Contacts of the helix formed by residues 393 - 410 (chain A) in PDB entry 4OE5
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 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A PHE* 4.1 6.6 - - - -
211A ASN* 3.1 31.3 + - - +
237A THR* 4.0 14.8 - - + -
391A VAL* 3.4 2.1 + - - +
392A ILE* 1.3 81.2 - - - +
394A ALA* 1.3 58.3 + - - +
395A LYS* 3.2 16.3 + - - +
396A SER* 2.9 35.9 + - - -
397A PHE* 3.0 27.9 + - - +
427A TYR* 3.8 18.5 - - - +
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Residues in contact with ALA 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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393A ASP* 1.3 74.2 - - - +
395A LYS* 1.3 61.2 + - - +
397A PHE* 3.3 4.2 + - - +
398A ALA* 2.9 29.6 + - - +
427A TYR* 3.6 34.4 - - + +
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Residues in contact with LYS 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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210A PHE* 4.7 10.5 - - + -
211A ASN* 3.7 10.8 - - - +
393A ASP* 3.2 15.6 + - - +
394A ALA* 1.3 78.0 - - - +
396A SER* 1.3 63.7 + - - +
398A ALA* 3.3 7.4 + - - +
399A ARG* 3.0 24.9 + - - +
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Residues in contact with SER 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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211A ASN* 3.9 7.0 + - - +
346A GLN* 5.0 1.7 + - - -
391A VAL* 4.4 9.0 - - - -
392A ILE* 3.6 19.3 - - - +
393A ASP* 2.9 27.6 + - - -
395A LYS* 1.3 76.0 - - - +
397A PHE* 1.3 63.5 + - - +
399A ARG* 3.2 33.3 + - - +
400A ILE* 2.9 33.0 + - - +
449A PHE* 5.6 2.4 - - - -
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Residues in contact with PHE 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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391A VAL* 4.1 7.5 - - + +
393A ASP 3.0 17.0 + - - +
394A ALA* 3.3 6.9 + - - +
396A SER* 1.3 77.0 - - - +
398A ALA* 1.3 61.8 + - + +
400A ILE* 3.5 4.0 + - - +
401A LYS* 2.9 32.1 + - + +
421A CYS* 3.7 28.5 - - + -
422A ASP* 3.7 5.2 - - - -
423A ASP* 3.5 45.8 - - + -
427A TYR* 3.7 34.8 - + + -
428A PHE 3.3 25.1 - - - -
429A VAL* 4.1 7.7 - - + +
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Residues in contact with ALA 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 ALA 2.9 16.2 + - - +
395A LYS* 3.6 8.1 - - - +
397A PHE* 1.3 79.6 - - + +
399A ARG* 1.3 65.2 + - - +
401A LYS* 3.3 7.9 + - - +
402A LYS* 3.0 23.4 + - - +
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Residues in contact with ARG 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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211A ASN* 5.3 4.2 - - - +
395A LYS* 3.0 15.7 + - - +
396A SER* 3.5 41.3 + - - +
398A ALA* 1.3 76.3 - - - +
400A ILE* 1.3 65.2 + - - +
402A LYS* 3.2 15.0 + - - +
403A TRP* 3.2 35.8 + - + +
447A GLU 4.9 4.5 + - - -
448A ILE* 2.8 33.1 + - - +
449A PHE* 3.4 26.3 + - - +
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Residues in contact with ILE 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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391A VAL* 3.6 38.4 - - + -
396A SER* 2.9 24.4 + - - +
397A PHE* 3.8 4.0 - - - +
399A ARG* 1.3 76.8 - - - +
401A LYS* 1.3 64.3 + - - +
403A TRP* 3.1 9.2 + - - +
404A LEU* 3.0 25.3 + - + +
429A VAL* 3.9 28.9 - - + -
448A ILE* 4.3 21.1 - - + +
449A PHE 4.5 3.8 - - - +
450A GLY* 4.0 7.2 - - - -
451A PRO* 3.8 11.4 - - + -
452A VAL* 4.3 18.4 - - + -
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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 PHE* 2.9 26.4 + - + +
398A ALA* 3.3 8.7 + - - +
400A ILE* 1.3 77.4 - - - +
402A LYS* 1.3 61.1 + - - +
404A LEU* 3.3 12.8 + - + +
405A GLU* 3.1 23.1 + - + +
421A CYS* 3.7 26.5 - - - -
