Contacts of the strand formed by residues 16 - 31 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C PRO* 5.9 0.4 - - + -
8C PRO* 4.0 15.3 - - + -
15C PRO* 1.3 69.4 - - - +
17C THR* 1.3 82.3 + - - +
18C VAL* 4.2 7.6 - - + -
47C TRP* 4.1 6.3 - - + -
48C LYS* 4.1 31.6 - - + +
72C TRP* 3.8 35.4 - - + -
138C ARG* 3.2 26.8 - - - +
139C ASN 3.2 14.1 + - - +
140C ILE* 3.5 8.4 - - + +
141C VAL* 2.9 29.3 + - - +
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Residues in contact with THR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO 3.7 4.4 + - - -
16C LEU* 1.3 89.7 - - - +
18C VAL* 1.3 58.7 + - - +
19C ASN* 3.1 27.8 + - - +
46C SER 4.2 0.9 - - - +
47C TRP* 4.0 8.5 - - - +
48C LYS 4.7 0.3 + - - -
141C VAL* 3.4 21.3 - - - +
143C ALA* 4.3 14.0 - - + +
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Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 4.0 9.4 - - + +
17C THR* 1.3 76.5 - - - +
19C ASN* 1.3 62.9 + - - +
20C THR* 3.5 4.6 + - - +
45C LEU* 4.5 9.4 - - + -
46C SER 3.7 14.8 - - - +
47C TRP* 4.3 8.7 - - + -
74C PRO* 3.9 29.8 - - + -
76C ILE* 4.4 9.4 - - + -
140C ILE* 3.4 32.8 - - + -
141C VAL 2.7 12.7 + - - +
142C LEU* 3.4 12.2 - - + -
143C ALA 2.9 27.4 + - - +
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Residues in contact with ASN 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 3.1 33.3 + - - +
18C VAL* 1.3 71.2 + - - +
20C THR* 1.3 61.4 + - - +
44C SER* 3.3 7.6 + - - +
45C LEU* 3.4 2.0 - - - -
46C SER* 2.7 50.3 + - - +
143C ALA* 3.4 11.7 + - - +
144C VAL 4.5 2.1 - - - +
145C ASP* 4.0 30.3 + - + +
148C LYS* 5.0 1.2 - - - -
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Residues in contact with THR 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C VAL 3.7 13.5 - - - +
19C ASN* 1.3 71.6 - - - +
21C GLY* 1.3 59.0 + - - +
44C SER* 3.2 7.0 - - - -
45C LEU* 3.8 21.3 - - + -
76C ILE* 5.1 0.4 - - + -
130C LEU* 4.1 15.0 - - + -
142C LEU* 4.0 20.4 - - + -
143C ALA 2.8 19.2 + - - +
144C VAL* 3.6 1.0 - - - +
145C ASP* 2.9 30.5 + - - +
184C LEU* 3.0 17.9 - - + +
186C TYR* 2.8 20.2 + - - -
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C THR* 1.3 76.5 - - - +
22C ILE* 1.3 61.9 + - - -
23C TYR 4.1 0.2 + - - -
42C PHE 3.5 1.6 - - - +
43C LEU* 3.5 4.9 - - - +
44C SER* 2.8 46.4 + - - -
148C LYS* 3.3 22.2 - - - +
149C VAL* 3.9 6.5 - - - -
186C TYR* 3.6 4.7 - - - -
177D GLU* 4.7 0.5 - - - +
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY* 1.3 75.3 - - - +
23C TYR* 1.3 61.9 + - - +
24C LEU* 4.0 15.0 - - + -
41C ALA* 3.9 17.7 - - + -
42C PHE 3.2 8.1 - - - +
43C LEU* 4.0 13.9 - - + -
78C PHE* 4.0 20.0 - - + -
106C PHE* 4.2 8.1 - - + -
128C ILE* 4.1 11.9 - - + -
130C LEU* 3.9 12.6 - - + -
148C LYS 3.5 2.6 + - - -
149C VAL* 3.5 3.2 - - - +
150C GLY 3.4 12.0 + - - -
165C PHE* 3.3 18.9 - - + -
186C TYR* 3.6 47.1 - - + -
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Residues in contact with TYR 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY 4.1 0.8 + - - -
22C ILE* 1.3 70.8 - - - +
24C LEU* 1.3 64.7 + - - +
25C ILE* 3.5 11.5 + - + +
41C ALA* 3.3 3.4 - - - -
42C PHE* 2.9 43.9 + + + -
149C VAL 4.7 0.9 - - - -
150C GLY* 3.4 22.0 - - - +
151C LYS 3.3 30.4 + - - -
152C ASN* 2.7 30.5 + - - -
174D PHE* 6.0 1.2 - - - -
176D LEU* 3.4 41.3 - - + +
