Contacts of the strand formed by residues 16 - 31 (chain B) in PDB entry 5J0Z
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 LEU 16 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PRO* 5.9 0.2 - - + -
8B PRO* 4.0 15.3 - - + -
15B PRO* 1.3 69.9 - - - +
17B THR* 1.3 80.1 + - - +
18B VAL* 4.2 10.1 - - + -
47B TRP* 4.1 11.7 - - + -
48B LYS* 4.1 23.3 - - + +
72B TRP* 3.8 36.1 - - + -
138B ARG* 3.2 26.5 - - - +
139B ASN 3.2 13.5 + - - +
140B ILE* 3.5 9.5 - - + +
141B VAL* 2.9 30.4 + - - +
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Residues in contact with THR 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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15B PRO 3.7 5.0 + - - +
16B LEU* 1.3 90.0 - - - +
18B VAL* 1.3 59.6 + - - +
19B ASN* 4.3 14.1 + - - -
46B SER 4.2 1.2 - - - +
47B TRP* 4.0 8.5 - - - +
48B LYS 4.8 0.5 + - - -
141B VAL* 3.4 22.0 - - + -
143B ALA* 5.1 9.9 - - + -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.0 9.6 - - + +
17B THR* 1.3 75.5 - - - +
19B ASN* 1.3 63.7 + - - +
20B THR* 3.5 4.2 + - - +
45B LEU* 4.5 9.0 - - + -
46B SER 3.7 15.3 - - - +
47B TRP* 4.3 8.3 - - + -
74B PRO* 3.9 29.8 - - + -
76B ILE* 4.4 10.1 - - + -
140B ILE* 3.4 32.3 - - + -
141B VAL 2.8 12.7 + - - +
142B LEU* 3.4 12.4 - - + -
143B ALA 2.9 24.9 + - - +
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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
----------------------------------------------------------
17B THR* 4.3 18.2 + - - -
18B VAL* 1.3 75.2 + - - +
20B THR* 1.3 59.2 + - - +
44B SER* 3.3 8.5 + - - +
45B LEU* 3.4 1.5 - - - -
46B SER* 2.7 50.2 + - - +
143B ALA* 3.5 15.7 + - - +
144B VAL 4.5 2.3 - - - +
145B ASP* 4.0 30.9 - - + +
148B LYS* 5.0 1.4 - - - -
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Residues in contact with THR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL 3.7 13.7 - - - +
19B ASN* 1.3 73.6 - - - +
21B GLY* 1.3 58.3 + - - +
44B SER* 3.3 7.4 - - - -
45B LEU* 3.8 21.1 - - + -
76B ILE* 5.1 0.9 - - + -
130B LEU* 4.1 15.5 - - + -
142B LEU* 4.0 19.7 - - + -
143B ALA 2.8 18.8 + - - +
144B VAL* 3.6 1.0 - - - +
145B ASP* 2.9 30.1 + - - +
184B LEU* 3.0 18.4 - - + +
186B TYR* 2.8 19.8 + - - -
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Residues in contact with GLY 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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20B THR* 1.3 75.9 - - - +
22B ILE* 1.3 62.5 + - - -
23B TYR 4.1 0.2 + - - -
42B PHE 3.5 1.4 - - - +
43B LEU* 3.5 3.8 - - - +
44B SER* 2.8 46.2 + - - +
148B LYS* 3.3 21.0 - - - +
149B VAL* 3.9 6.5 - - - -
186B TYR* 3.5 5.4 + - - -
177C GLU* 4.5 0.3 - - - +
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Residues in contact with ILE 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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21B GLY* 1.3 76.6 - - - +
23B TYR* 1.3 60.9 - - - +
24B LEU* 4.0 14.6 - - + -
41B ALA* 3.9 18.4 - - + -
42B PHE 3.2 7.9 - - - +
43B LEU* 4.0 13.5 - - + -
78B PHE* 4.0 20.6 - - + -
106B PHE* 4.2 8.1 - - + -
128B ILE* 4.1 11.9 - - + -
130B LEU* 3.9 12.8 - - + -
148B LYS 3.5 3.0 + - - -
149B VAL* 3.6 2.6 - - - +
150B GLY 3.4 12.0 + - - -
165B PHE* 3.3 19.1 - - + -
186B TYR* 3.7 45.8 - - + -
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Residues in contact with TYR 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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21B GLY 4.1 0.8 + - - -
22B ILE* 1.3 71.9 - - - +
24B LEU* 1.3 64.0 + - - +
25B ILE* 3.5 11.9 + - + +
41B ALA* 3.3 3.5 - - - -
42B PHE* 2.9 44.9 + + + -
149B VAL 4.7 0.2 - - - -
150B GLY* 3.4 22.9 - - - +
151B LYS 3.3 30.2 + - - -
152B ASN* 2.7 31.3 + - - -
174C PHE* 5.4 3.6 - - - -
176C LEU* 3.4 41.2 - - + +
177C GLU* 3.8 23.3 - - + +
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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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22B ILE* 4.0 4.7 - - + -
