Contacts of the helix formed by residues 395 - 408 (chain A) in PDB entry 1UA4
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 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A ASP* 4.7 6.4 + - + +
317A PRO* 4.1 31.0 - - + +
393A ASN* 3.4 11.0 - - - +
394A GLU* 1.3 77.0 - - + +
396A ALA* 1.3 60.9 + - - +
397A THR 3.1 1.3 + - - -
398A GLN* 3.4 20.8 + - - +
399A VAL* 3.6 13.8 + - - +
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Residues in contact with ALA 396 (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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345A GLY 3.5 13.9 - - - +
346A TYR* 5.0 0.2 - - + -
393A ASN* 3.0 26.4 - - - +
394A GLU 3.0 0.6 + - - -
395A LYS* 1.3 75.2 - - - +
397A THR* 1.3 59.5 + - - +
399A VAL* 3.2 12.4 + - + +
400A GLU* 2.9 30.8 + - - +
423A PHE* 4.0 4.3 - - + -
425A PRO* 3.5 31.8 - - + +
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Residues in contact with THR 397 (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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393A ASN 4.5 1.1 + - - -
394A GLU* 3.0 22.1 + - - -
396A ALA* 1.3 79.6 - - - +
398A GLN* 1.3 78.3 + - - +
400A GLU* 3.3 11.8 + - - +
401A GLU* 3.1 21.6 + - + +
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Residues in contact with GLN 398 (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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394A GLU 3.4 17.3 - - - +
395A LYS* 3.4 13.5 + - - +
396A ALA 3.3 0.2 - - - -
397A THR* 1.3 89.0 - - - +
399A VAL* 1.3 67.1 + - + +
401A GLU* 3.2 8.0 + - - +
402A LYS* 3.0 37.4 + - - +
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Residues in contact with VAL 399 (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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317A PRO* 3.6 35.7 - - + -
320A PRO* 3.7 32.7 - - + +
346A TYR* 3.8 19.1 - - + -
395A LYS 3.6 10.1 - - - +
396A ALA* 3.2 14.1 + - - +
398A GLN* 1.3 78.6 - - + +
400A GLU* 1.3 63.6 + - - +
402A LYS* 3.3 8.4 + - + +
403A LEU* 3.3 21.2 + - + +
423A PHE* 3.7 18.6 - - + -
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Residues in contact with GLU 400 (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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4A TRP* 3.1 41.5 + - - -
396A ALA 2.9 17.1 + - - +
397A THR* 3.6 10.3 - - - +
398A GLN 3.3 0.2 - - - -
399A VAL* 1.3 76.4 - - - +
401A GLU* 1.3 58.8 + - - +
403A LEU* 3.3 6.9 + - - +
404A ARG* 2.9 28.9 + - + +
409A ILE* 3.9 9.7 - - + +
411A GLU* 5.1 2.9 + - - -
412A GLY 4.5 5.5 + - - -
423A PHE* 3.6 25.1 - - + -
425A PRO* 5.8 0.9 - - + +
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Residues in contact with GLU 401 (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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397A THR* 3.1 14.8 + - + +
398A GLN* 3.5 11.7 - - - +
400A GLU* 1.3 76.2 - - - +
402A LYS* 1.3 67.5 + - + +
404A ARG* 2.6 46.7 + - - +
405A ALA* 3.0 26.1 + - + +
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Residues in contact with LYS 402 (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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319A ASP* 4.1 17.0 + - - +
320A PRO* 3.8 29.4 - - + -
321A ILE* 3.8 10.0 - - + +
398A GLN* 3.0 26.8 + - - +
399A VAL* 3.3 9.4 + - - +
401A GLU* 1.3 78.1 - - + +
403A LEU* 1.3 59.5 + - - +
405A ALA* 3.5 5.2 + - - +
406A GLU* 3.0 30.1 + - - +
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Residues in contact with LEU 403 (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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320A PRO* 3.6 27.1 - - + -
321A ILE* 3.9 15.0 - - + -
324A THR* 3.8 20.4 - - - +
348A LEU* 3.9 12.1 - - + -
399A VAL 3.3 13.8 + - - +
400A GLU 3.6 2.0 - - - +
401A GLU 3.2 0.2 - - - -
402A LYS* 1.3 74.7 - - - +
404A ARG* 1.3 60.1 + - - +
407A TYR* 2.8 41.7 + - + +
408A GLY 3.4 3.3 + - - -
409A ILE* 3.4 20.2 + - + -
421A ILE* 5.3 3.8 - - + -
423A PHE* 3.4 40.6 - - + -
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Residues in contact with ARG 404 (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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400A GLU* 2.9 20.0 + - + +
401A GLU* 2.6 44.9 + - - +
403A LEU* 1.3 77.0 - - - +
405A ALA* 1.3 75.7 + - - +
408A GLY* 2.7 30.3 + - - -
409A ILE* 3.7 28.9 - - + +
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Residues in contact with ALA 405 (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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401A GLU* 3.0 20.6 + - + +
402A LYS* 3.8 6.1 - - - +
404A ARG* 1.3 97.2 - - - +
406A GLU* 1.3 59.9 + - - +
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Residues in contact with GLU 406 (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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321A ILE* 3.4 30.7 - - + +
325A GLU* 5.3 2.4 - - - +
402A LYS 3.0 18.5 + - - +
403A LEU 4.0 0.4 - - - +
405A ALA* 1.3 79.8 - - - +
407A TYR* 1.3 92.4 + - + +
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Residues in contact with TYR 407 (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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321A ILE* 3.7 36.2 + - + +
324A THR* 3.4 39.0 - - + +
325A GLU* 3.9 9.4 + - - +
328A LEU* 5.0 1.8 - - + +
403A LEU* 2.8 31.2 + - + +
406A GLU* 1.3 96.4 + - + +
408A GLY* 1.3 60.4 + - - +
409A ILE* 4.5 10.8 - - + -
414A GLY* 4.9 0.2 - - - -
415A GLU 4.0 22.8 + - - +
416A VAL* 3.7 33.7 - - + -
421A ILE* 4.5 10.1 - - + -
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Residues in contact with GLY 408 (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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403A LEU 3.4 0.2 + - - -
404A ARG* 2.7 29.3 + - - -
406A GLU 3.8 0.4 - - - -
407A TYR* 1.3 73.6 - - - +
409A ILE* 1.3 67.3 + - - +
410A LYS* 3.5 5.2 + - - +
413A ILE 4.3 1.7 - - - +
414A GLY* 4.7 3.0 - - - -
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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