Contacts of the strand formed by residues 148 - 153 (chain E) in PDB entry 3EBL
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 148 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E ILE* 4.0 19.3 - - + -
81E TYR 3.4 12.3 - - - +
82E ARG* 4.4 12.8 - - + -
113E PHE* 3.7 27.3 - - + -
114E PRO 3.0 6.7 + - - +
115E VAL* 3.5 6.9 - - + -
116E ILE* 2.8 26.7 + - - +
147E GLY* 1.3 78.2 - - - +
149E VAL* 1.3 72.1 + - - +
150E VAL* 4.2 2.2 - - + -
182E MET* 4.0 24.5 - - + -
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Residues in contact with VAL 149 (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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79E ARG 3.6 0.7 - - - +
80E ILE* 3.3 3.3 - - - -
81E TYR* 2.7 44.5 + - + +
116E ILE* 3.3 23.1 - - + +
118E PHE* 4.2 8.1 - - + -
138E CYS* 3.7 33.0 - - + +
141E PHE* 3.7 26.7 - - + -
142E VAL* 3.7 25.5 - - + +
145E SER* 5.1 0.7 - - - +
148E VAL* 1.3 79.5 - - - +
150E VAL* 1.3 71.5 + - - +
151E SER 4.0 0.4 - - - -
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Residues in contact with VAL 150 (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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78E VAL* 3.7 37.5 - - + -
79E ARG 3.5 3.1 - - - +
80E ILE* 4.5 6.3 - - + -
115E VAL* 4.4 9.0 - - + -
116E ILE 2.7 10.8 + - - +
117E ILE* 3.2 9.8 - - + +
118E PHE 2.7 30.7 + - - +
148E VAL* 4.3 5.6 - - + -
149E VAL* 1.3 79.8 - - - +
151E SER* 1.3 55.2 + - - +
152E VAL* 4.6 5.6 - - + -
172E ALA* 5.6 0.9 - - + -
175E TRP* 4.4 3.8 - - + -
176E VAL* 4.1 30.3 - - + -
182E MET* 4.2 21.3 - - + -
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Residues in contact with SER 151 (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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78E VAL* 3.2 4.4 - - - -
79E ARG 2.7 42.0 + - - -
81E TYR* 3.9 8.1 - - - -
118E PHE* 3.3 22.0 + - - -
120E HIS* 5.1 3.1 + - - +
129E ALA* 3.5 26.7 + - - +
134E TYR* 5.4 1.4 - - - +
138E CYS* 3.8 23.8 - - - -
149E VAL 4.0 0.8 - - - -
150E VAL* 1.3 73.1 - - - +
152E VAL* 1.3 63.5 + - - +
153E ASN 3.8 0.5 + - - -
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Residues in contact with VAL 152 (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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76E LEU* 4.0 22.2 - - + -
77E GLU 4.0 4.3 - - - +
78E VAL* 4.3 9.6 - - + -
117E ILE* 3.8 15.5 - - + -
118E PHE 2.9 11.2 + - - +
119E PHE* 3.6 29.5 - - + -
120E HIS* 3.9 9.4 - - - -
129E ALA* 4.3 2.2 - - - -
150E VAL* 4.1 2.9 - - + +
151E SER* 1.3 75.3 + - - +
153E ASN* 1.3 62.1 + - - +
154E TYR* 2.9 27.6 + - + +
168E ASP 4.3 4.5 - - - +
172E ALA* 3.4 33.7 - - + -
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Residues in contact with ASN 153 (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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75E GLY 5.3 1.5 + - - +
76E LEU* 3.4 16.8 - - - +
77E GLU* 2.8 42.2 + - + +
78E VAL 5.8 0.2 - - - -
120E HIS* 4.7 1.3 + - - -
128E SER* 3.1 18.3 + - - -
129E ALA* 2.7 37.4 + - + +
130E SER 5.3 0.2 - - - -
151E SER 3.8 2.0 + - - -
152E VAL* 1.3 67.8 - - - +
154E TYR* 1.3 65.1 + - - +
155E ARG* 5.4 1.4 - - - +
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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