Contacts of the strand formed by residues 50 - 60 (chain E) in PDB entry 2WJ7
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 PHE 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E GLU* 3.4 34.0 - - + +
44E ARG* 3.5 4.5 - - - -
45E GLN* 3.3 54.3 - - + -
46E ASP* 4.0 0.7 - - - -
49E GLY* 1.3 82.6 - - - -
51E ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 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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41E HIS* 3.1 9.6 + - + +
43E GLU* 3.3 5.7 - - - -
44E ARG* 3.0 31.4 + - - +
46E ASP* 3.3 22.7 - - + +
50E PHE* 1.3 75.5 - - - +
52E SER* 1.3 73.3 + - - +
53E ARG* 3.3 57.7 - - + +
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Residues in contact with SER 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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41E HIS* 3.3 16.4 - - - -
42E GLU* 4.3 1.6 - - - -
43E GLU* 3.7 20.8 - - - +
51E ILE* 1.3 82.5 - - - +
53E ARG* 1.3 65.5 + - - +
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Residues in contact with ARG 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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20E HIS* 3.4 47.1 + - - +
21E PHE* 3.9 20.0 - - + -
40E LYS* 3.3 3.0 - - - +
41E HIS* 2.6 84.0 + - + +
44E ARG* 4.5 2.8 - - - +
46E ASP* 6.1 2.0 - - - +
51E ILE* 3.3 38.9 - - + +
52E SER* 1.3 78.9 - - - +
54E GLU* 1.3 62.2 + - - +
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Residues in contact with GLU 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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21E PHE* 5.0 0.9 - - - -
38E HIS* 2.8 28.8 + - + -
39E GLY 3.3 14.4 - - - +
40E LYS* 3.5 35.0 + - + +
53E ARG* 1.3 76.9 - - - +
55E PHE* 1.3 70.5 + - - +
56E HIS* 6.1 0.2 - - + -
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Residues in contact with PHE 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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16E LEU* 4.3 13.9 - - + -
17E ASP 5.9 0.7 - - - -
18E VAL* 4.4 10.3 - - + -
21E PHE* 3.7 39.3 - + - -
26E LEU* 4.4 3.1 - - + -
37E VAL* 3.7 39.0 - - + -
38E HIS* 3.2 7.6 + - - -
39E GLY* 2.8 49.1 + - - -
54E GLU* 1.3 79.5 - - - +
56E HIS* 1.3 66.6 + - - +
57E ARG* 4.0 15.5 - - + -
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Residues in contact with HIS 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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29E LYS* 4.8 1.3 - - - -
36E GLU* 3.3 45.0 + - + -
37E VAL 3.3 8.9 + - - -
38E HIS* 3.9 23.2 - + + +
55E PHE* 1.3 78.9 - - - +
57E ARG* 1.3 65.7 + - - +
58E LYS* 4.4 9.3 + - + +
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Residues in contact with ARG 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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16E LEU* 5.1 3.8 - - + -
35E ILE 3.5 0.2 - - - +
36E GLU* 3.2 5.9 - - - -
37E VAL* 2.9 41.1 + - + +
55E PHE* 4.0 16.1 - - + -
56E HIS* 1.3 75.1 + - - +
58E LYS* 1.3 82.1 + - - +
59E TYR* 3.4 48.5 + - + +
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Residues in contact with LYS 58 (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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34E VAL* 3.8 19.3 - - + -
35E ILE 3.2 4.3 - - - -
36E GLU* 4.3 13.0 - - + -
56E HIS* 4.4 11.6 + - + +
57E ARG* 1.3 99.1 + - - +
59E TYR* 1.3 65.6 + - - +
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Residues in contact with TYR 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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14E VAL* 3.5 33.1 - - + +
15E ASN 4.8 0.5 + - - -
16E LEU* 3.2 30.7 - - + +
34E VAL* 3.2 10.6 - - - +
35E ILE* 2.9 61.6 + - + -
37E VAL* 4.4 10.1 - - + -
57E ARG* 3.4 42.5 + - + -
58E LYS* 1.3 78.5 - - - +
60E ARG* 1.3 67.4 + - - +
82E VAL* 6.0 2.9 - - + -
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Residues in contact with ARG 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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33E ASP* 4.3 7.0 - - + +
34E VAL* 4.9 8.3 - - + +
35E ILE* 5.6 0.7 - - - +
59E TYR* 1.3 80.8 - - - +
61E ILE* 1.3 63.3 + - - +
62E PRO* 3.9 6.2 - - - +
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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