Contacts of the strand formed by residues 73 - 79 (chain E) in PDB entry 5DSV
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 73 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68E ASN* 3.6 10.4 - - - +
69E VAL* 3.2 33.0 + - + -
70E ASP* 3.5 16.2 + - + +
71E ARG 3.4 0.8 - - - -
72E HIS* 1.3 113.4 - - + +
74E GLY* 1.3 70.6 + - - +
106E ILE* 4.9 1.8 - - + -
108E LEU* 3.7 32.3 - - + -
111E LEU* 4.1 17.0 - - + -
137E LEU* 4.3 6.3 - - + -
138E GLY 3.4 3.4 - - - +
224E HIS* 4.0 3.8 - - - -
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Residues in contact with GLY 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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47E PHE* 3.9 6.6 - - - -
67E PHE 3.4 9.6 - - - -
69E VAL 5.0 0.4 - - - -
73E VAL* 1.3 78.4 - - - +
75E MET* 1.3 59.7 + - - -
136E MET 3.5 0.7 - - - +
137E LEU* 3.2 6.6 - - - -
138E GLY 2.8 34.3 + - - -
224E HIS* 3.4 23.9 - - - -
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Residues in contact with MET 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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47E PHE* 5.2 1.1 - - - -
65E ARG 3.8 0.7 - - - +
66E LEU* 3.3 7.0 - - - +
67E PHE* 2.9 40.0 + - + +
69E VAL* 3.7 29.4 - - + -
74E GLY* 1.3 74.6 - - - -
76E ALA* 1.3 64.2 + - - +
77E VAL* 3.7 26.0 - - + -
84E ALA* 3.9 22.0 - - - +
87E LEU* 4.3 5.6 - - + -
88E ALA* 3.8 22.7 - - + +
91E ALA* 4.9 2.5 - - - -
135E PHE* 3.7 27.4 - - + -
136E MET 3.2 4.0 - - - +
137E LEU* 3.8 16.6 - - + -
224E HIS* 4.7 0.5 + - - -
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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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36E ALA* 5.6 4.9 - - + -
37E ILE 5.5 1.3 - - - +
47E PHE* 3.6 28.5 - - + -
49E VAL* 5.2 3.1 - - + -
65E ARG 3.5 4.9 - - - -
66E LEU* 3.4 22.4 - - + -
75E MET* 1.3 75.5 - - - +
77E VAL* 1.3 59.4 + - - +
135E PHE* 3.1 2.4 - - - -
136E MET* 2.8 40.9 + - + +
165E ILE* 3.7 7.1 - - - +
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Residues in contact with VAL 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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36E ALA* 4.2 6.2 - - - +
65E ARG* 3.1 46.3 + - + +
67E PHE* 3.8 26.0 - - + -
75E MET* 3.7 33.0 - - + -
76E ALA* 1.3 78.4 - - - +
78E ALA* 1.3 63.0 + - - +
81E LEU* 4.1 16.8 - - + -
84E ALA* 3.8 16.4 - - + -
134E SER 3.7 5.6 - - - +
135E PHE* 3.8 4.7 - - + -
165E ILE* 4.1 2.0 - - - -
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Residues in contact with ALA 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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30E VAL* 3.8 14.7 - - + +
33E SER* 4.4 0.2 - - - +
34E SER 4.3 2.9 - - - +
36E ALA* 4.8 0.7 - - + -
65E ARG* 3.6 16.2 - - - +
77E VAL* 1.3 80.1 - - - +
79E GLY* 1.3 60.6 + - - +
133E CYS* 3.4 6.8 - - - +
134E SER 3.0 32.8 + - - +
165E ILE* 3.5 36.1 - - + +
166E GLY* 4.5 0.9 - - - +
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Residues in contact with GLY 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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29E ALA 3.6 14.4 - - - -
30E VAL* 3.8 6.7 - - - +
33E SER* 3.1 35.3 + - - -
65E ARG* 5.8 0.5 - - - -
78E ALA* 1.3 73.1 - - - +
80E LEU* 1.3 64.0 + - - -
81E LEU* 3.2 10.0 + - - +
84E ALA* 6.2 0.2 - - - -
132E GLY 3.8 1.3 - - - -
133E CYS* 4.6 0.2 - - - -
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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