Contacts of the helix formed by residues 390 - 403 (chain A) in PDB entry 5D3O
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 GLY 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386A GLU 3.3 13.4 + - - -
387A ARG 4.3 2.8 + - - -
389A SER* 1.3 76.5 - - - +
391A ASP* 1.3 58.8 + - - +
392A ARG 3.4 1.3 - - - -
393A ASN* 3.7 10.0 - - - -
394A PHE* 2.8 42.6 + - - -
420A PHE* 3.8 19.1 - - - -
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Residues in contact with ASP 391 (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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389A SER* 3.0 13.5 - - - +
390A GLY* 1.3 75.8 - - - +
392A ARG* 1.3 64.0 + - - +
394A PHE* 3.2 7.9 + - - +
395A ALA* 3.0 23.7 + - - +
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Residues in contact with ARG 392 (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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327A PHE* 3.7 31.4 - - + -
340A ASN* 3.8 28.7 - - - +
389A SER 4.5 3.3 + - - +
390A GLY* 3.4 0.6 - - - -
391A ASP* 1.3 78.9 - - - +
393A ASN* 1.3 58.5 + - - +
395A ALA* 3.4 8.2 - - + +
396A ILE* 3.1 40.0 + - + +
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Residues in contact with ASN 393 (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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340A ASN* 3.1 29.3 + - - +
344A ILE* 4.1 4.6 - - + +
386A GLU* 4.9 5.7 + - - -
389A SER 5.6 0.2 + - - -
390A GLY* 3.4 12.9 + - - +
391A ASP 3.2 0.6 - - - -
392A ARG* 1.3 77.8 + - - +
394A PHE* 1.3 59.9 + - - +
396A ILE* 3.4 15.6 + - - +
397A GLY 2.8 23.2 + - - -
416A LEU* 3.5 18.9 - - + +
419A TYR* 4.1 14.5 - - + -
420A PHE* 3.4 32.4 - - + -
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Residues in contact with PHE 394 (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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387A ARG* 5.0 8.7 - - + -
390A GLY* 2.8 37.4 + - - +
391A ASP* 3.2 9.2 + - - +
393A ASN* 1.3 69.2 - - - +
395A ALA* 1.3 57.2 + - - +
397A GLY* 3.2 1.2 + - - -
398A TYR* 2.7 60.0 + + + -
413A VAL* 4.2 28.0 - - + -
416A LEU* 3.3 26.6 - - + +
417A ASP 6.1 0.2 - - - -
420A PHE* 4.0 24.0 - + - -
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Residues in contact with ALA 395 (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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327A PHE* 5.6 5.4 - - + -
391A ASP 3.0 12.8 + - - +
392A ARG* 3.4 13.9 - - + +
394A PHE* 1.3 72.3 - - - +
396A ILE* 1.3 67.9 + - + +
398A TYR* 3.0 7.6 + - - +
399A TYR* 2.9 24.6 + - - +
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Residues in contact with ILE 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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327A PHE* 3.8 31.0 - - + -
340A ASN* 4.0 18.4 - - + -
341A ALA* 3.7 24.0 - - + +
344A ILE* 4.2 5.4 - - + -
392A ARG* 3.1 36.2 + - - +
393A ASN* 3.6 23.8 - - - +
394A PHE 3.3 0.2 - - - -
395A ALA* 1.3 75.7 - - - +
397A GLY* 1.3 63.7 + - - +
399A TYR* 3.1 7.2 + - + +
400A LEU* 2.9 49.2 + - + +
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Residues in contact with GLY 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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344A ILE* 5.0 0.6 - - - +
393A ASN 2.8 16.2 + - - -
394A PHE 3.4 4.5 - - - -
396A ILE* 1.3 76.2 - - - +
398A TYR* 1.3 60.5 + - - +
400A LEU* 3.5 10.0 + - - +
401A LYS* 3.1 18.7 + - - +
406A PHE* 5.1 2.0 - - - -
412A MET* 3.4 32.1 - - - +
416A LEU* 4.3 7.6 - - - +
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Residues in contact with TYR 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 PHE* 2.7 47.0 + + + +
395A ALA* 3.0 5.6 + - - +
397A GLY* 1.3 70.7 - - - +
399A TYR* 1.3 60.6 + - - +
401A LYS* 3.2 23.7 + - + +
402A GLU* 2.9 29.5 + - - +
412A MET* 3.6 21.5 - - + -
413A VAL* 4.3 14.0 - - + +
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Residues in contact with TYR 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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326A LEU* 4.5 8.9 + - - +
327A PHE* 4.4 23.3 - + + -
328A LEU* 3.7 37.9 - - + +
395A ALA 2.9 16.1 + - - +
396A ILE* 3.6 7.0 - - + +
398A TYR* 1.3 77.1 - - - +
400A LEU* 1.3 59.4 + - + +
402A GLU* 3.3 19.9 + - - +
403A LYS* 3.0 54.9 + - + +
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Residues in contact with LEU 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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328A LEU* 4.0 12.8 - - + -
334A PRO* 3.9 22.9 - - + -
341A ALA* 4.3 10.5 - - + +
344A ILE* 4.2 22.9 - - + -
345A VAL* 4.0 3.4 - - + -
396A ILE* 2.9 43.6 + - + +
397A GLY* 3.8 5.4 - - - +
399A TYR* 1.3 76.5 - - + +
401A LYS* 1.3 66.8 + - - +
403A LYS* 3.2 1.3 + - - -
404A LYS 3.2 4.9 + - - -
405A CYS* 3.0 58.2 + - + +
406A PHE* 4.0 13.0 - - + -
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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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397A GLY 3.1 15.0 + - - +
398A TYR* 3.2 27.1 + - + +
400A LEU* 1.3 77.2 - - - +
402A GLU* 1.3 61.8 + - - +
404A LYS* 3.3 15.8 + - - +
405A CYS 5.1 0.2 - - - +
406A PHE* 4.1 11.6 - - + -
412A MET* 4.1 32.5 - - + +
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Residues in contact with GLU 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 TYR 2.9 16.6 + - - +
399A TYR* 3.6 20.3 - - - +
400A LEU 3.1 0.2 - - - -
401A LYS* 1.3 73.8 - - - +
403A LYS* 1.3 80.6 + - - +
404A LYS* 3.0 24.7 + - - +
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Residues in contact with LYS 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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328A LEU* 4.0 10.1 - - + +
332A ASP* 4.0 27.2 + - - +
399A TYR* 3.0 57.4 + - + +
400A LEU 3.2 0.6 + - - -
402A GLU* 1.3 97.7 - - - +
404A LYS* 1.3 71.5 + - - +
405A CYS* 3.4 20.5 + - - -
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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