Contacts of the helix formed by residues 293 - 304 (chain A) in PDB entry 5VAI
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 LYS 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLU* 3.5 38.9 - - - +
249A ALA* 3.4 29.7 - - + +
250A SER* 3.8 4.3 - - - +
251A SER* 3.4 17.1 + - - +
265A ARG* 6.2 0.4 - - - +
292A ASN* 1.3 96.1 - - - +
294A GLN* 1.3 57.0 + - - +
295A ASP 3.5 1.8 - - - -
296A LEU* 3.5 30.0 - - + +
297A LEU* 2.6 37.5 + - - +
364A THR 3.2 1.4 + - - -
365A CYS* 3.6 15.9 - - - -
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Residues in contact with GLN 294 (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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250A SER* 3.5 7.2 + - - -
291A LEU* 2.2 55.3 + - - +
293A LYS* 1.3 74.3 - - - +
295A ASP* 1.3 65.6 + - - +
297A LEU* 3.0 10.6 + - - +
298A ALA* 2.9 22.1 + - - +
327A GLU* 5.5 4.5 - - - +
338A LYS* 3.5 22.8 - - + +
363A PHE* 3.2 32.7 - - + +
364A THR 2.9 31.0 + - - +
365A CYS* 3.8 0.6 - - - +
366A ALA* 4.3 15.0 - - + +
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Residues in contact with ASP 295 (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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293A LYS 4.0 0.2 - - - -
294A GLN* 1.3 76.2 - - - +
296A LEU* 1.3 82.6 + - - +
298A ALA* 3.1 7.2 + - - +
299A GLU* 2.9 41.5 + - + +
327A GLU* 5.7 8.7 + - - +
365A CYS* 3.0 36.3 - - - +
366A ALA* 4.8 6.7 - - - +
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Residues in contact with LEU 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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251A SER* 3.2 21.3 - - - +
293A LYS* 3.5 37.5 - - + +
294A GLN 3.3 0.4 - - - -
295A ASP* 1.3 87.7 + - - +
297A LEU* 1.3 57.6 + - - +
299A GLU* 4.7 12.3 - - + +
300A LYS* 2.8 41.4 + - + +
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Residues in contact with LEU 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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250A SER* 2.9 41.1 - - - +
251A SER* 3.5 10.7 - - - -
253A TYR* 4.4 7.0 - - + -
291A LEU* 6.2 2.0 - - + -
293A LYS 2.6 22.9 + - - +
294A GLN* 3.0 8.0 + - - +
296A LEU* 1.3 71.5 - - - +
298A ALA* 1.3 61.5 + - - +
300A LYS* 3.7 0.2 - - - +
301A VAL* 2.8 53.4 + - + +
308A ILE* 5.0 1.6 - - + -
337A ALA* 6.3 1.1 - - + -
338A LYS* 4.8 23.8 - - + +
341A ILE* 4.0 24.5 - - + -
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Residues in contact with ALA 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 GLN 2.9 12.4 + - - +
295A ASP* 3.6 10.3 - - - +
297A LEU* 1.3 78.9 - - - +
299A GLU* 1.3 65.8 + - + +
301A VAL* 3.1 5.0 + - - +
302A LEU* 3.0 30.8 + - + +
327A GLU* 5.7 4.5 - - - +
330A GLU* 5.3 1.6 - - - +
334A VAL* 3.4 32.1 - - + +
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Residues in contact with GLU 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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295A ASP* 2.9 33.7 + - - +
296A LEU* 4.2 12.1 - - + +
298A ALA* 1.3 72.9 - - + +
300A LYS* 1.3 64.5 + - - +
302A LEU* 2.9 23.1 + - + +
303A ALA* 2.9 12.2 + - - +
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Residues in contact with LYS 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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251A SER* 3.8 17.9 - - - +
253A TYR* 2.2 32.5 + - + -
254A ASN* 5.2 7.2 - - - +
296A LEU* 2.8 32.2 + - + +
297A LEU 3.7 2.7 - - - +
299A GLU* 1.3 73.4 - - - +
301A VAL* 1.3 56.2 - - - +
303A ALA* 3.1 22.2 - - - +
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Residues in contact with VAL 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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253A TYR* 3.1 10.1 + - + -
297A LEU* 2.8 42.9 + - + +
298A ALA* 3.4 7.0 - - - +
300A LYS* 1.3 77.3 - - - +
302A LEU* 1.3 71.3 + - + +
303A ALA 3.1 0.5 + - - -
304A GLY* 3.4 13.7 + - - -
307A LYS* 4.7 12.1 + - - +
308A ILE* 3.6 27.4 - - + -
333A ARG 6.2 0.4 - - - -
334A VAL* 4.9 8.5 - - + -
337A ALA* 5.4 14.1 - - + -
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Residues in contact with LEU 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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298A ALA* 3.0 17.4 + - + +
299A GLU* 2.9 13.1 + - + +
301A VAL* 1.3 79.5 - - + +
303A ALA* 1.3 65.0 + - - +
304A GLY* 4.3 1.3 - - - -
331A ASP* 4.8 19.3 - - + +
333A ARG* 6.5 0.4 - - + -
334A VAL* 3.5 28.3 - - + -
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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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253A TYR* 4.8 0.2 - - - +
299A GLU 2.9 10.6 + - - +
300A LYS* 3.1 17.7 - - - +
301A VAL 3.1 0.2 - - - -
302A LEU* 1.3 79.3 - - - +
304A GLY* 1.3 59.2 + - - +
305A LYS* 3.4 24.2 + - + +
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Residues in contact with GLY 304 (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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253A TYR* 4.2 1.4 + - - -
300A LYS 3.7 2.8 + - - -
301A VAL 3.4 13.2 + - - -
302A LEU 4.3 1.8 - - - -
303A ALA* 1.3 78.1 - - - +
305A LYS* 1.3 64.9 + - - +
306A SER 3.2 7.2 - - - -
307A LYS* 3.0 36.5 - - - +
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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