Contacts of the strand formed by residues 22 - 33 (chain E) in PDB entry 3BXB
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 HIS 22 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E THR* 3.3 4.3 - - - -
19E VAL 3.0 34.3 + - - +
20E ASN 3.2 2.6 - - - +
21E ASN* 1.3 78.8 - - - +
23E HIS* 1.3 73.4 + - - +
24E PHE* 3.8 4.7 - - - +
48E GLY* 2.6 33.0 + - - -
50E PRO 4.2 3.2 + - - -
51E LEU* 4.3 7.8 - - + +
52E PRO* 3.4 42.8 - - + +
53E PHE* 4.6 3.4 - - + -
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Residues in contact with HIS 23 (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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16E GLU* 3.3 35.6 + - + +
17E GLY 3.4 15.0 - - - -
18E THR* 4.1 6.0 + - - +
21E ASN 3.9 3.6 + - - -
22E HIS* 1.3 86.2 + - - +
24E PHE* 1.3 74.4 + - - +
25E LYS* 4.3 10.0 - - + -
47E GLU* 3.9 31.9 + - - +
48E GLY* 3.5 10.8 + - - -
120H LYS* 4.5 14.4 - - - +
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Residues in contact with PHE 24 (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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15E MET* 3.7 26.7 - - + -
16E GLU* 4.0 1.6 - - - +
17E GLY 3.0 64.2 + - - +
18E THR 3.7 3.4 - - - -
19E VAL* 4.0 17.7 - - + -
22E HIS* 3.8 10.8 - - - +
23E HIS* 1.3 84.0 - - - +
25E LYS* 1.3 70.5 + - - +
26E CYS* 3.9 13.9 - - - -
47E GLU 3.3 13.5 - - - +
48E GLY* 4.6 0.2 - - - -
51E LEU* 3.7 24.9 - - + -
53E PHE* 4.0 9.4 - + - -
58E LEU* 3.6 30.1 - - + -
121E ILE* 3.9 16.6 - - + -
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Residues in contact with LYS 25 (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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15E MET 3.2 13.2 - - - +
16E GLU* 3.8 29.2 + - + -
23E HIS* 4.3 6.5 - - + -
24E PHE* 1.3 79.8 - - - +
26E CYS* 1.3 61.2 + - - +
27E THR* 6.0 0.2 - - + -
45E VAL* 3.6 4.2 - - - +
46E VAL* 2.7 41.7 + - + -
47E GLU* 3.0 48.0 + - + +
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Residues in contact with CYS 26 (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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13E LEU* 5.0 0.7 - - - -
15E MET* 2.8 46.7 + - + +
24E PHE* 3.9 24.9 - - - -
25E LYS* 1.3 80.1 - - - +
27E THR* 1.3 68.8 + - - +
43E ILE* 4.1 13.5 - - + -
44E LYS 3.1 11.7 - - - +
45E VAL* 4.1 21.3 - - - -
46E VAL 4.2 0.9 - - - +
55E PHE* 4.7 0.7 - - - -
58E LEU* 4.6 6.5 - - - -
62E PHE* 4.2 12.6 - - + -
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Residues in contact with THR 27 (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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13E LEU* 3.3 13.2 - - - -
14E TYR* 4.1 21.8 - - + -
25E LYS* 6.0 0.4 - - + -
26E CYS* 1.3 80.8 - - - +
28E SER* 1.3 65.7 + - - +
43E ILE* 3.7 1.7 - - - +
44E LYS* 3.0 36.6 + - - +
46E VAL* 3.9 30.3 - - + +
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Residues in contact with SER 28 (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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12E LYS* 3.3 4.9 - - - +
13E LEU* 2.9 52.6 + - - +
27E THR* 1.3 79.7 - - - +
29E GLU* 1.3 65.2 + - - +
41E MET* 3.3 17.0 - - - +
42E ARG 3.0 20.4 - - - -
43E ILE* 3.5 20.1 - - - +
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Residues in contact with GLU 29 (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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11E MET 3.6 8.1 - - - +
12E LYS* 3.5 30.0 + - + +
28E SER* 1.3 79.9 - - - +
30E GLY* 1.3 58.4 + - - +
41E MET* 3.6 4.6 - - - -
42E ARG* 2.8 46.9 + - + +
44E LYS* 6.1 0.9 - - - -
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Residues in contact with GLY 30 (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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10E HIS* 3.3 8.0 + - - -
11E MET* 2.9 37.2 + - - +
29E GLU* 1.3 76.3 - - - +
31E GLU* 1.3 68.1 + - - +
40E THR 3.1 16.6 - - - -
41E MET* 4.2 0.9 - - - -
42E ARG* 4.1 10.9 - - - +
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Residues in contact with GLU 31 (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 ASN* 6.6 0.2 - - + -
9E MET 3.0 12.3 - - - +
10E HIS* 3.2 38.6 + - + +
11E MET* 3.4 9.9 - - - -
30E GLY* 1.3 72.0 - - - -
32E GLY* 1.3 60.5 + - - +
39E GLN* 3.6 0.5 - - - -
40E THR* 3.1 33.3 + - - +
42E ARG* 2.9 42.0 + - - -
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Residues in contact with GLY 32 (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 ASN* 3.5 7.3 - - - +
9E MET 2.8 35.3 + - - -
31E GLU* 1.3 77.9 - - - +
33E LYS* 1.3 63.8 + - - -
34E PRO* 3.2 1.2 - - - +
38E THR* 3.2 13.0 - - - -
39E GLN* 4.0 1.3 - - - -
69E PHE* 3.3 12.5 - - - -
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Residues in contact with LYS 33 (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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7E GLU* 3.4 15.5 - - - +
8E ASN* 2.5 37.2 + - - +
32E GLY* 1.3 76.5 - - - +
34E PRO* 1.3 63.1 - - - +
35E TYR 3.2 2.1 + - - -
36E GLU* 3.2 36.3 + - + +
37E GLY* 2.9 25.3 + - - -
38E THR* 2.7 28.6 + - - +
69E PHE* 4.0 0.9 - - - -
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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