Contacts of the helix formed by residues 397 - 409 (chain A) in PDB entry 4RIB
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 ASP 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A PHE* 1.3 75.5 - - - +
398A GLU* 1.3 64.0 + - - +
399A GLN* 3.3 12.4 + - - +
400A GLU* 2.9 37.9 + - - +
401A LYS* 3.1 22.1 + - - +
599A ARG* 3.5 26.8 + - - +
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Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A ASP* 1.3 72.3 - - - +
399A GLN* 1.3 67.7 + - - +
400A GLU 3.1 0.3 + - - -
401A LYS* 3.2 22.5 + - - +
402A GLY* 3.1 19.4 + - - -
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Residues in contact with GLN 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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397A ASP* 3.3 12.5 + - - +
398A GLU* 1.3 79.8 - - - +
400A GLU* 1.3 66.5 + - + +
402A GLY* 3.3 9.4 + - - -
403A ILE* 3.4 30.3 + - - +
406A LYS* 6.2 1.6 - - - +
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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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396A PHE* 3.3 15.4 - - + -
397A ASP* 2.9 38.0 + - - +
399A GLN* 1.3 76.5 - - - +
401A LYS* 1.3 61.0 + - - +
402A GLY 3.1 1.1 - - - -
403A ILE* 2.9 34.1 + - - +
404A VAL* 3.6 6.3 + - - +
544A VAL* 4.1 28.2 - - + +
547A ARG* 3.2 23.6 + - - -
599A ARG* 2.7 36.5 + - - -
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Residues in contact with LYS 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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393A MET* 3.0 58.0 + - + +
394A LEU* 5.3 1.2 - - - +
396A PHE* 3.5 18.0 + - + +
397A ASP 3.1 17.9 + - - +
398A GLU* 3.7 22.5 + - - +
400A GLU* 1.3 74.2 - - - +
402A GLY* 1.3 59.1 + - - +
404A VAL* 3.3 20.9 + - - +
405A THR* 2.8 18.9 + - - -
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Residues in contact with GLY 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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398A GLU 3.1 11.2 + - - -
399A GLN 3.3 6.7 + - - -
400A GLU 3.0 1.8 + - - -
401A LYS* 1.3 76.2 - - - +
403A ILE* 1.3 55.5 + - - +
405A THR* 3.3 9.5 + - - -
406A LYS* 2.9 38.6 + - - +
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Residues in contact with ILE 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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399A GLN* 3.4 41.5 - - - +
400A GLU* 2.9 13.0 + - + +
402A GLY* 1.3 73.1 - - - +
404A VAL* 1.3 65.3 + - - +
406A LYS* 3.5 14.2 + - + +
407A PHE* 3.2 16.8 + - - +
455A PHE* 3.5 31.8 - - + -
540A GLY 5.4 1.1 - - - +
541A PRO* 4.0 25.1 - - + +
544A VAL* 3.8 23.1 - - + -
545A PHE* 4.3 9.3 - - + -
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Residues in contact with VAL 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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383A LEU* 5.1 9.9 - - + -
387A LEU* 3.9 26.0 - - + -
393A MET* 6.0 2.2 - - + -
400A GLU 4.2 7.9 - - - +
401A LYS* 3.4 16.4 - - - +
402A GLY 3.3 0.4 - - - -
403A ILE* 1.3 76.8 - - + +
405A THR* 1.3 58.7 + - - +
407A PHE* 2.9 28.0 + - - +
408A TYR* 3.2 32.1 + - + -
544A VAL* 5.0 4.7 - - + -
545A PHE* 4.7 8.7 - - + -
548A ILE* 4.2 24.9 - - + -
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Residues in contact with THR 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 LYS 2.8 16.5 + - - -
402A GLY* 3.3 10.6 + - - -
404A VAL* 1.3 77.6 - - - +
406A LYS* 1.3 61.8 - - - +
407A PHE 3.1 0.5 + - - -
408A TYR* 3.2 15.6 + - + +
409A GLN* 3.0 41.3 + - + +
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Residues in contact with LYS 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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399A GLN* 6.2 1.8 - - - +
402A GLY* 2.9 26.0 + - - +
403A ILE* 3.6 17.3 - - + +
405A THR* 1.3 75.1 - - - +
407A PHE* 1.3 61.8 + - - +
409A GLN* 3.5 24.9 + - - +
410A LEU* 3.5 21.0 - - - +
453A ALA* 3.0 34.0 + - + +
455A PHE* 3.9 10.9 - - + -
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Residues in contact with PHE 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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376A LEU* 4.5 2.5 - - + -
379A PHE* 3.9 17.9 - + - -
380A LEU* 4.1 19.1 - - + -
383A LEU* 4.1 20.0 - - + -
403A ILE 3.2 11.0 + - - +
404A VAL* 2.9 12.6 + - - +
406A LYS* 1.3 74.0 - - - +
408A TYR* 1.3 70.8 + + - +
409A GLN 3.1 0.9 - - - -
410A LEU* 3.0 23.3 + - + +
415A GLN* 3.2 48.1 + - + +
418A TYR* 3.8 39.3 - + + -
419A VAL* 4.4 6.1 - - + -
455A PHE* 3.8 16.2 - + + -
545A PHE* 4.1 16.4 - + + -
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Residues in contact with TYR 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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380A LEU* 4.0 23.2 + - + -
383A LEU* 3.4 24.4 - - + +
384A LYS* 4.0 7.3 + - - +
387A LEU* 3.4 23.4 - - + +
404A VAL* 3.2 38.1 + - + -
405A THR* 3.2 14.0 + - + +
407A PHE* 1.3 80.4 - + - +
409A GLN* 1.3 57.6 + - + +
410A LEU 3.1 11.3 + - - +
415A GLN* 3.6 16.2 + - - +
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Residues in contact with GLN 409 (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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405A THR* 3.0 34.0 + - + +
406A LYS* 3.5 23.5 - - - +
407A PHE 3.1 0.8 - - - -
408A TYR* 1.3 75.8 - - + +
410A LEU* 1.3 61.5 + - + +
449A GLU* 4.8 0.5 - - - +
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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