Contacts of the helix formed by residues 295 - 303 (chain A) 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 HIS 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A LEU* 1.3 77.5 - - - +
296A ARG* 1.3 81.2 + - + +
298A LYS* 3.9 11.8 - - - +
299A ARG* 3.3 54.0 + - + +
232B PHE 4.8 9.4 - - - -
233B ASP 3.8 17.0 + - - -
234B GLU 5.1 0.7 - - - -
235B PRO* 4.6 21.8 - - + +
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL* 4.6 4.8 - - - +
244A GLU* 2.4 40.4 + - - +
274A TYR* 3.5 45.1 + - + -
295A HIS* 1.3 90.4 - - + +
297A PRO* 1.3 71.6 - - + +
298A LYS 3.3 0.3 + - - -
299A ARG* 3.3 10.4 + - - +
300A PHE* 3.1 20.0 + - - +
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Residues in contact with PRO 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ILE* 5.3 6.8 - - + +
270A LEU* 5.1 7.4 - - + -
271A ALA* 4.6 17.5 - - + +
274A TYR* 4.2 23.3 - - + -
294A LEU* 3.6 31.0 - - + +
296A ARG* 1.3 94.5 - - + +
298A LYS* 1.3 56.3 + - - +
300A PHE* 3.3 10.5 + - + +
301A PHE* 2.9 28.8 + - - +
335A PHE* 3.8 24.1 - - + -
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Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A LEU* 3.2 22.8 + - + +
295A HIS* 3.9 13.0 - - - +
296A ARG 3.2 0.8 - - - -
297A PRO* 1.3 79.7 - - - +
299A ARG* 1.3 58.1 + - - +
301A PHE* 3.3 4.9 + - - +
302A GLY* 2.8 26.2 + - - -
334A GLU* 4.9 15.6 + - + -
335A PHE* 4.1 16.1 - - + -
338A THR* 4.5 22.1 - - + +
210B ASP* 4.3 16.2 + - - -
232B PHE* 3.7 36.9 + - + -
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Residues in contact with ARG 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LYS* 5.7 4.7 + - - +
295A HIS* 3.3 37.8 + - + +
296A ARG* 3.3 13.1 + - - +
298A LYS* 1.3 74.7 - - + +
300A PHE* 1.3 64.3 + - - +
302A GLY 3.8 1.1 - - - +
303A ALA* 3.0 23.7 + - - +
232B PHE* 4.9 2.9 - - + +
233B ASP* 3.4 62.5 + - - +
234B GLU* 5.2 3.4 + - - -
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Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LEU* 5.1 5.6 - - + -
243A ALA* 3.9 16.4 - - + -
244A GLU* 5.3 3.1 - - - +
246A VAL* 5.7 1.1 - - + -
247A ILE* 3.5 44.4 - - + -
262A ILE* 5.1 10.1 - - + -
264A LEU* 3.5 44.0 - - + -
267A ILE* 6.4 1.3 - - + -
270A LEU* 4.5 15.3 - - + -
274A TYR* 6.1 2.0 - - + +
296A ARG 3.1 13.0 + - - +
297A PRO* 3.6 11.9 - - + +
299A ARG* 1.3 77.7 - - - +
301A PHE* 1.3 64.0 + + + +
303A ALA* 3.5 10.8 - - - +
315A ILE* 3.5 33.6 - - + +
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Residues in contact with PHE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 3.3 36.5 - - + +
174A GLY 3.1 30.3 - - - -
175A LEU* 3.5 33.2 - - + -
267A ILE* 4.4 18.6 - - + -
297A PRO 2.9 17.6 + - - +
298A LYS* 3.8 6.3 - - - +
300A PHE* 1.3 82.0 - + + +
302A GLY* 1.3 61.7 + - - +
303A ALA 3.1 1.8 + - - -
304A ALA* 3.4 10.6 + - - +
315A ILE* 3.8 25.6 - - + +
317A ALA* 4.7 3.6 - - + -
335A PHE* 4.5 8.5 - + + -
338A THR* 4.1 17.9 - - + -
339A GLY* 4.2 12.8 - - - -
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Residues in contact with GLY 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 3.8 14.9 + - - -
298A LYS 2.8 21.1 + - - -
299A ARG 3.8 2.7 - - - -
301A PHE* 1.3 71.6 - - - +
303A ALA* 1.3 63.6 + - - +
304A ALA 3.1 9.3 + - - +
305A ARG* 3.8 16.1 + - - -
338A THR* 5.2 2.4 - - - +
213B PRO* 5.3 2.1 - - - +
214B GLU* 5.5 0.9 - - - +
232B PHE* 3.7 24.9 - - - -
233B ASP* 5.4 1.6 - - - -
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.4 16.7 - - - -
247A ILE* 3.9 24.5 - - + -
251A LYS* 4.0 18.4 - - - +
299A ARG 3.0 17.3 + - - +
300A PHE* 3.5 11.4 - - - +
301A PHE 3.1 1.4 - - - -
302A GLY* 1.3 76.7 - - - +
304A ALA* 1.3 62.6 + - - +
305A ARG* 3.3 12.1 + - - +
313A LEU* 3.4 10.9 - - + +
315A ILE* 4.8 0.2 - - + -
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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