Contacts of the strand formed by residues 73 - 84 (chain E) in PDB entry 5LK5
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 ARG 73 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45E ASP* 3.4 29.5 + - - +
47E GLY* 3.8 15.7 - - - +
70E GLN* 3.9 32.8 + - + +
71E LYS 3.2 22.9 + - - +
72E ALA* 1.3 104.9 + - - +
74E PHE* 1.3 58.5 + - - +
75E TYR* 3.4 20.5 - - + -
319E TRP* 3.3 9.1 - - - -
320E GLN 3.0 28.6 + - - -
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Residues in contact with PHE 74 (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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43E LYS* 3.3 30.7 - - - +
45E ASP 5.2 1.4 + - - -
46E PHE* 3.3 15.9 - - + -
47E GLY 2.8 29.3 + - - -
73E ARG* 1.3 75.4 - - - +
75E TYR* 1.3 57.7 + - - +
318E LEU* 3.3 8.1 - - - -
319E TRP* 3.7 45.1 - + + -
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Residues in contact with TYR 75 (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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46E PHE* 4.4 3.0 - - - -
47E GLY* 3.5 33.9 - - - -
48E LYS 3.6 13.0 - - - -
49E PHE* 3.7 31.4 - + + -
68E THR* 3.5 29.9 - - + -
69E SER 3.5 2.3 + - - -
70E GLN* 2.5 42.9 + - - +
73E ARG* 3.4 27.6 - - + -
74E PHE* 1.3 74.0 - - - +
76E ALA* 1.3 64.4 + - - +
316E LEU 3.8 2.7 - - - +
317E ASP* 3.3 6.4 - - - +
318E LEU* 2.7 45.0 + - + +
320E GLN* 4.2 9.0 - - + -
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Residues in contact with ALA 76 (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 GLU* 3.8 4.0 - - - +
40E SER* 3.0 42.2 + - - +
46E PHE* 3.7 26.7 - - + +
47E GLY 5.2 1.4 + - - -
49E PHE* 4.5 2.0 - - - -
75E TYR* 1.3 78.7 - - - +
77E LEU* 1.3 60.0 + - - +
122E MET* 3.4 16.6 - - + +
316E LEU 3.3 6.1 - - - -
317E ASP* 3.9 7.2 - - - +
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Residues in contact with LEU 77 (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 TRP* 4.1 16.8 - - + -
37E TRP* 3.8 33.4 - - + +
38E ILE* 3.5 21.1 - - - +
39E GLU* 3.5 31.4 - - + +
49E PHE* 3.7 33.0 - - + -
66E LEU* 3.8 21.3 - - + -
76E ALA* 1.3 73.6 - - - +
78E SER* 1.3 61.9 + - - +
122E MET* 3.3 2.3 - - - +
316E LEU* 2.8 32.8 + - + +
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Residues in contact with SER 78 (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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37E TRP* 3.2 8.8 - - - -
38E ILE 2.8 37.9 + - - -
77E LEU* 1.3 77.2 - - - +
79E ALA* 1.3 59.9 + - - +
119E GLN* 3.1 38.4 + - - +
122E MET* 3.9 12.8 - - - +
313E VAL* 3.4 18.8 - - - +
314E LEU 3.3 8.5 - - - -
315E GLY* 3.8 7.0 - - - -
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Residues in contact with ALA 79 (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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23E PHE* 3.5 30.1 - - + -
36E ARG 3.6 12.6 - - - +
37E TRP* 3.5 27.1 - - + +
78E SER* 1.3 74.7 - - - +
80E SER* 1.3 61.5 + - - +
81E PHE* 3.9 4.2 - - - -
119E GLN* 4.0 2.5 - - - -
313E VAL* 3.4 2.4 - - - -
314E LEU* 2.9 38.7 + - - +
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Residues in contact with SER 80 (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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23E PHE* 4.3 8.3 - - - -
36E ARG 4.2 6.0 + - - +
79E ALA* 1.3 76.1 - - - +
81E PHE* 1.3 65.6 + - - +
115E ASN* 5.2 3.8 - - - -
119E GLN* 3.6 26.5 + - - -
312E GLY 3.2 12.6 - - - -
313E VAL* 4.1 5.2 - - - -
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Residues in contact with PHE 81 (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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22E TYR* 3.4 24.2 - - + +
23E PHE* 4.0 23.6 - + + -
79E ALA 3.9 4.3 - - - -
80E SER* 1.3 81.2 - - - +
82E GLU* 1.3 76.3 + - - +
83E PRO* 3.1 10.1 - - - +
84E PHE* 3.7 20.2 - + - -
112E LEU* 4.8 2.9 - - + -
115E ASN* 4.7 1.7 - - - +
311E PHE* 3.4 29.6 - - + -
312E GLY* 3.0 22.4 + - - +
313E VAL 3.6 7.9 - - - -
314E LEU* 3.5 30.3 - - + -
332E ILE* 4.4 15.3 - - + -
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Residues in contact with GLU 82 (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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22E TYR* 4.8 6.6 + - - +
81E PHE* 1.3 83.8 - - - +
83E PRO* 1.3 89.2 - - - +
84E PHE* 3.6 5.4 + - - +
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Residues in contact with PRO 83 (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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81E PHE 3.1 7.2 - - - +
82E GLU* 1.3 107.4 - - - +
84E PHE* 1.3 60.9 + - - +
115E ASN* 3.6 33.4 - - + +
310E ASN* 3.9 19.5 - - - +
311E PHE 3.0 15.7 - - - +
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Residues in contact with PHE 84 (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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22E TYR* 3.5 66.9 - + + -
81E PHE* 3.7 21.8 - + - -
82E GLU 4.2 1.3 - - - +
83E PRO* 1.3 77.0 - - - +
85E SER* 1.3 75.9 + - - +
86E ASN* 4.3 4.7 - - + -
91E LEU* 3.6 25.8 - - + -
112E LEU* 5.8 0.9 - - + -
309E ASP 4.2 2.5 - - - -
310E ASN* 3.4 3.4 - - - -
311E PHE* 2.7 66.2 + + + +
332E ILE* 3.9 7.9 - - + -
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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