Contacts of the helix formed by residues 15 - 32 (chain B) in PDB entry 1J3H
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 VAL 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLN* 3.9 18.1 - - + +
13B GLU 2.7 1.4 + - - +
14B SER* 1.3 77.2 - - - +
16B LYS* 1.3 61.9 + - - +
17B GLU 2.9 5.2 + - - -
18B PHE* 3.0 12.1 + - - +
19B LEU* 3.1 19.2 + - - +
155B GLU* 5.4 4.7 - - - +
292B LYS* 6.1 2.2 - - - +
352B MPD 3.9 28.4 + - + +
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Residues in contact with LYS 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 GLN 5.0 0.2 + - - -
13B GLU* 2.9 14.1 + - + +
15B VAL* 1.3 77.9 - - - +
17B GLU* 1.3 55.5 + - - +
19B LEU* 4.1 11.2 - - - +
20B ALA* 3.5 23.2 + - - +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU 3.2 11.4 + - - +
14B SER* 4.1 11.4 - - - +
15B VAL 2.9 0.6 - - - -
16B LYS* 1.3 77.3 - - - +
18B PHE* 1.3 62.1 + - - +
19B LEU 3.3 1.3 - - - -
20B ALA* 4.1 5.9 - - - +
21B LYS* 3.5 20.8 + - - +
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Residues in contact with PHE 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 SER 3.4 18.0 + - - +
15B VAL 3.0 4.8 + - - +
17B GLU* 1.3 78.4 - - - +
19B LEU* 1.3 75.4 + - + +
21B LYS* 3.6 6.6 + - + +
22B ALA* 3.2 26.9 + - + +
99B ASN 5.8 1.8 - - - -
100B PHE* 4.2 17.0 - + - -
156B TYR* 4.7 5.4 - + - -
306B TYR* 3.3 31.2 - + - -
352B MPD 3.8 48.5 - - + -
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Residues in contact with LEU 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 VAL 3.1 17.6 + - - +
16B LYS* 4.2 9.4 - - - +
18B PHE* 1.3 92.3 - - + +
20B ALA* 1.3 53.8 + - - +
21B LYS 3.1 0.2 - - - -
22B ALA* 2.9 6.7 + - + +
23B LYS* 2.8 35.7 + - - +
155B GLU* 4.3 28.5 - - + +
156B TYR* 4.5 12.3 - - + -
159B SER* 3.5 39.8 + - - +
352B MPD 5.1 4.9 - - + +
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Residues in contact with ALA 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 LYS 3.5 17.1 + - - +
17B GLU* 4.4 5.6 - - - +
18B PHE 3.6 0.2 - - - -
19B LEU* 1.3 77.9 - - - +
21B LYS* 1.3 60.4 + - - +
23B LYS* 3.6 9.5 + - - +
24B GLU* 3.3 19.8 + - - +
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Residues in contact with LYS 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 GLU 3.5 17.8 + - - +
18B PHE* 3.6 7.6 - - + +
19B LEU 3.1 0.2 - - - -
20B ALA* 1.3 77.4 - - - +
22B ALA* 1.3 58.8 + - - +
24B GLU* 3.1 14.6 + - - +
25B ASP* 3.0 25.6 + - - +
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Residues in contact with ALA 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 PHE* 3.2 19.8 + - + +
19B LEU* 2.9 12.9 + - + +
21B LYS* 1.3 77.2 - - - +
23B LYS* 1.3 58.6 + - - +
24B GLU 3.2 0.2 - - - -
25B ASP* 3.6 9.0 - - - +
26B PHE* 3.0 30.1 + - - +
156B TYR* 3.9 30.4 + - + +
159B SER* 5.7 0.4 - - - +
160B LEU* 3.9 5.0 - - + +
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Residues in contact with LYS 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 LEU 2.8 14.8 + - - +
20B ALA* 3.7 11.4 - - - +
21B LYS 3.2 0.2 - - - -
22B ALA* 1.3 76.9 - - - +
24B GLU* 1.3 57.9 + - - +
26B PHE* 3.8 1.3 - - - +
27B LEU* 3.1 62.7 + - + +