429A VAL* 6.0 0.2 - - - +
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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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398A ALA 3.0 11.5 + - - +
399A ARG* 3.6 10.3 - - - +
400A ILE 3.2 0.4 - - - -
401A LYS* 1.3 74.9 - - - +
403A TRP* 1.3 63.4 + - + +
405A GLU* 3.4 6.7 + - - +
406A HIS* 2.9 28.1 + - - +
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Residues in contact with TRP 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 ARG* 3.2 35.3 + - + +
400A ILE* 3.1 8.4 + - - +
402A LYS* 1.3 77.0 - - + +
404A LEU* 1.3 60.1 + - - +
406A HIS* 3.3 26.2 + + + +
407A ALA* 2.8 29.3 + - - +
442A PRO* 3.7 22.2 - - + -
443A ILE* 3.5 46.4 - - + +
446A GLU* 3.4 39.0 - - + -
447A GLU 4.9 2.4 + - - -
448A ILE* 3.7 43.0 - - + +
452A VAL* 5.2 5.4 - - + -
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Residues in contact with LEU 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 ILE* 3.0 20.5 + - + +
401A LYS* 3.6 9.2 - - + +
402A LYS 3.3 0.2 - - - -
403A TRP* 1.3 77.3 - - - +
405A GLU* 1.3 56.8 + - - +
407A ALA* 3.3 7.2 + - + +
408A ARG* 2.9 27.5 + - - +
415A ILE* 3.8 4.4 - - + +
419A GLY* 3.5 30.7 - - - +
420A LYS 4.0 10.5 - - - +
421A CYS* 4.2 17.9 - - - -
429A VAL* 4.1 17.3 - - + -
432A CYS* 3.6 39.3 - - + -
452A VAL* 4.3 14.4 - - + -
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Residues in contact with GLU 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* 3.1 16.5 + - + +
402A LYS* 3.9 7.0 - - - +
404A LEU* 1.3 72.7 - - - +
406A HIS* 1.3 61.3 + - - +
408A ARG* 2.7 47.6 + - - +
409A SER* 3.0 37.7 + - - +
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Residues in contact with HIS 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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402A LYS 2.9 14.8 + - - +
403A TRP* 3.4 38.1 - + + +
405A GLU* 1.3 77.8 - - - +
407A ALA* 1.3 61.4 + - - +
409A SER* 4.0 4.9 + - - -
410A SER* 3.0 42.6 + - - -
413A LEU* 3.4 14.6 - - + +
441A GLU* 3.2 33.6 + - - -
442A PRO* 4.5 10.7 - - + +
443A ILE* 4.5 1.1 - - + -
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Residues in contact with ALA 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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403A TRP 2.8 17.2 + - - +
404A LEU* 3.5 11.4 - - + +
406A HIS* 1.3 74.3 - - - +
408A ARG* 1.3 62.4 + - - +
410A SER 4.1 0.9 + - - -
413A LEU* 3.5 37.5 - - - +
415A ILE* 3.7 23.1 + - + +
432A CYS* 5.4 0.7 - - - -
434A VAL* 3.8 25.1 - - + -
443A ILE* 4.3 5.2 - - + -
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Residues in contact with ARG 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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404A LEU 2.9 16.6 + - - +
405A GLU* 2.7 45.2 + - - +
406A HIS 3.2 0.2 - - - -
407A ALA* 1.3 79.0 - - - +
409A SER* 1.3 72.7 + - - +
410A SER 4.6 2.3 - - - +
413A LEU 4.9 1.6 - - - +
415A ILE* 3.9 16.4 - - + +
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Residues in contact with SER 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 GLU* 3.0 34.0 + - - +
406A HIS* 3.7 6.1 + - - -
408A ARG* 1.3 88.3 - - - +
410A SER* 1.3 66.2 + - - +
411A PRO* 3.5 6.2 - - - +
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Residues in contact with SER 410 (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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406A HIS* 3.0 31.5 + - - -
407A ALA 4.3 0.2 - - - +
408A ARG 3.7 1.6 - - - +
409A SER* 1.3 78.6 + - - +
411A PRO* 1.3 72.5 - - - +
412A SER* 3.2 12.5 + - - -
413A LEU* 3.2 37.0 + - - +
441A GLU* 3.4 15.4 + - - -
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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