177D GLU* 3.3 25.4 - - + +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 4.0 5.4 - - + -
23C TYR* 1.3 73.9 - - - +
25C ILE* 1.3 61.0 + - - +
26C GLU 4.8 0.7 - - - +
27C CYS* 3.9 27.4 - - - -
39C VAL* 3.4 28.0 - - + -
40C ASN 4.1 0.2 - - - -
41C ALA* 3.7 10.8 - - + -
128C ILE* 4.4 4.7 - - + -
150C GLY 3.2 5.4 + - - +
151C LYS* 3.4 14.9 - - + -
152C ASN 3.1 24.6 + - - -
155C VAL* 3.9 2.9 - - + +
165C PHE* 3.6 54.1 - - + -
188C LEU* 4.2 12.6 - - + -
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Residues in contact with ILE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 3.6 20.0 - - + +
24C LEU* 1.3 73.7 - - - +
26C GLU* 1.3 68.3 + - + +
40C ASN* 2.8 11.3 + - - +
41C ALA* 3.8 4.5 - - - -
42C PHE* 3.6 38.6 - - + +
105C ARG* 3.4 48.0 - - + +
152C ASN* 4.2 15.9 + - - +
154C ASP* 5.1 2.3 - - - +
155C VAL* 3.4 14.4 + - - +
79D VAL* 4.0 24.9 - - + +
176D LEU* 5.9 1.1 - - + -
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 5.2 0.2 - - - -
25C ILE* 1.3 90.6 + - + +
27C CYS* 1.3 63.8 + - - +
28C TYR* 3.8 13.6 - - + -
39C VAL* 3.4 8.0 - - - +
40C ASN* 2.8 53.5 + - + +
154C ASP* 5.5 4.7 - - - +
155C VAL* 4.0 6.7 - - - +
156C PHE* 5.5 6.1 - - - -
79D VAL* 3.8 12.1 - - - +
80D ASN* 3.0 42.2 - - - +
81D VAL 3.3 8.2 + - - +
111D LEU* 4.0 18.1 - - + +
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Residues in contact with CYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 3.9 18.4 - - - -
26C GLU* 1.3 78.8 - - - +
28C TYR* 1.3 63.5 + - - +
37C PHE* 5.0 4.9 - - + -
38C LYS 3.5 7.4 - - - +
39C VAL* 4.6 4.9 - - - +
155C VAL* 3.6 28.7 - - + +
156C PHE 3.2 22.3 + - - +
157C LEU* 3.8 20.1 - - + +
162C ILE* 5.2 2.5 - - - -
188C LEU* 3.8 31.2 - - + -
111D LEU* 5.2 0.7 - - - +
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Residues in contact with TYR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C GLU* 3.8 20.4 - - + -
27C CYS* 1.3 79.8 - - - +
29C SER* 1.3 70.7 + - - +
30C LEU 3.5 2.4 + - - -
37C PHE* 3.8 1.9 - - - +
38C LYS* 2.8 76.6 + - + +
39C VAL 4.3 6.3 + - - -
40C ASN* 4.2 8.6 - - + +
107C SER* 4.5 5.9 - - - -
156C PHE 5.1 1.6 - - - +
157C LEU* 3.7 9.1 - - - +
158C THR 6.0 0.7 - - - +
82D GLU* 3.2 66.3 + - + +
111D LEU* 3.4 26.7 - - + -
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Residues in contact with SER 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C TYR* 1.3 83.9 - - - +
30C LEU* 1.3 63.3 + - - +
31C ASP* 2.9 14.1 + - - +
36C THR* 3.6 1.7 + - - +
37C PHE* 3.3 14.0 - - - -
38C LYS* 3.8 16.4 + - - +
157C LEU* 4.4 1.2 - - - +
401C SO4 3.1 35.8 + - - -
82D GLU* 4.7 1.6 + - - -
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C TYR 3.5 2.4 - - - -
29C SER* 1.3 73.5 - - - +
31C ASP* 1.3 59.8 + - - +
32C ASP* 3.6 17.5 + - - +
36C THR 3.4 11.2 - - - +
37C PHE* 3.9 4.9 - - + -
114C LEU* 3.7 28.3 - - + -
126C LEU* 4.1 18.4 - - + -
157C LEU* 3.9 20.0 - - + +
158C THR 5.8 0.7 - - - +
160C TRP* 3.7 36.4 + - + +
190C ILE* 3.3 33.4 - - + -
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Residues in contact with ASP 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B SO4 5.1 2.9 + - - -
29C SER* 2.9 7.2 + - - +
30C LEU* 1.3 71.8 - - - +
32C ASP* 1.3 53.1 + - - +
33C LYS* 3.2 12.5 + - - +
34C ALA* 3.1 27.3 + - - +
35C GLU* 2.7 32.7 + - - -
36C THR* 2.9 28.4 + - - +
109C 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