Contacts of the strand formed by residues 16 - 31 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D PRO* 5.9 0.4 - - + -
8D PRO* 4.0 14.4 - - + -
15D PRO* 1.3 70.5 - - - +
17D THR* 1.3 80.1 + - - +
18D VAL* 4.3 7.4 - - + -
47D TRP* 4.1 7.2 - - + -
48D LYS* 4.1 30.7 - - + +
72D TRP* 3.8 35.2 - - + -
138D ARG* 3.2 26.5 - - - +
139D ASN 3.2 14.1 + - - +
140D ILE* 3.5 9.1 - - + +
141D VAL* 2.9 30.4 + - - +
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Residues in contact with THR 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PRO 3.8 3.9 + - - -
16D LEU* 1.3 88.9 - - - +
18D VAL* 1.3 57.9 + - - +
19D ASN* 3.1 27.8 - - - +
46D SER 4.2 1.2 - - - +
47D TRP* 4.0 8.1 - - - +
48D LYS 4.8 0.3 + - - -
141D VAL* 3.4 21.1 - - - +
143D ALA* 4.3 13.7 - - + +
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Residues in contact with VAL 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 4.0 10.1 - - + +
17D THR* 1.3 75.6 - - - +
19D ASN* 1.3 64.0 + - - +
20D THR* 3.5 4.2 + - - +
45D LEU* 4.5 8.7 - - + -
46D SER 3.7 15.7 - - - +
47D TRP* 4.3 8.5 - - + -
74D PRO* 3.9 31.2 - - + -
76D ILE* 4.4 9.6 - - + -
140D ILE* 3.4 31.9 - - + -
141D VAL 2.8 12.3 + - - +
142D LEU* 3.4 13.9 - - + -
143D ALA 2.9 27.0 + - - +
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Residues in contact with ASN 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D THR* 3.1 33.3 - - - +
18D VAL* 1.3 70.5 + - - +
20D THR* 1.3 60.3 + - - +
44D SER* 3.3 8.0 + - - +
45D LEU* 3.4 2.1 - - - -
46D SER* 2.7 50.3 + - - +
143D ALA* 3.5 13.1 + - - +
144D VAL 4.5 2.4 - - - +
145D ASP* 4.0 31.6 + - + +
148D LYS* 5.0 1.2 - - - -
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Residues in contact with THR 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D VAL 3.7 13.5 - - - +
19D ASN* 1.3 72.2 - - - +
21D GLY* 1.3 58.4 + - - +
43D LEU* 5.2 0.2 - - - -
44D SER* 3.3 7.2 - - - -
45D LEU* 3.8 21.1 - - + -
76D ILE* 5.1 0.4 - - + -
130D LEU* 4.1 16.2 - - + -
142D LEU* 4.0 19.7 - - + -
143D ALA 2.8 17.8 + - - +
144D VAL* 3.6 0.7 - - - +
145D ASP* 2.8 30.6 + - - -
184D LEU* 3.0 18.2 - - + +
186D TYR* 2.8 19.4 + - - -
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Residues in contact with GLY 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D THR* 1.3 75.8 - - - +
22D ILE* 1.3 62.2 + - - -
23D TYR 4.1 0.2 + - - -
42D PHE 3.5 1.7 - - - +
43D LEU* 3.5 4.4 - - - +
44D SER* 2.8 46.3 + - - -
148D LYS* 3.2 22.6 - - - +
149D VAL* 3.9 6.7 - - - -
186D TYR* 3.5 5.6 + - - -
177E GLU* 4.7 0.2 - - - +
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Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D GLY* 1.3 75.3 - - - +
23D TYR* 1.3 62.4 + - - +
24D LEU* 4.0 14.8 - - + -
41D ALA* 3.9 17.9 - - + -
42D PHE 3.2 8.1 - - - +
43D LEU* 4.0 13.9 - - + -
78D PHE* 4.0 20.4 - - + -
106D PHE* 4.2 7.9 - - + -
128D ILE* 4.1 11.9 - - + -
130D LEU* 3.9 12.8 - - + -
148D LYS 3.4 2.5 + - - -
149D VAL* 3.6 3.4 - - - +
150D GLY 3.4 11.8 + - - -
165D PHE* 3.3 19.4 - - + -
186D TYR* 3.7 47.5 - - + -
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Residues in contact with TYR 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D GLY 4.1 0.8 + - - -
22D ILE* 1.3 71.0 - - - +
24D LEU* 1.3 67.0 + - - +
25D ILE* 3.4 10.5 + - + +
41D ALA* 3.3 3.8 - - - -
42D PHE* 2.9 42.7 + + + -
149D VAL 4.7 0.9 - - - -
150D GLY* 3.4 22.0 - - - +
151D LYS 3.3 30.3 + - - -
152D ASN* 2.7 30.5 + - - -
176E LEU* 3.3 42.2 - - + +
177E GLU* 3.3 24.9 - - + +
