Contacts of the helix formed by residues 12 - 27 (chain B) in PDB entry 3ADB
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 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLY 3.2 0.4 + - - -
11B VAL* 1.3 80.3 - - - +
13B LYS* 1.3 58.5 + - - +
15B THR* 4.0 0.9 - - - -
16B PHE* 2.9 32.7 + - - +
102B LEU* 3.6 6.4 - - - +
150B THR* 4.8 2.1 - - - +
2002B ANP 3.0 43.7 + - - -
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Residues in contact with LYS 13 (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 LEU* 3.6 11.7 - - + +
6B THR 4.3 1.3 - - - -
7B GLY 3.0 29.9 + - - +
8B LEU 3.1 8.5 + - - -
11B VAL* 3.6 11.7 - - + -
12B GLY* 1.3 74.3 - - - +
14B SER* 1.3 56.7 + - - +
16B PHE* 3.2 1.4 + - - +
17B SER* 2.7 37.8 + - - -
74B ASP* 3.0 15.0 - - - +
75B ASP* 3.3 24.9 - - - +
76B THR* 3.4 26.2 + - - +
102B LEU* 3.7 16.8 - - + -
2002B ANP 2.7 44.9 + - - +
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Residues in contact with SER 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 LYS* 1.3 72.3 - - - +
15B THR* 1.3 64.9 + - - +
17B SER* 3.2 5.4 + - - -
18B LYS* 3.1 34.2 + - - +
74B ASP* 2.9 21.3 + - - -
2002B ANP 2.7 19.8 + - - -
2004B MG 2.1 27.9 - - - -
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Residues in contact with THR 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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12B GLY 4.0 0.2 - - - -
14B SER* 1.3 76.2 - - - +
16B PHE* 1.3 64.0 + - - +
18B LYS* 3.2 11.0 + - - +
19B ASN* 3.1 41.7 + - - +
2002B ANP 3.0 55.2 + - + +
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Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.0 26.0 - - + -
12B GLY 2.9 21.7 + - - +
13B LYS 3.5 2.9 - - - +
15B THR* 1.3 76.6 - - - +
17B SER* 1.3 60.2 + - - +
19B ASN* 3.3 1.1 + - - +
20B LEU* 2.8 54.7 + - + +
100B ILE* 4.1 9.0 - - + -
102B LEU* 3.8 16.4 - - + -
148B ILE* 3.5 33.0 - - + -
150B THR* 5.7 0.4 - - + -
154B ILE* 3.9 17.9 - - + -
156B PHE* 3.3 35.6 - + - -
159B ILE* 3.7 16.8 - - + -
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.2 16.8 - - - +
13B LYS 2.7 20.0 + - - -
14B SER* 3.3 11.0 - - - -
16B PHE* 1.3 81.3 - - - +
18B LYS* 1.3 53.2 + - - +
20B LEU* 3.7 2.5 - - - +
21B ALA* 2.7 38.6 + - - +
33B VAL* 3.7 25.4 - - - -
72B ILE* 3.9 14.1 - - - +
74B ASP* 3.4 12.1 - - - +
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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
----------------------------------------------------------
44A PRO* 5.1 0.2 - - - +
14B SER* 3.1 21.6 + - - +
15B THR* 3.6 10.1 - - - +
17B SER* 1.3 80.9 - - - +
19B ASN* 1.3 61.7 + - - +
21B ALA* 3.4 6.6 + - - +
22B LYS* 2.9 39.0 + - + +
33B VAL* 5.1 4.7 - - + -
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Residues in contact with ASN 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 THR* 3.1 33.6 + - - +
16B PHE 3.7 1.1 - - - +
18B LYS* 1.3 76.7 - - - +
20B LEU* 1.3 66.0 + - - +
22B LYS* 3.1 14.3 + - - +
23B ILE* 3.1 29.1 + - + +
156B PHE* 3.5 43.1 - - + -
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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
----------------------------------------------------------
3B ILE* 4.2 6.7 - - + -
16B PHE* 2.8 43.2 + - + +
