Contacts of the strand formed by residues 34 - 45 (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 VAL 34 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E VAL* 3.5 3.5 - - - -
31E LEU* 3.1 32.8 + - + +
32E GLY 3.2 1.4 - - - -
33E ASP* 1.3 110.6 - - - +
35E ILE* 1.3 73.6 + - - +
36E GLU* 3.7 8.5 + - + +
58E LYS* 3.8 23.1 - - + -
59E TYR 3.2 18.6 - - - +
60E ARG* 5.4 7.0 - - + -
61E ILE* 4.3 1.8 - - - -
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Residues in contact with ILE 35 (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 PHE* 4.1 13.9 - - + -
14E VAL* 6.1 2.5 - - + -
28E VAL* 4.3 18.6 - - + -
29E LYS 3.8 3.8 - - - +
30E VAL* 4.6 7.9 - - + +
33E ASP 4.1 0.6 + - - -
34E VAL* 1.3 72.3 - - - +
36E GLU* 1.3 69.3 + - - +
37E VAL* 4.0 5.8 + - + -
57E ARG 3.5 0.7 - - - +
58E LYS* 3.2 5.9 - - - -
59E TYR* 2.9 63.1 + - + +
60E ARG 5.6 0.2 - - - +
61E ILE* 3.9 27.1 - - + -
70E ILE* 4.1 12.3 - - + -
82E VAL* 3.8 30.1 - - + -
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Residues in contact with GLU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LYS 3.6 1.6 - - - +
28E VAL* 3.4 6.8 - - - +
29E LYS* 2.9 63.2 + - - +
31E LEU* 3.7 22.8 - - + +
34E VAL* 4.4 11.2 - - + +
35E ILE* 1.3 76.4 - - - +
37E VAL* 1.3 61.2 + - - +
38E HIS 4.1 0.2 - - - -
56E HIS* 3.3 31.5 + - + -
57E ARG 3.2 3.4 - - - -
58E LYS* 4.3 12.3 - - + -
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Residues in contact with VAL 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU* 4.2 11.2 - - + -
26E LEU* 5.0 2.7 - - + -
27E LYS 3.5 5.6 - - - +
28E VAL* 4.4 12.1 - - + -
35E ILE* 4.4 15.0 - - + -
36E GLU* 1.3 76.5 - - - +
38E HIS* 1.3 68.1 + - - +
55E PHE* 3.7 28.2 - - + -
56E HIS* 3.3 3.7 + - - -
57E ARG* 2.9 36.9 + - + -
59E TYR* 4.4 16.6 - - + -
80E LEU* 3.9 24.5 - - + -
82E VAL* 4.9 6.3 - - + -
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Residues in contact with HIS 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E GLU 3.8 0.2 - - - +
26E LEU* 3.4 6.8 - - - +
27E LYS* 2.8 76.2 + - + +
29E LYS* 5.3 6.5 - - - +
36E GLU 4.1 0.2 - - - -
37E VAL* 1.3 79.7 - - - +
39E GLY* 1.3 59.4 + - - +
40E LYS* 3.9 12.3 - - - +
54E GLU* 2.8 40.1 + - + -
55E PHE* 3.2 11.7 + - - -
56E HIS* 3.9 25.6 - + + +
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Residues in contact with GLY 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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21E PHE* 3.8 7.2 - - - -
25E GLU 3.4 8.1 - - - -
26E LEU* 4.0 5.6 - - - -
38E HIS* 1.3 76.4 - - - +
40E LYS* 1.3 64.1 + - - +
54E GLU* 3.3 2.6 - - - +
55E PHE* 2.8 54.8 + - - +
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Residues in contact with LYS 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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21E PHE* 3.2 6.5 - - - -
25E GLU* 3.0 30.8 + - - +
27E LYS* 5.0 5.2 - - - +
38E HIS* 3.9 11.8 + - + +
39E GLY* 1.3 77.0 - - - +
41E HIS* 1.3 81.7 + - - +
42E GLU* 3.6 22.0 - - - +
53E ARG 3.3 12.6 - - - +
54E GLU* 3.5 35.8 + - + +
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Residues in contact with HIS 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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20E HIS 3.5 13.6 + - - -
21E PHE* 3.9 6.0 - - + -
25E GLU* 3.4 24.9 - - - +
40E LYS* 1.3 84.8 - - - +
42E GLU* 1.3 80.7 + - - +
44E ARG* 3.6 24.1 - - - +
51E ILE* 3.1 21.1 + - - +
52E SER* 3.3 6.4 - - - -
53E ARG* 2.6 77.1 + - + +
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Residues in contact with GLU 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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25E GLU* 4.9 1.8 + - - -
40E LYS* 3.6 30.3 - - - +
41E HIS* 1.3 92.1 - - - +
43E GLU* 1.3 72.4 + - - +
44E ARG* 3.4 3.3 + - - +
52E SER* 3.8 3.6 - - - -
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Residues in contact with GLU 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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42E GLU* 1.3 79.3 - - - +
44E ARG* 1.3 64.2 + - - +
50E PHE* 3.4 37.0 - - + +
51E ILE 3.3 14.6 - - - +
52E SER* 3.7 11.7 - - - +
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Residues in contact with ARG 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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20E HIS* 2.8 29.4 + - - +
22E SER* 4.8 3.4 + - - +
25E GLU* 3.3 35.2 + - - -
41E HIS* 3.6 27.4 - - - -
42E GLU 3.7 4.7 + - - +
43E GLU* 1.3 82.2 - - - +
45E GLN* 1.3 81.9 + - - +
46E ASP* 5.7 0.4 - - - -
50E PHE* 3.5 5.3 - - - -
51E ILE* 3.0 32.9 + - - +
53E ARG* 4.5 3.4 - - - +
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Residues in contact with GLN 45 (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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44E ARG* 1.3 95.6 - - - +
46E ASP* 1.3 67.0 + - - +
47E GLU 4.9 1.6 - - - +
49E GLY 3.2 12.1 - - - +
50E PHE* 3.3 35.2 - - + -
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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