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Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 4.0 5.2 - - + -
23D TYR* 1.3 75.7 - - - +
25D ILE* 1.3 60.7 + - - +
26D GLU 4.8 0.7 - - - +
27D CYS* 3.9 27.1 - - - -
39D VAL* 3.4 29.4 - - + -
40D ASN 4.1 0.2 - - - -
41D ALA* 3.7 10.8 - - + -
128D ILE* 4.4 4.3 - - + -
150D GLY 3.2 5.8 + - - +
151D LYS* 3.4 15.6 - - + -
152D ASN 3.1 24.6 + - - -
155D VAL* 3.9 2.6 - - + +
165D PHE* 3.6 55.0 - - + -
188D LEU* 4.2 12.3 - - + -
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Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D TYR* 3.6 18.2 - - + +
24D LEU* 1.3 74.6 - - - +
26D GLU* 1.3 64.5 + - + +
40D ASN* 2.8 13.8 + - - +
41D ALA* 3.8 4.9 - - - -
42D PHE* 3.6 32.5 - - + +
105D ARG* 3.4 46.4 - - + +
152D ASN* 4.2 15.4 + - - +
154D ASP* 5.2 1.9 - - - +
155D VAL* 3.4 14.5 + - - +
79E VAL* 4.1 23.8 - - + +
403E ACT 4.1 20.9 - - + -
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Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 5.2 0.2 - - - -
25D ILE* 1.3 92.7 + - + +
27D CYS* 1.3 62.8 + - - +
28D TYR* 3.8 13.5 - - + -
39D VAL* 3.4 7.8 - - - +
40D ASN* 2.8 55.1 + - + +
154D ASP* 5.5 4.7 - - - +
155D VAL* 4.0 7.4 - - - +
156D PHE* 5.6 6.1 - - - -
79E VAL* 3.9 12.4 - - - +
80E ASN* 3.1 41.8 - - - +
81E VAL 3.3 6.1 + - - +
111E LEU* 4.2 17.5 - - + +
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Residues in contact with CYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 3.9 19.1 - - - -
26D GLU* 1.3 78.2 - - - +
28D TYR* 1.3 64.1 + - - +
37D PHE* 5.0 4.5 - - + -
38D LYS 3.5 8.1 - - - +
39D VAL* 4.5 4.9 - - + +
155D VAL* 3.5 28.7 - - + +
156D PHE 3.2 22.0 + - - +
157D LEU* 3.8 20.1 - - + +
162D ILE* 5.2 2.7 - - - -
188D LEU* 3.8 30.3 - - + -
111E LEU* 5.4 0.2 - - - +
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Residues in contact with TYR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLU* 3.8 25.4 - - + -
27D CYS* 1.3 78.9 - - - +
29D SER* 1.3 75.1 + - - +
30D LEU 3.5 1.5 + - - -
37D PHE* 3.8 1.7 - - - +
38D LYS* 2.8 75.1 + - + +
39D VAL 4.3 6.5 + - - -
40D ASN* 4.2 9.0 - - + +
107D SER* 4.5 6.4 - - - -
156D PHE 5.1 1.8 - - - +
157D LEU* 3.7 10.2 - - - +
158D THR 6.0 0.2 - - - +
82E GLU* 3.4 65.3 + - + +
111E LEU* 3.5 23.3 - - + -
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Residues in contact with SER 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D TYR* 1.3 86.9 - - - +
30D LEU* 1.3 62.9 + - - +
31D ASP* 2.9 15.1 + - - +
36D THR* 3.6 1.9 + - - +
37D PHE* 3.3 13.3 - - - -
38D LYS* 4.1 16.9 - - - +
157D LEU* 4.4 1.2 - - - +
82E GLU* 4.8 2.3 + - - -
402E SO4 3.6 31.3 + - - -
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D TYR 3.5 2.8 - - - -
29D SER* 1.3 73.9 - - - +
31D ASP* 1.3 58.8 + - - +
32D ASP* 3.6 30.7 + - - +
36D THR 3.4 10.8 - - - +
37D PHE* 3.9 5.2 - - + -
114D LEU* 3.7 18.2 - - + -
126D LEU* 4.2 18.4 - - + -
157D LEU* 3.9 19.3 - - + +
158D THR 5.8 1.1 - - - +
160D TRP* 3.7 28.2 + - + +
190D ILE* 3.3 34.1 - - + -
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Residues in contact with ASP 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D SER* 2.9 7.4 + - - +
30D LEU* 1.3 71.2 - - - +
32D ASP* 1.3 53.2 + - - +
33D LYS* 3.2 12.4 + - - +
34D ALA* 3.1 28.0 + - + +
35D GLU 2.7 31.9 + - - -
36D THR* 2.9 29.3 + - - +
109D ARG* 4.3 5.9 + - - +
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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