Contacts of the strand formed by residues 264 - 270 (chain E) in PDB entry 5CEV
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 ILE 264 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91E PHE* 3.7 22.6 - - + -
119E ILE* 4.5 2.5 - - + -
221E VAL* 3.4 28.0 - - + +
223E LEU* 4.1 18.2 - - + -
258E LEU* 4.0 38.8 + - + +
262E GLN* 3.7 2.6 - - - +
263E ILE* 1.3 78.2 - - + +
265E THR* 1.3 60.0 + - - +
266E SER 3.3 25.6 - - - +
267E ALA* 4.4 1.1 - - + -
293E LEU* 3.9 28.0 - - + -
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Residues in contact with THR 265 (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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2E LYS* 6.1 0.3 - - - +
91E PHE* 3.5 17.8 - - - -
92E PRO* 3.9 9.5 - - - +
109E VAL* 5.5 0.2 - - - +
113E TYR* 3.4 30.0 + - + +
116E LEU* 4.3 3.1 - - - +
219E ASP 4.9 1.8 - - - +
220E GLY* 3.4 16.1 - - - -
221E VAL 2.8 27.2 + - - -
262E GLN 5.9 0.7 - - - +
263E ILE 3.8 10.5 - - - +
264E ILE* 1.3 76.4 - - - +
266E SER* 1.3 64.2 + - - +
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Residues in contact with SER 266 (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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91E PHE* 3.4 12.2 - - - -
92E PRO* 3.7 22.2 - - - -
105E THR* 5.5 0.4 - - - -
109E VAL* 3.8 22.4 - - - +
221E VAL 3.6 1.0 + - - -
222E HIS* 2.7 37.0 + - - +
223E LEU 2.9 21.8 + - - -
264E ILE* 3.3 5.7 - - - +
265E THR* 1.3 80.9 + - - +
267E ALA* 1.3 63.9 + - - +
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Residues in contact with ALA 267 (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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91E PHE* 3.5 17.0 - - + -
92E PRO 3.3 9.7 + - - +
93E LEU* 3.5 11.0 - - + -
94E VAL* 2.9 24.4 + - - +
105E THR* 5.1 0.2 - - - +
222E HIS* 3.7 5.0 + - - -
223E LEU* 3.1 16.2 - - + +
264E ILE* 4.4 0.2 - - + -
266E SER* 1.3 79.2 - - - +
268E GLU* 1.3 62.2 + - - +
269E PHE* 4.4 4.3 - - + -
293E LEU* 4.0 21.8 - - + -
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Residues in contact with GLU 268 (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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94E VAL* 3.0 23.1 - - + +
101E ILE* 3.9 7.6 - - - +
102E ALA* 3.5 26.7 + - - +
105E THR* 2.9 21.2 + - - -
222E HIS* 2.7 24.2 + - + +
223E LEU 2.9 6.3 + - - +
224E SER* 2.7 31.4 + - - +
225E LEU* 2.9 26.9 + - - +
267E ALA* 1.3 75.5 - - - +
269E PHE* 1.3 67.6 + - - +
270E VAL* 4.1 13.9 - - + -
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Residues in contact with PHE 269 (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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27E MET* 3.7 25.2 - - - +
93E LEU* 4.3 7.0 - - + -
94E VAL 3.0 6.1 + - - -
95E LEU* 3.7 3.3 - - + -
96E GLY 2.8 23.7 + - - -
223E LEU* 4.3 20.0 - - + -
225E LEU* 3.4 37.7 - - + -
227E LEU* 4.2 4.3 - - + -
255E MET* 4.4 3.6 - - - -
267E ALA* 4.4 6.3 - - + -
268E GLU* 1.3 81.3 - - - +
270E VAL* 1.3 61.2 + - - +
286E ALA* 3.9 24.5 - - + -
289E LEU* 4.0 9.4 - - + -
290E MET* 3.5 42.2 - - + -
293E LEU* 4.2 17.9 - - + -
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Residues in contact with VAL 270 (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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96E GLY* 4.2 2.5 - - - -
97E GLY 3.3 9.6 - - - +
99E HIS* 3.6 38.8 - - + +
101E ILE* 3.7 34.8 - - + -
225E LEU 2.9 19.1 + - - +
226E ASP* 3.6 11.0 - - - -
227E LEU* 3.2 24.2 + - - +
268E GLU* 4.3 14.8 - - + -
269E PHE* 1.3 78.4 - - - +
271E GLU* 1.3 73.9 + - + +
272E VAL* 3.2 5.6 + - - -
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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