Contacts of the strand formed by residues 16 - 31 (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 LEU 16 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E PRO* 5.9 0.4 - - + -
8E PRO* 4.0 15.0 - - + -
15E PRO* 1.3 71.4 - - - +
17E THR* 1.3 80.4 + - - +
18E VAL* 4.2 7.6 - - + -
47E TRP* 4.1 6.7 - - + -
48E LYS* 4.1 30.7 - - + +
72E TRP* 3.7 35.7 - - + -
138E ARG* 3.2 27.6 - - - +
139E ASN 3.2 13.1 + - - +
140E ILE* 3.5 9.2 - - + +
141E VAL* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 17 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E PRO 3.7 4.7 + - - -
16E LEU* 1.3 89.0 - - - +
18E VAL* 1.3 58.5 + - - +
19E ASN* 3.1 28.1 + - - +
46E SER 4.2 0.9 - - - +
47E TRP* 4.0 8.8 - - - +
48E LYS 4.8 0.2 + - - -
141E VAL* 3.4 20.3 - - - +
143E ALA* 4.3 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU* 4.0 9.9 - - + +
17E THR* 1.3 76.9 - - - +
19E ASN* 1.3 63.2 + - - +
20E THR* 3.5 4.6 + - - +
45E LEU* 4.5 9.0 - - + -
46E SER 3.7 15.5 - - - +
47E TRP* 4.3 7.6 - - + -
74E PRO* 3.9 31.2 - - + -
76E ILE* 4.4 9.9 - - + -
140E ILE* 3.4 32.1 - - + -
141E VAL 2.7 12.1 + - - +
142E LEU* 3.4 12.1 - - + -
143E ALA 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E THR* 3.1 33.1 - - - +
18E VAL* 1.3 70.8 + - - +
20E THR* 1.3 61.0 + - - +
44E SER* 3.3 8.3 + - - +
45E LEU* 3.4 1.7 - - - -
46E SER* 2.7 50.4 + - - +
143E ALA* 3.5 11.1 + - - +
144E VAL 4.5 2.8 - - - +
145E ASP* 4.0 31.0 + - + +
148E LYS* 5.0 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E VAL* 3.7 13.5 - - + +
19E ASN* 1.3 71.6 - - - +
21E GLY* 1.3 58.6 + - - +
44E SER* 3.3 7.4 - - - -
45E LEU* 3.8 20.4 - - + -
76E ILE* 5.1 0.9 - - + -
130E LEU* 4.1 15.9 - - + -
142E LEU* 4.0 19.7 - - + -
143E ALA 2.8 18.4 + - - +
144E VAL* 3.6 0.9 - - - +
145E ASP* 2.9 30.3 + - - -
184E LEU* 3.0 17.9 - - + +
186E TYR* 2.8 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLU* 4.9 0.5 - - - +
20E THR* 1.3 75.9 - - - +
22E ILE* 1.3 62.6 + - - -
23E TYR 4.1 0.2 + - - -
42E PHE 3.5 1.4 - - - +
43E LEU* 3.5 4.0 - - - +
44E SER* 2.8 46.7 + - - -
148E LYS* 3.3 22.2 - - - +
149E VAL* 3.9 5.8 - - - -
186E TYR* 3.6 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E GLY* 1.3 76.4 - - - +
23E TYR* 1.3 62.1 + - - +
24E LEU* 4.0 15.5 - - + -
41E ALA* 3.9 17.5 - - + -
42E PHE 3.2 8.3 - - - +
43E LEU* 4.0 13.7 - - + -
78E PHE* 4.0 20.6 - - + -
106E PHE* 4.2 8.1 - - + -
128E ILE* 4.1 11.7 - - + -
130E LEU* 3.9 12.3 - - + -
148E LYS 3.4 3.0 + - - -
149E VAL* 3.6 3.2 - - - +
150E GLY 3.4 12.5 + - - -
165E PHE* 3.3 19.1 - - + -
186E TYR* 3.7 47.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 5.8 2.3 - - - -
176A LEU* 3.6 41.5 - - + +
177A GLU* 3.5 22.7 - - + +
21E GLY 4.1 0.6 + - - -
22E ILE* 1.3 71.8 - - - +
24E LEU* 1.3 67.0 + - - +
25E ILE* 3.4 11.4 + - + +
41E ALA* 3.3 3.2 - - - -
42E PHE* 2.9 46.0 + + + -
148E LYS 5.8 0.2 - - - -
149E VAL 4.7 0.9 - - - -
