Contacts of the strand formed by residues 105 - 110 (chain E) in PDB entry 5DPW
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 105 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ILE* 4.2 6.5 - - + -
28E PRO 3.0 14.0 + - - +
29E VAL* 3.3 11.8 - - + +
30E VAL 2.6 33.8 + - - -
79E VAL* 4.2 12.8 - - + -
94E ILE* 3.7 25.1 - - + +
95E TYR* 3.3 43.1 - - + -
98E TYR 4.7 5.4 - - - +
99E LYS* 4.7 4.9 - - - -
104E PHE* 1.3 72.4 - - - +
106E TYR* 1.3 57.1 + - - +
107E MET* 4.2 19.3 - - + -
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Residues in contact with TYR 106 (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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3E PHE* 3.5 15.4 - + + -
4E LYS* 3.3 28.6 - - + +
12E ARG* 3.4 12.5 - - - -
30E VAL* 3.5 28.7 - - + -
32E GLU* 5.2 3.6 - - - -
79E VAL* 3.5 4.0 - - - +
80E ASN* 2.7 50.8 + - - +
81E ASN 4.5 0.4 + - - -
100E ASP* 3.7 26.9 - - + -
102E ASP* 2.6 34.2 + - - -
104E PHE* 3.5 20.7 + - + +
105E VAL* 1.3 71.7 - - - +
107E MET* 1.3 59.5 + - - +
108E THR* 5.5 0.4 - - - -
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Residues in contact with MET 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E VAL* 4.0 9.2 - - + -
30E VAL* 2.6 23.2 + - - +
31E VAL* 4.2 12.3 - - + -
32E GLU* 3.2 17.5 + - - +
56E MET* 3.5 39.3 - - + -
59E PHE* 3.7 24.2 - - + -
77E LEU* 4.4 13.7 - - + -
78E LEU 3.3 6.1 - - - +
79E VAL* 4.3 10.8 - - + -
91E MET* 3.7 25.1 - - + -
94E ILE* 4.3 5.4 - - + -
105E VAL* 4.2 16.4 - - + -
106E TYR* 1.3 78.6 - - - +
108E THR* 1.3 65.2 - - - +
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Residues in contact with THR 108 (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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31E VAL* 5.4 0.4 - - - -
32E GLU* 3.2 14.1 - - - +
33E ARG 4.9 0.9 - - - -
34E TYR* 3.9 21.0 - - - +
35E PRO* 5.8 1.8 - - - -
77E LEU* 3.6 7.0 - - - +
78E LEU* 2.8 47.2 + - + +
81E ASN* 3.4 42.9 + - + +
106E TYR 5.3 0.2 - - - +
107E MET* 1.3 76.5 - - - +
109E TYR* 1.3 64.7 + - - +
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Residues in contact with TYR 109 (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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31E VAL* 4.1 13.0 - - + -
32E GLU 3.3 21.3 + - - -
33E ARG* 3.3 46.4 - - + +
34E TYR* 3.1 20.1 + - - +
37E GLU* 4.9 0.3 - - - +
40E LEU* 3.8 25.5 - - + +
41E PRO 2.8 19.9 + - - -
42E PRO* 3.4 11.4 - - - +
43E LEU* 3.9 15.1 + - + -
63E ILE* 5.1 1.6 - - + -
67E MET* 3.3 27.8 - - + +
75E PHE* 3.5 18.6 - + + -
76E TYR 3.2 13.7 - - - +
77E LEU* 4.1 5.8 - - + -
78E LEU* 5.6 0.2 - - - -
108E THR* 1.3 76.8 + - - +
110E ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 110 (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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34E TYR* 3.6 28.7 - - + -
37E GLU* 3.9 4.9 - - - -
40E LEU* 4.1 2.2 - - - -
75E PHE* 3.4 4.9 - - - +
76E TYR* 2.9 34.2 + - + +
78E LEU* 4.6 18.3 - - + +
109E TYR* 1.3 78.1 - - - +
111E SER* 1.3 63.2 + - - +
112E GLN* 3.8 14.4 - - - +
113E GLU* 4.7 1.3 - - + -
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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