159B SER* 3.4 26.5 + - - +
160B LEU* 3.9 16.4 - - + +
161B ASP* 3.4 22.2 + - - -
190B ARG* 4.0 15.7 - - - +
192B LYS* 5.9 1.0 - - - +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA 3.3 9.5 + - - +
21B LYS* 3.1 13.5 + - - +
23B LYS* 1.3 79.4 - - - +
25B ASP* 1.3 65.1 + - - +
27B LEU* 4.3 5.0 - - - +
28B LYS* 3.3 37.1 + - - +
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Residues in contact with ASP 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 LYS 3.0 13.0 + - - +
22B ALA* 3.7 12.3 - - - +
23B LYS 3.3 0.4 - - - -
24B GLU* 1.3 78.6 - - - +
26B PHE* 1.3 63.2 + - - +
28B LYS* 3.3 12.1 + - - +
29B LYS* 3.2 20.2 + - - +
97B ALA 5.0 2.0 - - - +
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA 3.0 17.6 + - - +
23B LYS* 3.8 1.6 - - + +
25B ASP* 1.3 77.0 - - - +
27B LEU* 1.3 62.3 + - + +
29B LYS* 3.0 5.9 + - - +
30B TRP* 2.6 71.5 + + - +
94B ILE* 4.7 3.6 - - - -
97B ALA* 3.4 46.1 + - + +
98B VAL* 4.1 3.4 - - + -
156B TYR* 5.0 1.8 - - - +
160B LEU* 3.8 31.9 - - + -
162B LEU* 4.2 20.0 - - + -
190B ARG* 3.8 37.0 - - - -
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Residues in contact with LEU 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 LYS* 3.1 39.0 + - + +
24B GLU* 4.3 5.4 - - - +
26B PHE* 1.3 86.5 - - + +
28B LYS* 1.3 54.3 + - - +
30B TRP* 3.4 11.0 - - + +
31B GLU* 2.6 38.2 + - - +
190B ARG* 3.7 31.6 - - - +
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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
----------------------------------------------------------
24B GLU* 3.3 28.2 + - - +
25B ASP* 3.3 14.9 + - - +
27B LEU* 1.3 77.6 - - - +
29B LYS* 1.3 61.4 + - - +
31B GLU* 3.5 3.3 + - - +
32B THR* 3.3 34.6 + - + +
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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 ASP 3.2 8.2 + - - +
26B PHE 3.0 7.4 + - - +
28B LYS* 1.3 79.2 - - - +
30B TRP* 1.3 56.8 + - - +
32B THR 4.2 4.9 - - - -
33B PRO* 3.0 18.5 - - - +
96B GLN* 2.7 33.7 - - - +
97B ALA* 3.7 21.3 - - - +
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Residues in contact with TRP 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 PHE* 2.6 50.9 + + + +
27B LEU* 3.4 17.3 - - + +
29B LYS* 1.3 72.9 - - - +
31B GLU* 1.3 60.0 + - - +
33B PRO* 3.6 4.0 - - - +
90B ASN* 4.7 8.5 - - - -
93B ARG* 2.7 98.8 + - + +
94B ILE* 3.8 28.7 - - + -
96B GLN* 5.0 1.6 - - - +
97B ALA* 3.9 3.3 - - + +
190B ARG* 3.5 49.8 - - + +
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Residues in contact with GLU 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 LEU 2.6 20.4 + - - +
28B LYS* 3.9 5.6 - - - +
30B TRP* 1.3 75.3 - - - +
32B THR* 1.3 71.4 + - + +
33B PRO* 3.4 5.4 - - - +
93B ARG* 4.6 5.3 + - - +
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Residues in contact with THR 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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28B LYS* 3.3 22.9 + - + +
29B LYS* 3.4 7.9 - - - +
31B GLU* 1.3 93.1 - - + +
33B PRO* 1.3 65.9 + - - +
34B SER 3.8 0.7 + - - -
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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