Contacts of the helix formed by residues 294 - 303 (chain E) in PDB entry 6XAV
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 294 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271E ALA* 4.2 25.8 - - + +
285E LEU* 6.3 3.4 - - + -
289E VAL* 3.7 26.9 - - + -
290E ASP 4.6 1.6 + - - +
291E ALA 5.1 1.7 + - - +
292E ASN* 3.3 0.6 - - - +
293E ALA* 1.3 76.5 - - + +
295E HIS* 1.3 65.3 + - - +
296E ARG 3.2 2.2 - - - -
297E PRO* 3.3 6.8 - - + +
298E LYS* 3.2 40.9 + - + +
330E VAL* 5.4 8.7 - - + +
331E ILE* 4.4 15.7 - - + -
334E GLU* 4.1 31.2 - - + +
335E PHE* 4.5 7.9 - - + -
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Residues in contact with HIS 295 (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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291E ALA 5.4 0.4 + - - -
292E ASN* 3.4 27.9 + - + +
293E ALA 3.4 1.4 - - - -
294E LEU* 1.3 78.3 - - - +
296E ARG* 1.3 82.7 + - - +
298E LYS* 4.1 11.9 - - - +
299E ARG* 3.3 29.2 + - + +
232F PHE 4.4 2.0 - - - +
233F ASP* 2.8 35.4 + - - +
234F GLU* 4.0 13.6 + - - -
235F PRO* 4.0 15.8 - - + +
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Residues in contact with ARG 296 (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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240E VAL* 5.3 1.8 - - - +
244E GLU* 2.4 35.2 + - - +
274E TYR* 3.5 44.4 + - + -
292E ASN 4.7 8.1 - - - +
293E ALA 4.3 0.4 + - - -
295E HIS* 1.3 100.3 - - - +
297E PRO* 1.3 72.5 - - + +
299E ARG* 3.0 21.0 + - - +
300E PHE* 3.1 12.0 + - - +
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Residues in contact with PRO 297 (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 ILE* 5.1 5.8 - - + +
270E LEU* 5.0 7.4 - - + -
271E ALA* 4.2 28.0 - - + +
274E TYR* 3.8 15.9 - - + -
293E ALA 3.2 17.5 - - - +
294E LEU* 3.3 19.7 - - - +
296E ARG* 1.3 93.4 - - + +
298E LYS* 1.3 56.0 + - - +
300E PHE* 3.4 8.2 + - + +
301E PHE* 2.9 30.5 + - - +
335E PHE* 4.1 19.9 - - + -
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Residues in contact with LYS 298 (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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294E LEU* 3.2 31.1 + - + +
295E HIS* 4.1 6.8 - - - +
296E ARG 3.2 0.6 - - - -
297E PRO* 1.3 74.2 - - - +
299E ARG* 1.3 59.5 + - - +
301E PHE* 4.3 5.8 - - - -
302E GLY* 2.9 24.3 + - - -
334E GLU* 4.0 22.8 + - + +
335E PHE* 3.6 25.6 - - + -
338E THR* 5.2 6.7 - - + +
210F ASP* 3.5 21.3 + - - +
232F PHE* 3.2 56.3 + - + +
233F ASP* 5.1 0.4 - - - -
234F GLU 5.3 1.6 + - - -
239F HIS* 5.9 0.2 + - - -
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Residues in contact with ARG 299 (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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134E GLU* 6.0 2.8 + - - +
251E LYS* 5.3 11.8 + - - +
295E HIS* 3.3 19.2 + - + +
296E ARG* 3.0 18.7 + - - +
298E LYS* 1.3 79.5 - - - +
300E PHE* 1.3 61.6 + - - +
303E ALA* 3.3 20.3 + - - +
233F ASP* 3.1 62.3 + - + +
234F GLU* 4.1 10.3 + - - -
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Residues in contact with PHE 300 (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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207E LEU* 4.9 3.4 - - + -
243E ALA* 4.5 10.1 - - + -
244E GLU* 5.7 3.4 - - - +
247E ILE* 3.5 49.1 - - + -
251E LYS* 6.3 0.4 - - - +
262E ILE* 4.6 17.7 - - + -
264E LEU* 3.6 31.4 - - + -
267E ILE* 6.4 3.1 - - + -
270E LEU* 4.1 18.6 - - + -
274E TYR* 5.6 4.7 - - - +
296E ARG 3.1 8.5 + - - +
297E PRO* 3.9 8.7 - - + +
299E ARG* 1.3 79.2 - - - +
301E PHE* 1.3 68.4 + + - +
303E ALA* 3.3 18.2 + - - +
315E ILE* 3.8 31.2 - - + +
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Residues in contact with PHE 301 (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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173E ARG* 3.2 58.8 - - + +
174E GLY 4.5 5.8 - - - -
175E LEU* 3.6 42.4 - - + -
267E ILE* 3.9 20.4 - - + -
297E PRO 2.9 17.9 + - - +
298E LYS* 3.9 6.1 - - - +
299E ARG 3.3 0.2 - - - -
300E PHE* 1.3 84.4 - + + +
302E GLY* 1.3 61.9 + - - +
303E ALA 3.1 1.6 + - - -
304E ALA* 3.5 8.1 + - - +
315E ILE* 4.6 13.4 - - + +
317E ALA* 5.2 3.1 - - + -
335E PHE* 5.5 6.3 - + + -
338E THR* 3.9 31.2 - - + -
339E GLY* 3.9 11.2 - - - -
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Residues in contact with GLY 302 (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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173E ARG* 4.5 8.3 - - - -
298E LYS 2.9 17.0 + - - -
299E ARG 4.0 1.8 - - - -
301E PHE* 1.3 75.0 - - - +
303E ALA* 1.3 64.0 + - - +
304E ALA 3.1 8.8 + - - +
305E ARG* 3.5 17.1 + - - -
213F PRO* 4.6 8.1 - - - +
214F GLU* 5.0 3.5 - - - +
232F PHE* 4.1 19.7 - - - -
233F ASP* 5.0 5.2 - - - -
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Residues in contact with ALA 303 (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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133E PHE* 3.5 15.8 - - - -
247E ILE* 3.9 15.0 - - + -
251E LYS* 3.8 30.3 - - - +
299E ARG 3.3 11.2 + - - +
300E PHE* 3.3 14.9 + - - +
301E PHE 3.1 1.6 - - - -
302E GLY* 1.3 76.9 - - - +
304E ALA* 1.3 63.2 + - - +
305E ARG* 3.2 11.3 + - - +
313E LEU* 3.3 13.2 - - + +
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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