Contacts of the strand formed by residues 36 - 48 (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 THR 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B SER 4.2 0.2 + - - -
30B LEU* 3.4 7.1 - - - +
31B ASP* 2.9 31.6 + - - +
34B ALA* 3.3 23.1 - - + +
35B GLU* 1.3 82.7 - - - +
37B PHE* 1.3 68.3 + - - +
82B GLU* 3.5 23.8 - - - +
109B ARG* 2.5 36.8 + - - +
110B VAL 3.2 15.0 - - - +
111B LEU* 4.4 3.8 - - + +
112B SER 4.7 2.0 - - - +
114B LEU* 5.1 2.2 - - - +
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Residues in contact with PHE 37 (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 CYS* 5.0 5.8 - - + -
28B TYR 4.1 3.4 - - - +
29B SER 3.3 9.0 - - - -
30B LEU* 3.9 19.5 - - + +
36B THR* 1.3 83.7 - - - +
38B LYS* 1.3 72.9 + - - +
39B VAL* 4.0 23.1 + - + -
109B ARG* 4.6 0.9 - - - -
110B VAL* 2.9 65.1 + - + +
112B SER* 4.4 6.1 - - - -
126B LEU* 3.7 50.7 - - + -
127B HIS 4.7 0.4 - - - -
128B ILE* 4.1 14.1 - - + -
157B LEU* 5.2 2.2 - - + -
188B LEU* 4.4 13.5 - - + -
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B CYS* 3.5 2.9 - - - -
28B TYR* 2.8 74.2 + - + +
29B SER* 3.8 19.9 + - - +
37B PHE* 1.3 79.0 - - - +
39B VAL* 1.3 60.7 + - - +
83B ASN* 5.1 3.2 + - - -
108B ALA 3.5 5.6 - - - +
109B ARG* 3.7 47.4 - - + +
403B SO4 3.8 25.7 + - - +
82C GLU* 5.0 1.1 - - - +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.4 33.2 - - + -
26B GLU 3.4 10.3 - - - +
27B CYS* 4.8 4.3 - - - -
28B TYR* 4.4 4.2 + - - -
37B PHE* 4.0 14.8 - - + -
38B LYS* 1.3 74.2 - - - +
40B ASN* 1.3 64.9 + - - +
41B ALA* 4.4 3.8 - - + -
106B PHE* 3.8 25.8 - - + -
107B SER* 3.1 5.2 - - - -
108B ALA 3.0 39.4 + - - +
110B VAL* 4.0 15.9 - - + -
128B ILE* 4.3 11.4 - - + -
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Residues in contact with ASN 40 (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* 4.1 0.2 - - - -
25B ILE* 2.7 31.5 + - - +
26B GLU* 2.8 35.6 + - + +
28B TYR* 4.2 5.6 - - + -
39B VAL* 1.3 76.0 - - - +
41B ALA* 1.3 55.1 + - - +
105B ARG* 3.1 37.9 + - - +
106B PHE 3.3 12.5 - - - +
107B SER* 3.9 13.3 - - - -
81C VAL* 2.9 27.5 + - - +
82C GLU 4.1 6.3 + - - -
84C ALA* 5.5 4.8 - - - +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.9 9.9 - - + -
23B TYR 3.3 15.9 - - - +
24B LEU* 3.7 16.2 - - + -
25B ILE* 3.8 9.0 - - - -
39B VAL* 4.3 1.3 - - + -
40B ASN* 1.3 76.9 + - - +
42B PHE* 1.3 57.9 + - - +
105B ARG* 3.4 1.0 - - - +
106B PHE* 2.8 63.0 + - + +
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Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 3.5 0.5 - - - +
22B ILE* 3.2 9.4 - - - +
23B TYR* 2.9 52.5 + + + +
25B ILE* 3.7 9.8 - - + +
41B ALA* 1.3 71.4 - - - +
43B LEU* 1.3 59.2 + - - +
44B SER 4.0 0.2 - - - -
90B VAL* 4.5 1.1 - - + -
103B LEU* 3.9 30.5 - - + -
104B GLU 3.3 8.3 - - - +
105B ARG* 3.6 32.1 - - + -
106B PHE* 4.2 0.9 - - - -
77C ARG* 3.3 31.6 - - - -
133C ARG* 4.8 3.6 - - - -
176C LEU* 3.9 24.9 - - + -
177C GLU* 4.0 18.6 - - - +
181C GLU* 3.6 14.4 - - - -
