Contacts of the strand formed by residues 191 - 198 (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 ARG 191 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E PRO* 5.7 1.1 - - + -
113E PHE 3.6 18.3 + - - +
114E PRO* 3.5 4.0 - - - +
115E VAL* 2.7 30.4 + - - +
182E MET 4.3 4.0 + - - -
184E SER* 4.3 9.6 + - - +
190E ALA* 1.3 68.1 - - - +
192E VAL* 1.3 56.7 + - - +
193E PHE* 3.7 3.0 - - - -
219E CYS* 3.8 20.2 - - - -
352E LEU* 3.8 24.0 - - + +
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Residues in contact with VAL 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E VAL* 3.4 7.2 - - + -
117E ILE* 4.0 13.5 - - + -
173E LEU* 3.6 24.9 - - + -
176E VAL* 4.0 26.0 - - + -
177E MET* 4.0 19.5 - - + -
190E ALA* 3.3 20.4 + - + +
191E ARG* 1.3 73.6 - - - +
193E PHE* 1.3 70.2 + - - +
194E LEU* 4.3 6.3 - - + -
217E LYS 4.6 4.4 + - - +
218E VAL* 3.6 6.6 - - + +
219E CYS* 2.8 36.6 + - - +
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Residues in contact with PHE 193 (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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114E PRO* 3.7 24.2 - - + -
115E VAL 2.8 13.2 + - - +
116E ILE* 3.5 6.0 - - + +
117E ILE* 2.8 28.4 + - - +
191E ARG 3.7 10.3 - - - -
192E VAL* 1.3 76.2 - - - +
194E LEU* 1.3 63.2 + - - +
219E CYS* 3.6 28.5 - - + -
220E GLY* 3.1 25.8 - - - +
222E ILE* 4.3 14.4 - - + -
347E PHE* 3.8 23.1 - + - -
348E LEU* 3.6 42.0 - - + -
351E ASN* 3.9 14.6 - - + -
352E LEU* 4.5 5.2 - - + -
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Residues in contact with LEU 194 (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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117E ILE* 3.6 35.2 - - + +
119E PHE* 4.5 5.8 - - + -
173E LEU* 4.2 11.4 - - + -
192E VAL* 4.3 2.7 - - + -
193E PHE* 1.3 74.5 - - - +
195E SER* 1.3 59.9 + - - +
204E ALA* 3.7 20.2 - - + +
207E VAL* 3.9 23.1 - - + +
208E ALA* 3.6 34.8 - - + +
218E VAL* 4.0 19.7 - - + +
220E GLY 2.9 6.5 + - - +
221E ASN* 3.2 18.4 - - - +
222E ILE* 2.9 24.4 + - - +
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Residues in contact with SER 195 (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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116E ILE* 3.8 26.2 - - - -
117E ILE 2.8 9.2 + - - +
118E PHE* 3.7 14.5 - - - -
119E PHE* 2.9 28.1 + - - -
141E PHE* 4.0 11.3 - - - -
194E LEU* 1.3 76.8 - - - +
196E GLY* 1.3 61.2 + - - +
204E ALA* 4.0 7.5 - - - +
222E ILE* 3.2 27.9 + - - +
224E LEU* 4.5 2.6 - - - +
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Residues in contact with GLY 196 (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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118E PHE* 3.6 9.4 - - - -
119E PHE 3.1 16.4 - - - -
195E SER* 1.3 78.7 + - - +
197E ASP* 1.3 60.4 + - - -
200E GLY 3.5 9.7 + - - -
201E GLY* 3.3 14.2 - - - -
204E ALA* 4.3 1.8 - - - +
222E ILE 3.2 3.8 + - - +
223E LEU* 3.7 1.7 - - - -
224E LEU* 3.1 22.4 + - - -
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Residues in contact with ASP 197 (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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118E PHE* 3.6 9.1 - - + -
119E PHE 3.5 1.0 + - - -
121E GLY* 2.8 28.0 + - - -
134E TYR* 2.7 33.0 + - - -
196E GLY* 1.3 72.3 - - - -
198E SER* 1.3 63.7 + - - +
200E GLY* 2.7 25.5 + - - -
201E GLY 3.7 0.2 - - - -
224E LEU* 3.0 19.7 - - + +
329E TYR* 2.4 41.3 + - + +
401E GA4 3.4 4.3 - - - +
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Residues in contact with SER 198 (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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121E GLY* 3.6 12.8 - - - -
122E GLY 4.0 0.2 - - - -
123E SER* 3.4 9.7 + - - -
197E ASP* 1.3 73.5 - - - +
199E SER* 1.3 65.4 + - - -
201E GLY* 2.8 19.1 + - - -
202E ASN 3.5 0.5 + - - -
224E LEU 3.0 12.1 + - - -
225E ASN* 3.1 16.5 + - - +
227E MET* 3.1 26.9 + - - +
329E TYR* 4.7 0.4 + - - -
401E GA4 2.9 44.9 + - - -
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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