Contacts of the helix formed by residues 263 - 275 (chain E) in PDB entry 5UQ9
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 THR 263 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103E ASN* 4.2 13.3 + - + +
184E LYS* 4.5 0.7 - - + +
185E MET* 3.9 17.9 - - - +
188E ASN* 3.2 39.0 + - + +
192E TYR* 4.5 2.8 + - - -
262E GLY* 1.3 81.9 + - - +
264E GLY* 1.3 67.4 + - - +
265E LYS 3.2 2.9 - - - +
266E TRP* 3.0 21.7 + - + +
267E THR* 3.0 24.8 + - - -
501F 8HS 4.2 22.2 + - - +
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Residues in contact with GLY 264 (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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188E ASN* 4.8 0.4 - - - +
189E GLY* 4.4 5.4 - - - -
192E TYR* 3.8 28.3 - - - -
263E THR* 1.3 76.1 - - - +
265E LYS* 1.3 64.3 + - - +
267E THR* 3.3 10.4 + - - -
268E ALA* 3.2 18.4 + - - +
281E ILE* 4.5 0.5 - - - +
285E VAL* 3.2 26.7 - - - +
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Residues in contact with LYS 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E TYR* 5.0 1.6 + - - -
260E GLN* 4.7 18.5 - - + +
262E GLY* 4.7 11.2 - - - -
263E THR 3.2 5.7 - - - +
264E GLY* 1.3 77.7 - - - +
266E TRP* 1.3 81.7 + - + +
268E ALA* 3.5 1.9 + - - +
269E ILE* 3.0 49.4 + - + +
285E VAL* 4.0 18.1 - - + +
272F LEU* 3.1 34.9 - - + +
273F GLU* 4.0 20.6 + - - +
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Residues in contact with TRP 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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77E ALA* 5.3 4.9 - - + -
103E ASN* 3.2 34.3 - - + -
104E SER 4.2 1.6 - - - -
105E GLU* 3.5 53.2 + - + -
106E TYR* 5.8 0.2 - - - -
185E MET* 3.6 19.3 - - + +
261E LYS 5.4 1.6 - - - -
262E GLY* 3.1 29.3 + - - -
263E THR* 3.0 18.2 + - + +
265E LYS* 1.3 107.9 - - + +
267E THR* 1.3 58.6 + - - +
269E ILE* 3.8 8.9 - - + +
270E SER* 2.9 31.7 + - - -
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Residues in contact with THR 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E MET* 2.8 34.6 + - - +
186E VAL* 4.0 17.9 - - + -
189E GLY* 3.7 9.0 - - - -
263E THR 3.0 10.4 + - - -
264E GLY 3.3 7.8 + - - -
266E TRP* 1.3 77.9 - - - +
268E ALA* 1.3 60.8 + - - +
270E SER* 3.5 0.7 + - - -
271E ALA* 3.2 21.8 + - - +
278E VAL* 5.1 1.7 - - + +
281E ILE* 4.1 26.9 - - + -
341E LEU* 3.7 21.8 - - + +
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Residues in contact with ALA 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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264E GLY 3.2 12.6 + - - +
265E LYS 4.1 0.4 - - - +
267E THR* 1.3 76.7 - - - +
269E ILE* 1.3 66.4 + - - +
271E ALA* 3.3 7.0 + - - +
272E LEU* 3.1 28.1 + - + +
278E VAL* 5.6 2.0 - - - -
281E ILE* 4.9 2.4 - - - +
282E GLY* 3.9 26.5 - - - +
285E VAL* 4.7 1.6 - - + -
272F LEU* 3.6 28.9 - - + -
286F PHE* 4.5 5.3 - - + -
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Residues in contact with ILE 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E LYS* 3.0 45.5 + - + +
266E TRP* 3.8 9.0 - - + +
268E ALA* 1.3 77.9 - - - +
270E SER* 1.3 57.7 + - - +
272E LEU* 3.4 2.6 + - - +
273E GLU* 3.0 39.8 + - - +
266F TRP* 6.2 0.2 - - + -
