Contacts of the strand formed by residues 48 - 60 (chain E) in PDB entry 2BG9
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 ALA 48 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D ILE* 5.8 1.6 - - + -
41E SER 3.4 1.0 - - - +
42E LEU* 4.0 1.4 - - - +
43E ASN* 3.0 36.6 + - + +
46E GLU* 4.4 8.7 - - + +
47E GLU* 1.3 78.8 - - - +
49E LEU* 1.3 61.8 + - - +
96E ASP* 6.3 0.2 - - + -
124E ARG* 4.2 19.1 - - + +
125E SER 2.8 15.3 - - - +
126E THR* 3.9 6.7 - - - +
127E CYS 5.2 0.9 - - - -
129E ILE* 3.9 3.7 - - - +
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Residues in contact with LEU 49 (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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39E LEU* 3.2 16.2 - - + -
41E SER 2.9 13.0 - - - +
42E LEU* 4.0 14.6 - - + -
48E ALA* 1.3 76.4 - - - +
50E THR* 1.3 74.1 + - - +
51E THR* 2.9 33.7 - - - +
94E ASN* 4.0 15.5 - - - +
123E TYR* 5.5 0.2 - - + -
124E ARG* 2.8 13.2 - - - +
125E SER* 2.5 52.3 + - - +
127E CYS* 4.6 3.8 - - + -
141E CYS* 4.5 11.9 - - - -
143E LEU* 4.1 13.0 - - + -
212E LEU* 5.4 3.6 - - + -
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Residues in contact with THR 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E LEU* 3.3 2.1 - - - -
40E ILE* 2.5 59.7 + - + -
41E SER* 2.6 29.7 + - - -
49E LEU* 1.3 76.2 - - - +
51E THR* 1.3 56.2 + - - +
100E GLU* 4.7 4.0 - - - +
122E ILE* 4.4 2.5 - - + -
123E TYR* 2.9 29.8 - - - +
124E ARG* 3.0 21.1 + - + +
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Residues in contact with THR 51 (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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36E LEU* 2.9 33.9 - - + +
38E ASN 2.6 18.2 + - - +
39E LEU* 3.1 16.3 - - - +
40E ILE* 4.9 1.8 - - - -
49E LEU* 2.9 27.1 - - - +
50E THR* 1.3 69.8 - - - +
52E ASN* 1.3 64.6 + - - +
53E VAL* 3.4 12.3 + - + -
121E ALA 2.4 22.2 - - - +
122E ILE* 3.3 6.3 - - - -
123E TYR* 3.2 25.6 + - - -
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Residues in contact with ASN 52 (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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95A ASN 5.7 1.4 - - - +
96A ALA* 5.9 2.6 - - - +
37E THR* 3.1 38.8 + - + +
38E ASN* 2.7 34.1 + - + +
40E ILE* 5.1 0.2 - - - +
51E THR* 1.3 68.7 - - - +
53E VAL* 1.3 58.6 + - - +
54E TRP* 5.4 3.2 - - - +
120E PRO* 3.1 35.0 - - - +
121E ALA 2.8 12.3 - - - +
122E ILE* 3.5 25.6 - - + +
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Residues in contact with VAL 53 (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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34E LEU* 4.0 30.3 - - + -
35E THR 4.0 4.5 - - - +
36E LEU* 5.0 3.1 - - + -
51E THR* 3.5 16.2 - - + -
52E ASN* 1.3 73.7 - - - +
54E TRP* 1.3 59.5 + - - +
55E ILE* 3.1 8.1 + - + +
99E PHE* 3.9 25.1 - - + -
119E PRO 3.4 2.8 - - - +
120E PRO* 3.6 0.9 - - - +
121E ALA* 2.8 32.5 + - + -
123E TYR* 3.2 40.6 - - + +
210E PHE* 6.1 0.4 - - + -
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Residues in contact with TRP 54 (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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149A TRP* 5.5 5.8 - + - -
33E LYS 3.2 0.2 - - - +
34E LEU* 3.0 26.3 - - - -
35E THR* 3.0 59.6 + - + +
36E LEU 3.6 3.6 - - - -