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Residues in contact with LEU 43 (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 3.5 9.0 - - - +
22B ILE* 4.0 8.7 - - + -
41B ALA 3.8 2.6 + - - -
42B PHE* 1.3 71.5 - - - +
44B SER* 1.3 63.6 + - - +
45B LEU* 4.2 23.7 + - + -
76B ILE* 4.2 16.4 - - + -
78B PHE* 4.7 4.7 - - + -
85B ARG* 4.1 17.5 - - - +
102B TYR* 4.3 1.2 - - - +
103B LEU* 3.6 2.4 - - - +
104B GLU* 2.8 65.6 + - + +
106B PHE* 3.9 11.4 - - + -
130B LEU* 4.0 30.1 - - + -
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Residues in contact with SER 44 (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 3.3 2.1 - - - +
20B THR* 3.3 5.4 - - - -
21B GLY* 2.8 46.5 + - - -
42B PHE 5.4 0.2 - - - -
43B LEU* 1.3 73.7 - - - +
45B LEU* 1.3 63.6 + - - +
102B TYR 3.4 6.5 - - - -
103B LEU* 3.5 19.3 - - - -
148B LYS* 3.2 35.3 - - - +
177C GLU* 3.9 6.7 + - - -
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Residues in contact with LEU 45 (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 VAL* 4.5 4.9 - - + -
19B ASN 3.4 3.6 - - - -
20B THR* 3.8 26.2 - - + -
43B LEU* 4.3 16.2 - - + -
44B SER* 1.3 77.1 - - - +
46B SER* 1.3 63.5 + - - +
47B TRP* 4.1 8.3 - - + -
73B ILE* 5.1 2.7 - - + -
74B PRO* 4.9 9.2 - - + +
76B ILE* 3.5 45.5 - - + -
85B ARG* 5.6 1.3 - - - +
101B GLN* 3.7 3.3 + - - -
102B TYR* 2.8 70.9 + - + +
148B LYS* 5.1 1.1 - - - -
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Residues in contact with SER 46 (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 THR 4.2 1.0 - - - +
18B VAL* 3.7 1.1 - - - +
19B ASN* 2.7 52.6 + - - +
45B LEU* 1.3 78.1 - - - +
47B TRP* 1.3 63.7 + - - +
99B THR* 4.4 9.2 - - - +
100B VAL 3.0 18.0 + - - -
101B GLN* 3.0 21.6 + - - -
145B ASP* 5.1 5.3 + - - -
148B LYS* 5.2 1.8 - - - -
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Residues in contact with TRP 47 (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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8B PRO* 4.6 0.2 - - + -
16B LEU* 4.1 10.5 - - + -
17B THR 4.0 15.7 - - - +
18B VAL* 4.3 9.6 - - + -
45B LEU* 4.1 7.2 - - + -
46B SER* 1.3 82.9 - - - +
48B LYS* 1.3 62.8 + - - +
49B ASP* 4.0 17.5 + - + +
71B ILE* 3.7 6.3 - - + -
72B TRP* 3.2 49.4 + + - -
73B ILE* 3.7 15.5 - - + -
74B PRO* 3.6 29.8 - - + -
92B ILE* 5.5 0.2 - - + -
99B THR* 3.4 6.4 - - - +
100B VAL* 2.7 71.7 + - + +
102B TYR* 3.6 27.6 - + + -
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Residues in contact with LYS 48 (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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8B PRO* 3.7 16.3 - - - +
14B GLU* 6.0 0.4 - - - -
16B LEU* 4.1 14.3 - - + +
17B THR 4.8 0.6 + - - -
47B TRP* 1.3 75.7 - - - +
49B ASP* 1.3 59.4 + - - +
50B ARG* 3.5 46.5 + - + +
97B ASP* 4.5 13.2 - - - +
98B GLY 3.6 4.9 - - - +
99B THR* 4.1 19.7 - - + +
138B ARG* 5.0 1.7 + - - -
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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