269F ILE* 3.7 26.9 - - + +
272F LEU* 3.6 21.5 - - + -
273F GLU* 3.9 27.1 - - + +
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Residues in contact with SER 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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106E TYR* 3.6 15.5 + - - -
182E PHE* 3.4 26.3 - - - -
185E MET* 4.1 14.6 - - - -
266E TRP 2.9 17.9 + - - -
267E THR 3.8 4.9 - - - -
269E ILE* 1.3 79.2 - - - +
271E ALA* 1.3 60.1 + - - +
273E GLU* 3.5 8.9 + - - +
274E TYR* 3.3 30.9 + - - +
341E LEU* 4.0 7.0 - - - +
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Residues in contact with ALA 271 (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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267E THR 3.2 13.7 + - - +
268E ALA* 3.7 9.2 - - - +
269E ILE 3.2 0.2 - - - -
270E SER* 1.3 75.2 - - - +
272E LEU* 1.3 60.9 + - - +
274E TYR 3.4 0.9 + - - -
275E GLY 2.9 25.3 + - - -
276E VAL* 3.0 31.3 + - - +
278E VAL* 3.6 26.5 - - + -
341E LEU* 4.2 10.7 - - + +
286F PHE* 4.1 4.9 - - + -
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Residues in contact with LEU 272 (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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268E ALA 3.1 20.7 + - - +
269E ILE 3.9 0.2 - - - +
271E ALA* 1.3 78.1 - - - +
273E GLU* 1.3 62.2 + - - +
274E TYR 3.4 0.7 + - - -
275E GLY* 3.5 8.6 + - - -
286E PHE* 6.3 0.2 - - + -
260F GLN* 4.7 2.9 + - - -
265F LYS* 3.2 24.8 + - + +
268F ALA* 3.7 27.8 - - + -
269F ILE* 3.7 22.2 - - + -
272F LEU* 3.7 21.8 - - + -
282F GLY* 4.3 2.7 - - - +
285F VAL* 3.7 32.5 - - + +
286F PHE* 3.5 31.4 - - + -
289F CYS* 5.7 0.7 - - - -
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Residues in contact with GLU 273 (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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107E ARG* 3.0 32.8 + - - -
269E ILE* 3.0 30.6 + - - +
270E SER* 3.9 8.7 - - - +
271E ALA 3.2 0.2 - - - -
272E LEU* 1.3 77.1 - - - +
274E TYR* 1.3 73.9 + - + +
265F LYS* 3.9 19.5 + - + -
266F TRP* 3.8 34.4 - - + -
269F ILE* 4.3 3.8 - - + -
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Residues in contact with TYR 274 (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 TYR* 3.7 14.4 - - - -
107E ARG* 3.1 32.6 + - - -
182E PHE* 5.6 1.6 - + - -
270E SER* 3.3 28.0 + - - +
271E ALA 4.6 0.7 - - - +
272E LEU 3.3 0.2 - - - -
273E GLU* 1.3 90.8 - - + +
275E GLY* 1.3 63.1 + - - +
276E VAL* 3.6 5.6 - - + +
341E LEU* 5.6 3.4 - - + -
344E GLN* 3.8 28.7 + - + -
345E ALA* 5.9 2.5 - - - -
348E GLU* 3.6 37.0 - - + +
349E PHE* 3.1 35.5 - + - -
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Residues in contact with GLY 275 (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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271E ALA 2.9 9.6 + - - -
272E LEU 3.5 6.5 + - - -
273E GLU 3.6 0.2 - - - -
274E TYR* 1.3 80.5 - - - +
276E VAL* 1.3 58.0 + - - +
277E PRO* 4.0 2.4 - - - +
344E GLN* 5.7 0.3 - - - -
260F GLN* 5.1 3.8 - - - -
265F LYS* 6.0 0.4 - - - +
289F CYS* 3.5 36.8 - - - +
293F LEU* 5.8 3.3 - - - +
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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