23B TYR* 1.3 74.2 - - - +
25B ILE* 1.3 60.4 + - - +
26B GLU 4.8 1.3 - - - +
27B CYS* 3.9 26.7 - - - -
39B VAL* 3.4 28.0 - - + -
40B ASN 4.1 0.2 - - - -
41B ALA* 3.7 11.9 - - + -
128B ILE* 4.4 4.0 - - + -
150B GLY 3.2 5.8 + - - +
151B LYS* 3.4 15.4 - - + -
152B ASN 3.1 25.1 + - - -
155B VAL* 3.9 3.0 - - + +
165B PHE* 3.6 55.2 - - + -
188B LEU* 4.2 12.3 - - + -
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Residues in contact with ILE 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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23B TYR* 3.6 20.0 - - + +
24B LEU* 1.3 75.1 - - - +
26B GLU* 1.3 67.7 + - + +
40B ASN* 2.7 11.7 + - - +
41B ALA* 3.8 4.3 - - - -
42B PHE* 3.7 38.1 - - + +
105B ARG* 3.4 37.0 - - + +
152B ASN* 4.2 14.8 + - - +
154B ASP* 5.1 2.3 - - - +
155B VAL* 3.4 13.7 + - - +
79C VAL* 3.7 39.1 - - + +
176C LEU* 6.1 0.4 - - + -
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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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25B ILE* 1.3 91.9 - - + +
27B CYS* 1.3 63.8 + - - +
28B TYR* 3.8 14.5 - - + -
39B VAL* 3.4 6.8 - - - +
40B ASN* 2.8 52.0 + - + +
154B ASP* 5.5 4.9 - - - +
155B VAL* 4.0 6.7 - - - +
156B PHE* 5.5 5.5 - - - -
79C VAL* 3.8 11.5 - - - +
80C ASN* 3.0 37.5 - - - +
81C VAL 3.1 16.7 + - - +
111C LEU* 3.9 18.4 - - + +
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Residues in contact with CYS 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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24B LEU* 3.9 18.6 - - - -
26B GLU* 1.3 79.3 - - - +
28B TYR* 1.3 65.0 + - - +
37B PHE* 5.0 4.9 - - + -
38B LYS 3.5 6.7 - - - +
39B VAL* 4.6 4.7 - - + +
155B VAL* 3.5 28.1 - - + +
156B PHE 3.2 22.2 + - - +
157B LEU* 3.8 20.3 - - + +
162B ILE* 5.2 2.2 - - - -
188B LEU* 3.8 31.4 - - + -
111C LEU* 5.2 0.9 - - - +
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Residues in contact with TYR 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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26B GLU* 3.8 19.3 - - + -
27B CYS* 1.3 79.4 - - - +
29B SER* 1.3 74.9 + - - +
30B LEU 3.5 2.2 + - - -
37B PHE* 3.8 1.6 - - - +
38B LYS* 2.8 73.6 + - + +
39B VAL 4.4 5.8 + - - -
40B ASN* 4.2 9.1 - - + +
107B SER* 4.5 5.9 - - - -
156B PHE 5.1 1.8 - - - +
157B LEU* 3.7 9.1 - - - +
158B THR 6.0 0.7 - - - +
82C GLU* 3.2 66.8 + - + +
111C LEU* 3.5 26.7 - - + -
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Residues in contact with SER 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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28B TYR* 1.3 86.6 - - - +
30B LEU* 1.3 61.7 + - - +
31B ASP* 2.9 15.6 + - - +
36B THR* 3.6 1.4 + - - +
37B PHE* 3.3 13.5 + - - -
38B LYS* 3.8 21.2 - - - +
109B ARG* 4.9 2.1 + - - -
157B LEU* 4.4 1.2 - - - +
403B SO4 2.7 28.3 + - - -
82C GLU* 4.8 2.6 + - - -
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Residues in contact with LEU 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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28B TYR 3.5 2.8 - - - -
29B SER* 1.3 73.1 - - - +
31B ASP* 1.3 59.6 + - - +
32B ASP* 3.6 17.4 + - - +
36B THR 3.4 9.4 - - - +
37B PHE* 3.9 5.2 - - + -
114B LEU* 3.7 28.3 - - + -
126B LEU* 4.2 17.7 - - + -
157B LEU* 3.9 20.0 - - + +
158B THR 5.8 0.9 - - - +
160B TRP* 3.7 35.6 + - + +
190B ILE* 3.3 34.3 - - + -
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Residues in contact with ASP 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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29B SER* 2.9 8.0 + - - +
30B LEU* 1.3 70.4 - - - +
32B ASP* 1.3 52.2 + - - +
33B LYS* 3.2 12.1 + - - +
34B ALA* 3.1 27.2 + - - +
35B GLU* 2.7 32.9 + - - -
36B THR* 2.9 29.0 + - - +
109B ARG* 4.5 8.4 + - - +
402B SO4 5.0 1.9 + - - -
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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