Contacts of the helix formed by residues 294 - 303 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271B ALA* 4.2 19.1 - - + +
275B ASN* 6.2 0.9 - - + -
289B VAL* 3.7 27.6 - - + -
290B ASP 4.4 2.8 + - - +
291B ALA 4.9 3.0 + - - +
292B ASN* 3.6 0.4 - - - +
293B ALA* 1.3 77.9 - - + +
295B HIS* 1.3 63.6 + - - +
296B ARG 3.4 0.7 - - - -
297B PRO* 3.5 5.3 - - - +
298B LYS* 3.1 24.3 + - - +
330B VAL* 5.0 5.8 - - + +
331B ILE* 3.9 34.1 - - + -
334B GLU* 4.2 31.9 - - + +
335B PHE* 4.4 12.9 - - + -
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Residues in contact with HIS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B ALA 5.4 1.5 + - - +
292B ASN* 4.1 20.5 + - + +
293B ALA 3.2 1.2 - - - -
294B LEU* 1.3 79.1 - - - +
296B ARG* 1.3 75.5 + - + +
298B LYS* 3.3 6.7 + - - +
299B ARG* 3.2 43.7 + - - +
232C PHE 3.9 15.3 - - - -
233C ASP 2.7 30.2 + - - -
234C GLU 3.8 15.4 - - - -
235C PRO* 3.9 14.5 - - + +
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B VAL* 4.8 5.3 - - - +
244B GLU* 2.4 40.8 + - - +
274B TYR* 3.5 41.4 + - + -
292B ASN 5.2 5.2 - - - +
293B ALA 4.0 3.1 + - - +
295B HIS* 1.3 90.2 - - + +
297B PRO* 1.3 71.4 - - + +
298B LYS 3.3 0.2 + - - -
299B ARG* 3.4 9.4 + - - +
300B PHE* 3.1 21.1 + - - +
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Residues in contact with PRO 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B ILE* 4.7 9.1 - - + +
270B LEU* 5.2 3.1 - - + -
271B ALA* 3.9 23.8 - - + +
274B TYR* 3.6 22.4 - - + -
293B ALA 3.2 19.5 - - - +
294B LEU* 3.5 9.4 - - - +
296B ARG* 1.3 92.3 - - + +
298B LYS* 1.3 56.1 + - - +
300B PHE* 3.8 10.1 - - + +
301B PHE* 2.9 31.0 + - - +
335B PHE* 3.8 23.9 - - + -
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LEU 3.1 19.8 + - - +
295B HIS* 3.4 9.2 - - - +
296B ARG 3.1 0.4 - - - -
297B PRO* 1.3 77.2 - - - +
299B ARG* 1.3 56.4 + - - +
301B PHE* 3.9 2.1 - - + +
302B GLY 3.0 23.4 + - - -
334B GLU* 4.4 17.8 + - + +
335B PHE* 3.7 24.2 - - + -
338B THR* 3.3 32.7 - - + +
210C ASP* 3.7 17.0 + - - -
232C PHE* 3.4 58.9 - - + +
233C ASP* 4.3 1.1 - - - -
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLU* 6.1 3.0 - - - +
251B LYS* 5.4 8.0 + - - +
295B HIS* 3.2 29.4 + - + +
296B ARG* 3.4 9.8 + - - +
298B LYS* 1.3 73.0 - - - +
300B PHE* 1.3 64.9 + - - +
302B GLY 3.9 0.2 - - - -
303B ALA* 3.1 25.3 + - - +
232C PHE 5.0 0.2 - - - +
233C ASP* 3.4 57.8 + - - +
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Residues in contact with PHE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B LEU* 4.1 21.5 - - + -
243B ALA* 3.6 24.7 - - + -
244B GLU* 5.3 3.8 - - - +
246B VAL* 5.2 2.9 - - + -
247B ILE* 3.6 38.3 - - + +
262B ILE* 5.2 11.7 - - + -
264B LEU* 3.7 28.9 - - + -
267B ILE* 5.1 3.1 - - + -
270B LEU* 3.7 24.5 - - + -
274B TYR* 5.4 5.4 - - - +
296B ARG 3.1 17.4 + - - +
297B PRO* 3.8 7.9 - - + +
298B LYS 3.3 0.2 - - - -
299B ARG* 1.3 77.4 - - - +
301B PHE* 1.3 65.6 + + - +
303B ALA* 3.8 8.0 - - - +
315B ILE* 3.6 24.2 - - + +
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ARG* 3.2 41.8 - - + +
174B GLY 3.4 24.7 - - - -
175B LEU* 3.5 34.3 - - + -
264B LEU* 5.8 0.9 - - + -
267B ILE* 4.9 14.1 - - + -
297B PRO 2.9 18.1 + - - +
298B LYS* 3.9 4.9 - - - +
300B PHE* 1.3 77.7 - - - +
302B GLY* 1.3 57.3 + - - +
303B ALA 3.1 9.3 + - - -
304B ALA* 3.5 9.2 + - - +
315B ILE* 4.0 23.9 - - + +
317B ALA* 4.1 11.2 - - + -
335B PHE* 4.7 15.9 - + + -
338B THR* 4.2 18.6 - - + -
339B GLY* 4.6 9.9 - - - -
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Residues in contact with GLY 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ARG* 4.0 12.6 + - - -
298B LYS 3.0 16.9 + - - -
299B ARG 3.9 1.8 - - - -
301B PHE* 1.3 74.3 - - - +
303B ALA* 1.3 62.3 + - - +
304B ALA 3.1 9.3 + - - +
305B ARG* 4.2 13.6 + - - -
338B THR* 5.5 0.6 - - - +
213C PRO* 4.4 8.2 - - - +
214C GLU* 5.2 0.5 - - - +
232C PHE* 3.9 23.3 - - - -
233C ASP* 5.3 3.1 - - - -
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PHE* 3.4 26.0 - - + -
247B ILE* 3.7 30.3 - - + -
251B LYS* 4.2 18.2 - - - +
299B ARG 3.1 17.7 + - - +
300B PHE 3.8 4.5 - - - +
301B PHE 3.1 2.0 + - - -
302B GLY* 1.3 77.7 - - - +
304B ALA* 1.3 62.8 + - - +
305B ARG* 3.3 8.8 + - - +
313B LEU* 3.4 4.2 - - + +
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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