Contacts of the strand formed by residues 36 - 48 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E SER 4.2 1.4 + - - -
30E LEU* 3.4 6.9 - - - +
31E ASP* 2.9 34.6 + - - +
34E ALA* 3.3 23.6 - - + +
35E GLU* 1.3 82.6 - - - +
37E PHE* 1.3 70.4 + - - +
38E LYS* 6.1 0.2 - - - -
82E GLU* 3.5 24.7 - - - +
109E ARG* 3.4 26.9 + - - +
110E VAL 3.2 15.0 - - - +
111E LEU* 4.1 3.4 - - + +
112E SER 4.2 2.4 + - - +
114E LEU* 5.1 1.6 - - - +
126E LEU* 6.2 0.2 - - - -
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Residues in contact with PHE 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E CYS* 5.0 6.7 - - + -
28E TYR 4.1 3.4 - - - +
29E SER 3.3 9.2 - - - -
30E LEU* 3.9 19.1 - - + -
36E THR* 1.3 83.4 - - - +
38E LYS* 1.3 71.3 + - - +
39E VAL* 4.0 22.7 - - + -
109E ARG* 4.6 1.3 - - - -
110E VAL* 2.9 64.1 + - + +
112E SER* 4.4 6.5 - - - -
126E LEU* 3.7 50.5 - - + -
127E HIS 4.7 0.4 - - - -
128E ILE* 4.1 14.1 - - + -
157E LEU* 5.2 3.1 - - + -
188E LEU* 4.4 12.8 - - + -
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Residues in contact with LYS 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 4.9 1.6 - - - +
406A SO4 4.0 18.6 - - - +
27E CYS* 3.5 2.8 - - - -
28E TYR* 2.8 72.5 + - + +
29E SER* 3.8 21.9 + - - +
36E THR* 6.1 0.4 - - - -
37E PHE* 1.3 78.1 - - - +
39E VAL* 1.3 61.5 + - - +
83E ASN* 5.1 3.4 + - - -
108E ALA 3.5 6.1 - - - +
109E ARG* 3.7 44.6 - - + +
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Residues in contact with VAL 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E LEU* 3.4 33.0 - - + -
26E GLU 3.3 10.8 - - - +
27E CYS* 4.8 4.9 - - - -
28E TYR* 4.3 4.2 + - - -
37E PHE* 4.0 14.8 - - + -
38E LYS* 1.3 76.5 - - - +
40E ASN* 1.3 64.3 + - - +
41E ALA* 4.4 4.0 - - + -
106E PHE* 3.9 26.2 - - + -
107E SER* 3.1 5.7 - - - -
108E ALA 3.0 38.7 + - - +
110E VAL* 4.0 16.4 - - + -
128E ILE* 4.3 9.9 - - + -
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Residues in contact with ASN 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A VAL* 2.9 27.7 + - - +
82A GLU* 4.1 5.9 + - - +
84A ALA* 5.6 4.2 - - - +
24E LEU* 4.1 0.2 - - - -
25E ILE* 2.8 30.7 + - - +
26E GLU* 2.8 35.3 + - + +
28E TYR* 4.2 5.2 - - + -
39E VAL* 1.3 76.6 - - - +
41E ALA* 1.3 55.8 + - - +
105E ARG* 3.1 38.5 + - - +
106E PHE 3.3 12.8 - - - +
107E SER* 3.9 13.7 - - - -
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Residues in contact with ALA 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ILE* 3.9 9.6 - - + -
23E TYR 3.3 17.5 - - - +
24E LEU* 3.7 15.9 - - + -
25E ILE* 3.7 8.7 - - - -
39E VAL* 4.3 1.3 - - + -
40E ASN* 1.3 77.1 + - - +
42E PHE* 1.3 56.9 + - - +
105E ARG* 3.5 1.1 - - - -
106E PHE* 2.8 63.0 + - + +
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Residues in contact with PHE 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ARG* 3.6 12.8 - - - -
133A ARG* 4.3 6.7 - - - -
176A LEU* 3.8 21.5 - - + -
177A GLU* 4.7 9.0 - - - +
181A GLU* 3.7 8.3 - - - -
407A ACT 3.1 40.4 - - - -
21E GLY 3.5 0.3 - - - +
22E ILE* 3.2 9.5 - - - +
23E TYR* 2.9 55.7 + + + +