37E THR* 2.6 44.2 - - + -
52E ASN* 4.1 2.3 + - - +
53E VAL* 1.3 70.8 - - - +
55E ILE* 1.3 56.8 + - - +
56E GLU* 3.1 3.3 + - - +
118E LEU* 3.1 31.4 - - + -
119E PRO 4.1 0.4 - - - -
120E PRO* 4.8 15.5 - - + +
176E ASP* 4.6 9.6 - - + -
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Residues in contact with ILE 55 (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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32E LEU* 4.7 5.8 - - + -
33E LYS 4.6 0.2 - - - +
34E LEU* 3.3 20.4 - - + -
53E VAL* 3.1 10.8 + - + +
54E TRP* 1.3 66.5 - - - +
56E GLU* 1.3 65.2 + - - +
57E ILE* 3.0 36.0 + - + +
89E VAL* 3.9 26.2 - - + -
102E ALA* 4.2 13.2 - - + +
117E TRP 3.2 6.6 - - - +
118E LEU* 3.0 12.2 - - - +
119E PRO* 2.8 50.2 + - + +
121E ALA* 5.2 0.2 - - + -
145E PHE* 3.9 13.7 - - + -
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Residues in contact with GLU 56 (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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32E LEU* 2.8 36.2 - - - +
33E LYS* 2.6 52.9 + - + +
35E THR* 5.3 4.9 + - - +
54E TRP* 3.1 4.3 + - + +
55E ILE* 1.3 70.2 - - - +
57E ILE* 1.3 53.7 + - - +
58E GLN* 2.6 34.3 + - + +
116E TYR* 4.6 11.8 + - + -
118E LEU* 3.1 28.7 - - + +
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Residues in contact with ILE 57 (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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30E VAL* 5.6 0.9 - - + -
31E THR 3.7 2.2 - - - -
32E LEU* 4.0 6.1 - - + -
55E ILE* 3.1 38.4 - - + +
56E GLU* 1.3 70.5 - - - +
58E GLN* 1.3 71.0 + - - +
59E TRP* 3.7 15.2 - - + -
87E PRO* 3.4 37.0 - - + +
89E VAL* 4.5 3.6 - - + -
102E ALA 4.9 1.1 - - - +
116E TYR* 3.6 0.3 - - - -
117E TRP* 2.7 84.5 + - + +
119E PRO* 4.5 1.8 - - + -
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Residues in contact with GLN 58 (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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30E VAL* 3.3 3.5 - - - +
31E THR* 2.4 73.1 + - - +
56E GLU* 2.6 36.7 + - + +
57E ILE* 1.3 86.8 - - - +
59E TRP* 1.3 64.9 + - - +
115E MET 3.1 15.5 - - - +
116E TYR* 3.9 27.9 - - + +
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Residues in contact with TRP 59 (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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20E PRO* 4.8 0.9 - - + -
28E ILE* 4.4 1.1 - - + -
29E ASP 3.4 7.0 - - - +
30E VAL* 3.6 23.6 - - + -
31E THR* 3.7 0.6 + - - -
57E ILE* 3.7 25.6 - - + -
58E GLN* 1.3 85.2 - - - +
60E ASN* 1.3 89.6 + - - +
61E ASP* 4.5 3.7 - - + +
84E LEU* 2.9 35.3 - - + +
85E TRP* 4.1 37.4 + + + +
107E VAL* 2.8 37.2 - - + -
109E VAL* 5.8 0.4 - - + -
115E MET* 2.8 67.4 + - + +
116E TYR 3.5 1.6 - - - -
117E TRP* 4.4 1.6 - + + -
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Residues in contact with ASN 60 (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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20E PRO* 3.3 2.8 - - - +
28E ILE* 2.5 34.6 - - - +
29E ASP* 3.7 32.4 + - - +
31E THR* 4.8 4.4 + - - -
59E TRP* 1.3 118.7 + - - +
61E ASP* 1.3 58.9 + - - +
62E TYR 5.6 0.2 - - - +
113E GLY 3.9 7.4 - - - +
114E SER* 5.1 5.6 - - - +
115E MET 5.0 0.8 - - - +
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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