Contacts of the strand formed by residues 50 - 63 (chain E) in PDB entry 1XWD
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 THR 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D SER* 3.6 8.3 - - - +
55D SER* 3.6 17.3 - - - +
56D GLU 4.6 0.7 - - - +
57D SER* 3.3 33.8 - - - +
87D CYS* 4.7 1.2 - - - -
90D HIS* 3.3 20.8 - - + +
32E CYS* 3.5 6.7 - - - -
48E GLN 4.3 0.2 + - - -
49E LYS* 1.3 74.7 + - - +
51E CYS* 1.3 79.8 + - - +
52E THR* 3.4 4.0 + - - -
84E CYS* 3.4 2.3 - - - -
85E GLY 3.0 35.9 + - - +
87E CYS* 4.8 7.2 - - + -
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Residues in contact with CYS 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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34D SER* 2.7 33.3 + - - +
35D ARG* 3.8 17.6 - - - +
36D ALA* 4.2 0.2 - - - +
55D SER* 4.5 0.3 + - - -
3E CYS* 2.0 57.7 - - + -
4E GLU 4.0 0.9 - - - -
28E CYS* 3.9 4.9 - - - -
29E ALA 3.6 27.6 - - - -
30E GLY 4.0 4.0 - - - +
32E CYS* 3.5 3.8 - - - -
50E THR* 1.3 80.8 - - - +
52E THR* 1.3 62.7 + - - +
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Residues in contact with THR 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ALA* 4.2 9.1 - - - +
53D VAL* 5.6 0.2 - - - +
55D SER* 4.9 3.4 - - - -
28E CYS* 3.0 15.6 - - - -
50E THR* 4.4 4.3 - - - -
51E CYS* 1.3 76.8 - - - +
53E PHE* 1.3 89.3 + - - +
83E HIS* 3.1 41.2 + - + +
85E GLY 4.0 19.7 - - - +
86E LYS 4.0 13.9 - - - +
87E CYS* 4.3 15.6 - - - +
88E ASP 5.2 1.0 + - - +
92E THR* 4.7 3.5 + - - +
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Residues in contact with PHE 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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53D VAL* 3.6 23.1 - - + -
27E TRP* 3.6 29.4 - + + -
28E CYS* 3.2 6.6 - - - -
52E THR* 1.3 98.3 + - - +
54E LYS* 1.3 72.0 + - - +
55E GLU* 4.1 8.3 - - - +
56E LEU* 3.5 33.7 - - + -
79E ALA* 4.4 2.5 - - + -
81E GLN 3.1 10.5 - - - +
83E HIS* 3.9 4.8 + - - -
88E ASP* 4.9 9.4 - - + -
91E SER* 3.7 22.0 - - - -
92E THR* 3.7 14.6 - - - -
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Residues in contact with LYS 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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52E THR 3.9 1.0 + - - -
53E PHE* 1.3 79.4 - - - +
55E GLU* 1.3 76.8 + - + +
81E GLN* 2.5 46.0 + - + +
83E HIS* 3.9 37.2 - - + +
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Residues in contact with GLU 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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53E PHE* 4.1 4.3 - - - +
54E LYS* 1.3 95.6 - - + +
56E LEU* 1.3 68.7 + - - +
79E ALA* 3.8 0.9 - - - -
80E THR* 2.9 41.0 + - + -
81E GLN* 3.5 29.5 + - + +
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Residues in contact with LEU 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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52D ASN* 6.2 0.2 - - + -
53D VAL* 3.9 17.7 - - + -
27E TRP* 3.5 20.6 - - + -
53E PHE* 3.5 38.8 - - + -
55E GLU* 1.3 78.1 + - - +
57E VAL* 1.3 69.2 + - - +
58E TYR* 5.4 10.9 - - + +
77E PRO* 3.9 14.1 - - + -
78E VAL 3.0 36.8 - - - +
79E ALA* 3.6 6.3 - - - -
80E THR* 4.1 0.9 - - - -
91E SER* 5.8 1.3 - - - +
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Residues in contact with VAL 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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56E LEU* 1.3 79.6 - - - +
58E TYR* 1.3 68.9 + - - +
59E GLU* 4.0 0.4 + - + -
77E PRO* 3.4 4.0 - - - +
78E VAL* 2.8 45.5 + - + +
79E ALA 5.7 0.2 - - - -
80E THR* 3.6 20.2 - - + +
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Residues in contact with TYR 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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52D ASN* 3.4 26.8 + - - +
56E LEU* 5.4 9.6 - - + +
57E VAL* 1.3 79.2 - - - +
59E GLU* 1.3 61.6 + - - +
60E THR* 4.4 2.1 + - - -
75E THR* 4.3 26.2 - - + -
76E TYR 4.1 2.9 - - - -
77E PRO* 3.8 40.1 - - + +
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Residues in contact with GLU 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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57E VAL* 4.0 1.6 + - + -
58E TYR* 1.3 76.5 - - - +
60E THR* 1.3 71.2 + - - +
75E THR* 3.4 2.8 - - - -
76E TYR* 2.9 67.3 + - + +
78E VAL* 3.9 13.2 - - + -
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Residues in contact with THR 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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58E TYR 5.1 1.2 + - - -
59E GLU* 1.3 85.3 + - - +
61E VAL* 1.3 65.2 + - - +
73E LEU* 3.8 39.7 - - + -
74E TYR 3.7 16.2 - - - +
75E THR* 3.3 19.8 - - + +
76E TYR* 4.1 2.2 + - - -
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Residues in contact with VAL 61 (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 ILE* 4.2 14.4 - - + -
21E ILE* 5.0 2.2 - - + -
23E ILE* 3.6 36.3 - - + -
60E THR* 1.3 77.7 - - - +
62E ARG* 1.3 85.7 + - + +
63E VAL* 3.4 13.8 + - + +
73E LEU* 3.5 19.8 - - - +
74E TYR 3.6 12.5 + - - +
76E TYR* 4.1 11.4 - - + +
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Residues in contact with ARG 62 (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 ILE* 3.7 17.4 - - + +
61E VAL* 1.3 80.7 - - + +
63E VAL* 1.3 60.7 + - - +
64E PRO* 3.2 20.0 - - + +
71E ASP* 5.9 2.5 - - - +
73E LEU* 4.9 4.7 - - - -
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Residues in contact with VAL 63 (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 ILE* 4.8 14.6 - - + -
13E GLU 5.3 0.9 - - - -
14E LYS* 3.4 39.2 - - + +
19E PHE* 6.3 1.1 - - + -
21E ILE* 5.4 1.6 - - + -
61E VAL* 3.4 12.2 + - + +
62E ARG* 1.3 72.8 - - - +
64E PRO* 1.3 69.5 - - + +
71E ASP* 3.3 6.4 + - - +
72E SER* 3.0 44.3 + - - +
74E TYR* 3.7 34.3 - - + +
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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