17B SER 3.7 2.9 - - - +
19B ASN* 1.3 73.5 - - - +
21B ALA* 1.3 63.0 + - - +
23B ILE* 3.4 3.2 + - + +
24B LEU* 3.1 36.8 + - + +
72B ILE* 3.8 21.8 - - + -
100B ILE* 4.2 9.2 - - + -
156B PHE* 3.8 15.1 - - + +
159B ILE* 3.9 17.0 - - + -
160B ALA* 4.4 11.4 - - + +
163B LEU* 3.8 33.4 - - + -
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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
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44A PRO* 3.4 30.3 - - + +
17B SER 2.7 19.7 + - - +
18B LYS* 3.5 7.0 - - - +
20B LEU* 1.3 77.9 - - - +
22B LYS* 1.3 61.4 + - - +
24B LEU* 3.4 1.3 + - - -
25B SER 3.2 16.6 + - - -
31B VAL* 3.6 15.9 - - + +
33B VAL* 3.9 20.4 - - + -
72B ILE* 4.0 6.5 - - + +
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Residues in contact with LYS 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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44A PRO* 4.1 21.3 - - + +
45A VAL* 6.3 0.7 - - + -
18B LYS* 2.9 26.4 + - + +
19B ASN* 3.1 14.0 + - - +
21B ALA* 1.3 74.1 - - - +
23B ILE* 1.3 70.5 + - + +
25B SER* 3.3 6.7 + - - -
26B LYS* 3.3 25.9 + - - +
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Residues in contact with ILE 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 ASN* 3.1 16.2 + - + +
20B LEU* 3.9 4.3 - - - +
21B ALA 3.4 0.2 - - - -
22B LYS* 1.3 78.2 - - + +
24B LEU* 1.3 60.3 + - - +
26B LYS* 3.1 34.6 + - + +
27B ASN* 2.7 31.7 + - - +
156B PHE* 3.7 39.3 - - + +
157B ASN* 3.9 22.4 - - - +
160B ALA* 3.7 13.2 - - + -
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Residues in contact with LEU 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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3B ILE* 4.3 11.4 - - + -
20B LEU* 3.1 32.4 + - + +
21B ALA 3.7 4.5 - - - +
22B LYS 3.3 0.2 - - - -
23B ILE* 1.3 75.8 - - - +
25B SER* 1.3 63.4 + - - +
27B ASN* 3.0 16.0 + - - +
29B ILE* 3.2 35.6 + - + +
31B VAL* 3.9 27.1 - - + -
70B TRP* 3.8 37.9 - - + -
72B ILE* 4.3 1.6 - - + -
160B ALA* 4.0 29.8 - - + +
163B LEU* 4.9 1.8 - - + -
164B ILE* 4.6 2.2 - - + -
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Residues in contact with SER 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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44A PRO* 3.0 28.4 - - - +
45A VAL* 3.5 29.3 - - - +
21B ALA 3.2 8.0 + - - -
22B LYS* 3.4 11.7 - - - -
23B ILE 3.1 0.6 - - - -
24B LEU* 1.3 72.5 - - - +
26B LYS* 1.3 54.1 - - - +
27B ASN 2.8 5.1 + - - -
28B ASN* 2.8 27.0 + - - -
29B ILE 3.7 12.5 + - - -
31B VAL* 4.5 0.2 - - - +
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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 LYS* 3.3 13.9 + - - +
23B ILE* 3.1 31.9 + - + +
25B SER* 1.3 77.6 - - - +
27B ASN* 1.3 60.5 + - - +
28B ASN 3.3 2.7 + - - -
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Residues in contact with ASN 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 ILE* 2.7 37.6 + - - +
24B LEU* 3.0 10.5 + - - +
25B SER 2.8 1.4 + - - -
26B LYS* 1.3 82.6 - - - +
28B ASN* 1.3 69.9 + - - +
29B ILE* 3.1 10.1 + - + +
160B ALA* 4.4 8.7 - - - +
164B ILE* 3.9 27.2 - - + +
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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