25E ILE* 3.6 3.5 - - + +
41E ALA* 1.3 70.7 - - - +
43E LEU* 1.3 58.7 + - - +
44E SER 4.0 0.4 - - - +
90E VAL* 4.5 2.7 - - + -
103E LEU* 3.9 33.2 - - + -
104E GLU 3.3 7.9 - - - +
105E ARG* 3.6 28.0 - - + -
106E PHE* 4.2 1.1 - - - -
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Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLY 3.5 8.5 - - - +
22E ILE* 4.0 9.2 - - + -
41E ALA 3.8 2.2 + - - -
42E PHE* 1.3 72.2 - - - +
44E SER* 1.3 64.5 + - - +
45E LEU* 4.2 24.1 + - + -
76E ILE* 4.1 17.3 - - + -
78E PHE* 4.6 4.9 - - + -
85E ARG* 4.1 17.0 - - - +
102E TYR* 4.2 1.2 - - - +
103E LEU* 3.6 3.0 - - - +
104E GLU* 2.8 64.0 + - + +
106E PHE* 3.9 11.6 - - + -
130E LEU* 4.0 29.8 - - + -
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Residues in contact with SER 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU* 4.1 6.7 - - - -
19E ASN 3.3 1.6 - - - +
20E THR* 3.3 4.9 - - - -
21E GLY* 2.8 47.8 + - - -
42E PHE 5.4 0.4 - - - -
43E LEU* 1.3 73.5 - - - +
45E LEU* 1.3 64.7 + - - +
102E TYR 3.4 6.5 - - - -
103E LEU* 3.6 19.1 - - - -
148E LYS* 3.2 34.1 + - - +
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Residues in contact with LEU 45 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E VAL* 4.5 4.7 - - + -
19E ASN 3.4 3.6 - - - -
20E THR* 3.8 26.9 - - + -
43E LEU* 4.2 16.8 - - + -
44E SER* 1.3 79.1 - - - +
46E SER* 1.3 63.8 + - - +
47E TRP* 4.0 9.0 - - + -
73E ILE* 5.1 2.9 - - + -
74E PRO* 4.9 8.5 - - + +
76E ILE* 3.4 45.1 - - + -
85E ARG* 5.6 1.6 - - - +
101E GLN* 3.7 3.6 + - - -
102E TYR* 2.8 69.0 + - + +
148E LYS* 5.1 0.6 - - - -
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Residues in contact with SER 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E THR 4.2 0.9 - - - +
18E VAL* 3.7 1.2 - - - +
19E ASN* 2.7 53.1 + - - +
45E LEU* 1.3 79.1 - - - +
47E TRP* 1.3 63.4 + - - +
99E THR* 4.4 9.4 - - - +
100E VAL 3.0 17.9 + - - -
101E GLN* 3.0 21.5 + - - +
145E ASP* 5.0 5.5 + - - -
148E LYS* 5.2 1.3 - - - -
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Residues in contact with TRP 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E PRO* 4.6 0.2 - - + -
16E LEU* 4.1 10.3 - - + -
17E THR 4.0 15.3 - - - +
18E VAL* 4.3 9.9 - - + -
45E LEU* 4.0 7.0 - - + -
46E SER* 1.3 82.7 + - - +
48E LYS* 1.3 61.6 + - - +
49E ASP* 4.0 16.7 - - + +
71E ILE* 3.7 5.8 - - + -
72E TRP* 3.1 49.6 + + - -
73E ILE* 3.7 15.7 - - + -
74E PRO* 3.6 30.5 - - + -
92E ILE* 5.5 0.2 - - + -
99E THR* 3.4 7.2 - - - +
100E VAL* 2.7 71.4 + - + +
102E TYR* 3.6 27.8 - + + -
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Residues in contact with LYS 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E PRO* 3.7 16.6 - - - +
14E GLU* 5.9 0.4 - - - -
16E LEU* 4.1 15.8 - - + +
17E THR 4.8 0.6 + - - -
47E TRP* 1.3 75.0 - - - +
49E ASP* 1.3 60.8 + - - +
50E ARG* 3.5 46.7 + - + +
97E ASP* 4.5 13.5 - - - +
98E GLY 3.6 4.9 - - - +
99E THR* 4.1 20.2 - - + +
138E ARG* 5.0 1.2 + - - -
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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