Contacts of the strand formed by residues 71 - 77 (chain E) in PDB entry 5HJD
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 TYR 71 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E PHE* 3.3 4.7 - - - +
36E VAL* 2.8 49.3 + - + +
37E ARG* 5.4 0.2 - - - -
44E ILE* 3.7 27.6 - - + -
45E GLN* 2.9 32.8 + - - -
48E VAL* 3.8 25.7 + - + +
49E GLU 5.2 0.2 - - - -
50E LYS* 4.8 0.7 - - - -
51E VAL* 3.5 29.4 - - + -
53E PHE* 3.4 6.5 - - + -
66E CYS* 3.6 29.4 - - + -
67E LYS 4.2 2.8 + - - -
68E ASP* 3.9 15.4 - - - -
69E PRO* 3.5 20.9 - - + +
70E PRO* 1.3 69.4 - - + +
72E LYS* 1.3 59.1 + - - +
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Residues in contact with LYS 72 (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 MET* 3.7 30.4 - - + +
34E VAL 3.2 13.5 - - - +
35E PHE* 4.2 2.0 - - + -
53E PHE* 4.0 4.9 - - - -
66E CYS* 3.3 22.1 - - - -
70E PRO* 3.2 38.4 + - + +
71E TYR* 1.3 75.3 - - - +
73E VAL* 1.3 61.2 + - - +
74E GLU* 3.5 40.0 + - - +
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Residues in contact with VAL 73 (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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32E TRP* 3.7 16.1 - - + -
33E MET* 3.4 5.2 - - - +
34E VAL* 3.2 45.2 + - + -
53E PHE* 4.4 9.6 - - + -
55E LEU* 4.2 10.5 - - + -
64E ARG* 3.5 50.0 - - + +
72E LYS* 1.3 75.6 - - - +
74E GLU* 1.3 66.5 + - - +
75E GLU* 4.3 9.2 - - + -
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Residues in contact with GLU 74 (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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32E TRP 3.8 4.5 - - - +
33E MET* 4.2 11.7 - - + -
64E ARG* 4.8 0.9 + - - -
72E LYS* 3.5 38.7 + - - +
73E VAL* 1.3 77.3 - - - +
75E GLU* 1.3 73.1 + - - +
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Residues in contact with GLU 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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28E PHE* 6.1 0.2 - - - -
31E ASP* 3.6 3.3 - - - +
32E TRP* 2.9 66.9 + - + +
55E LEU* 4.4 1.3 - - + -
59E PHE* 3.6 24.9 - - + -
60E PRO* 5.6 1.3 - - - +
61E ARG* 5.6 0.2 + - - -
64E ARG* 3.1 37.0 + - - +
73E VAL* 4.0 4.2 + - + -
74E GLU* 1.3 81.1 - - - +
76E SER* 1.3 73.6 + - - +
18F KCR 5.7 0.2 - - - +
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Residues in contact with SER 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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20E ARG* 4.6 2.0 + - - -
24E THR* 4.7 8.1 - - - +
28E PHE* 3.9 32.1 - - - -
30E HIS 3.4 9.2 - - - -
31E ASP* 2.4 25.9 + - - +
32E TRP* 4.3 4.0 - - - +
59E PHE* 3.8 15.8 - - - -
75E GLU* 1.3 81.5 + - - +
77E GLY* 1.3 58.0 + - - +
18F KCR 4.1 2.9 - - - +
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Residues in contact with GLY 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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28E PHE* 4.2 12.9 - - - +
29E THR 3.5 2.9 + - - -
30E HIS* 2.9 37.0 + - - +
32E TRP* 4.1 13.6 - - - +
59E PHE* 4.8 0.2 - - - -
76E SER* 1.3 74.9 - - - +
78E TYR* 1.3 58.9 + - - -
79E ALA 3.7 2.0 - - - -
106E LEU* 5.1 1.3 - - - -
18F KCR 3.5 14.6 - - - -
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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