Contacts of the strand formed by residues 116 - 121 (chain E) in PDB entry 4CEV
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 LEU 116 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106E LEU* 3.8 29.2 - - + -
109E VAL* 3.9 15.9 - - + -
110E ALA* 3.7 31.0 - - + +
113E TYR* 3.9 27.1 + - + +
114E GLU 4.1 0.4 - - - -
115E ARG* 1.3 72.2 - - - +
117E GLY* 1.3 69.7 + - - +
163E LYS 4.8 2.8 + - - +
164E ILE* 3.6 24.8 - - + +
168E HIS* 3.6 13.6 + - - +
218E THR* 4.3 0.9 - - - -
219E ASP* 3.7 0.8 + - - -
220E GLY* 3.4 29.8 - - - +
221E VAL 3.9 2.9 - - - +
222E HIS* 3.9 8.3 - - + +
265E THR* 4.3 2.9 - - - +
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Residues in contact with GLY 117 (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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115E ARG 3.4 2.8 + - - -
116E LEU* 1.3 78.6 - - - +
118E VAL* 1.3 67.6 + - - +
168E HIS 3.1 12.8 - - - -
214E LEU* 4.2 3.8 - - - -
218E THR* 3.6 17.0 - - - +
220E GLY 2.8 13.1 + - - -
221E VAL* 4.1 5.6 - - - -
222E HIS 3.0 22.2 + - - -
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Residues in contact with VAL 118 (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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106E LEU* 3.9 15.9 - - + -
117E GLY* 1.3 80.2 - - - +
119E ILE* 1.3 70.7 + - - +
120E TRP* 3.7 34.3 - - + +
143E LEU* 4.7 4.3 - - + -
164E ILE* 3.7 35.4 - - + -
168E HIS 2.8 8.7 + - - +
169E VAL* 3.4 12.3 - - + +
170E VAL* 2.9 27.2 + - - +
214E LEU* 4.3 3.1 - - - +
221E VAL* 4.4 1.2 - - - +
222E HIS* 3.4 17.7 - - + +
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Residues in contact with ILE 119 (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 VAL* 1.3 71.5 - - - +
120E TRP* 1.3 60.1 + - - +
121E TYR* 3.7 9.5 + - + +
170E VAL* 3.5 4.7 - - + +
172E ILE* 4.0 24.7 - - + -
207E MET* 4.9 2.0 - - + -
210E THR* 3.8 19.1 - - + -
214E LEU* 3.5 26.0 - - + -
221E VAL* 4.0 12.1 - - + +
222E HIS 3.0 8.9 + - - +
223E LEU* 3.8 20.8 - - + +
224E SER* 2.9 28.4 + - - +
258E LEU* 3.7 35.7 - - + -
263E ILE* 4.7 2.9 - - + -
264E ILE* 4.3 1.6 - - + -
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Residues in contact with TRP 120 (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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99E HIS* 3.2 20.4 - + - -
102E ALA* 3.5 28.3 - - + -
106E LEU* 4.3 13.9 - - + -
118E VAL* 3.7 16.3 - - + -
119E ILE* 1.3 70.3 - - - +
121E TYR* 1.3 62.3 + - - +
122E ASP* 3.2 26.6 + - + +
124E HIS 4.1 1.6 - - - -
125E GLY 3.9 0.9 + - - -
126E ASP* 3.0 41.7 + - + +
142E PRO* 3.8 4.7 - - + -
143E LEU* 3.7 38.6 - - + -
169E VAL* 5.0 1.8 - - + -
170E VAL 2.9 11.6 + - - +
171E LEU* 3.4 34.0 - - + +
172E ILE 2.9 25.0 + - - +
174E VAL* 5.3 0.2 - - - +
224E SER* 3.6 25.8 - - - -
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Residues in contact with TYR 121 (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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119E ILE* 3.7 6.5 + - + +
120E TRP* 1.3 68.8 - - - +
122E ASP* 1.3 62.2 + - - +
172E ILE* 3.5 26.0 - - + +
203E MET* 3.6 12.9 - - + +
207E MET* 5.8 0.4 - - - -
223E LEU* 4.6 6.1 - - + -
224E SER 3.1 9.4 + - - +
225E LEU* 3.8 35.2 - - + -
226E ASP* 2.9 33.7 + - - +
229E GLY* 4.8 3.1 - - - -
230E LEU* 4.3 11.2 - - + -
246E LEU* 3.4 32.9 - - + +
251E SER* 2.8 42.1 + - - -
254E ALA* 4.0 18.8 - - + -
255E MET* 4.5 8.1 - - + -
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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