.2 + - - +
19B GLY* 3.4 11.9 - - - +
20B LEU 3.2 0.2 - - - -
21B ALA* 1.3 78.9 - - - +
23B VAL* 1.3 57.6 + - - +
25B LYS* 3.3 33.7 - - - +
26B LYS* 3.1 25.3 + - - +
292B ALA* 4.5 12.8 - - + -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY 3.6 14.8 - - - +
20B LEU* 3.2 8.2 + - - +
22B GLU* 1.3 74.8 - - - +
24B GLY* 1.3 64.8 + - - +
26B LYS* 3.4 10.3 - - + +
27B PHE* 3.1 18.0 + - - +
279B PHE* 3.6 23.3 - - + -
283B TYR* 3.9 31.6 - - + +
284B LEU* 4.2 12.1 - - + +
288B GLU 5.0 0.9 - - - +
289B GLY* 3.6 30.5 - - - +
292B ALA* 4.2 7.0 - - + -
293B VAL* 4.7 0.2 - - + -
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU 2.8 14.2 + - - -
21B ALA* 2.9 9.2 + - - -
23B VAL* 1.3 80.7 - - - +
25B LYS* 1.3 54.9 + - - -
27B PHE* 3.3 15.2 + - - +
28B GLU* 3.2 21.2 + - - +
35B VAL* 3.8 20.3 - - - +
279B PHE* 4.0 12.3 - - - -
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 2.8 22.0 + - + +
22B GLU* 3.3 45.1 - - - +
24B GLY* 1.3 68.3 - - - -
26B LYS* 1.3 62.5 + - - +
28B GLU* 3.6 29.6 - - + +
29B LYS* 3.3 39.1 + - - +
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Residues in contact with LYS 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 GLU 3.1 14.7 + - - +
23B VAL* 3.4 16.2 - - + +
24B GLY 3.2 0.2 - - - -
25B LYS* 1.3 76.3 - - - +
27B PHE* 1.3 64.5 + - - +
28B GLU 3.2 0.9 + - - -
29B LYS* 3.5 25.9 + - + +
30B ASP* 3.5 40.1 + - - +
283B TYR* 4.2 17.0 - - + -
288B GLU* 6.5 1.6 - - - -
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Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 4.5 8.7 - - + -
23B VAL 3.1 9.4 + - - +
24B GLY 3.4 9.6 - - - +
26B LYS* 1.3 80.0 - - - +
28B GLU* 1.3 58.8 + - - +
30B ASP 3.6 1.6 + - - -
31B THR* 2.7 51.5 + - + -
33B ILE* 3.8 31.4 - - + -
35B VAL* 3.8 17.5 - - + -
275B LEU* 4.3 16.2 - - + -
278B GLU* 3.7 30.5 - - + -
279B PHE* 3.7 24.0 - + + -
283B TYR* 3.5 38.8 - + + -
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Residues in contact with GLU 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 GLY 3.2 19.0 + - - +
25B LYS* 3.6 22.2 - - + +
26B LYS 3.1 0.6 - - - -
27B PHE* 1.3 73.6 - - - +
29B LYS* 1.3 61.2 + - + +
30B ASP 3.0 4.0 - - - -
32B GLY* 2.6 33.3 + - - -
33B ILE 3.0 27.6 - - - +
34B LYS* 3.4 22.8 - - + +
35B VAL* 2.9 24.5 + - - +
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Residues in contact with LYS 29 (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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25B LYS* 3.3 41.0 + - - +
26B LYS* 3.5 24.8 + - + +
28B GLU* 1.3 79.0 - - + +
30B ASP* 1.3 70.5 + - - +
32B GLY 4.9 0.5 + - - -
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Residues in contact with ASP 30 (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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26B LYS* 3.5 38.5 + - - +
27B PHE 4.2 0.4 - - - +
28B GLU 3.0 1.0 - - - -
29B LYS* 1.3 90.7 - - - +
31B THR* 1.3 65.4 + - - +
283B TYR* 3.4 29.5 + - + +
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Residues in contact with THR 31 (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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27B PHE* 2.7 49.5 + - + -
30B ASP* 1.3 82.3 - - - +
32B GLY* 1.3 64.4 + - - +
33B ILE* 3.6 20.3 - - + +
275B LEU* 6.3 0.4 - - + -
278B GLU* 5.3 7.2 - - + +
283B TYR* 4.3 12.8 - - - +
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Residues in contact with GLY 32 (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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5B GLY 5.3 0.7 - - - +
28B GLU* 2.6 25.1 + - - -
29B LYS 4.6 1.2 + - - -
31B THR* 1.3 73.3 - - - +
33B ILE* 1.3 61.0 + - - +
34B LYS* 4.3 4.3 + - - +
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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