150E GLY* 3.4 22.4 - - - +
151E LYS 3.3 30.3 + - - -
152E ASN* 2.7 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ILE* 4.0 5.2 - - + -
23E TYR* 1.3 73.5 - - - +
25E ILE* 1.3 60.7 + - - +
26E GLU 4.8 0.7 - - - +
27E CYS* 3.9 27.1 - - - -
39E VAL* 3.4 28.9 - - + -
41E ALA* 3.7 11.2 - - + -
128E ILE* 4.4 4.7 - - + -
150E GLY 3.2 5.5 + - - -
151E LYS* 3.4 14.7 - - + -
152E ASN 3.1 25.3 + - - -
155E VAL* 3.9 3.1 - - + +
165E PHE* 3.6 55.2 - - + -
188E LEU* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.9 25.3 - - + +
407A ACT 4.1 12.8 - - + +
23E TYR* 3.6 19.3 - - + +
24E LEU* 1.3 74.3 - - - +
26E GLU* 1.3 68.0 + - + +
40E ASN* 2.8 11.7 + - - +
41E ALA* 3.7 4.5 - - - -
42E PHE* 3.6 35.2 - - + +
105E ARG* 3.4 47.3 - - + +
152E ASN* 4.2 15.9 + - - +
154E ASP* 5.1 2.3 - - - +
155E VAL* 3.4 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 4.0 10.5 - - - +
80A ASN* 3.1 41.2 - - - +
81A VAL 3.2 9.3 + - - +
111A LEU* 3.9 25.9 - - + +
25E ILE* 1.3 91.4 + - + +
27E CYS* 1.3 63.4 + - - +
28E TYR* 3.8 14.8 - - + -
39E VAL* 3.3 7.4 - - - +
40E ASN* 2.8 54.1 + - + +
154E ASP* 5.5 4.5 - - - +
155E VAL* 4.0 7.2 - - - +
156E PHE* 5.6 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 5.3 2.9 - - - +
24E LEU* 3.9 18.6 - - - -
26E GLU* 1.3 79.0 - - - +
28E TYR* 1.3 63.7 + - - +
37E PHE* 5.0 4.5 - - + -
38E LYS 3.5 7.4 - - - +
39E VAL* 4.5 4.7 - - + +
155E VAL* 3.6 28.2 - - + +
156E PHE 3.2 22.2 + - - +
157E LEU* 3.8 20.5 - - + +
162E ILE* 5.2 2.7 - - - -
188E LEU* 3.8 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 3.2 67.0 + - + +
111A LEU* 3.6 22.2 - - + -
26E GLU* 3.8 24.0 - - + -
27E CYS* 1.3 80.0 - - - +
29E SER* 1.3 74.1 + - - +
30E LEU 3.5 2.0 + - - -
37E PHE* 3.8 1.9 - - - +
38E LYS* 2.8 71.8 + - + +
39E VAL 4.3 6.3 + - - -
40E ASN* 4.2 9.3 - - + +
107E SER* 4.5 5.4 - - - -
156E PHE 5.1 1.8 - - - +
157E LEU* 3.7 9.7 - - - +
158E THR 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 4.9 0.5 + - - -
406A SO4 3.3 30.4 + - - -
28E TYR* 1.3 86.1 - - - +
30E LEU* 1.3 61.7 - - - +
31E ASP* 2.9 14.4 + - - +
36E THR* 3.6 1.9 + - - +
37E PHE* 3.3 13.9 + - - -
38E LYS* 3.8 22.5 + - - +
157E LEU* 4.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR 3.5 2.6 - - - -
29E SER* 1.3 74.0 - - - +
31E ASP* 1.3 59.6 + - - +
32E ASP* 3.6 17.0 + - - +
36E THR 3.4 10.3 - - - +
37E PHE* 3.9 5.6 - - + -
114E LEU* 3.7 27.8 - - + -
126E LEU* 4.1 18.4 - - + -
157E LEU* 3.9 20.4 - - + +
158E THR 5.8 0.4 - - - +
160E TRP* 3.7 34.5 + - + +
190E ILE* 3.3 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E SER* 2.9 7.2 + - - +
30E LEU* 1.3 71.5 - - - +
32E ASP* 1.3 52.5 + - - +
33E LYS* 3.2 12.6 + - - +
34E ALA* 3.1 27.2 + - + +
35E GLU* 2.7 32.4 + - - -
36E THR* 2.9 27.9 + - - +
109E ARG* 4.3 6.4 + - - +
402E SO4 5.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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