Contacts of the helix formed by residues 421 - 435 (chain A) in PDB entry 4YCV
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 SER 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A GLN 4.8 1.8 - - - -
418A PRO 3.0 8.9 + - - -
419A PHE* 2.6 35.2 + - - -
420A ASP* 1.3 90.0 + - - +
422A ASN* 1.3 70.1 + - - +
423A GLU* 2.8 5.2 + - - +
424A THR* 2.9 17.1 + - - -
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Residues in contact with ASN 422 (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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420A ASP 3.1 5.7 + - - -
421A SER* 1.3 69.4 - - - +
423A GLU* 1.3 69.4 + - + +
425A ILE* 2.9 23.3 + - - +
426A GLU* 3.0 12.6 + - - +
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Residues in contact with GLU 423 (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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421A SER 2.8 3.7 + - - +
422A ASN* 1.3 81.1 - - + +
424A THR* 1.3 51.3 + - - +
426A GLU* 2.9 12.4 + - - +
427A LYS* 2.7 38.3 + - - +
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Residues in contact with THR 424 (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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415A LEU* 3.9 11.9 - - + -
416A GLU* 3.2 47.7 + - - +
417A GLN 3.9 4.0 + - - -
419A PHE* 3.1 38.8 + - + +
421A SER* 2.9 11.0 + - - -
423A GLU* 1.3 74.1 - - - +
425A ILE* 1.3 51.6 + - - +
427A LYS* 3.0 12.6 + - - +
428A MET* 2.7 36.7 + - + +
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Residues in contact with ILE 425 (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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420A ASP* 2.9 27.3 + - + +
422A ASN* 2.9 16.0 + - - +
424A THR* 1.3 75.3 - - - +
426A GLU* 1.3 56.3 + - - +
428A MET* 3.0 12.0 + - - +
429A ILE* 2.7 53.1 + - + +
443A PRO 3.4 15.5 - - - +
444A THR* 4.3 1.6 - - - -
445A ALA* 3.5 22.0 - - + +
448A LEU* 3.4 23.0 - - + +
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Residues in contact with GLU 426 (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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422A ASN 3.0 5.9 + - - +
423A GLU* 2.9 14.0 + - - +
425A ILE* 1.3 82.2 - - + +
427A LYS* 1.3 68.1 + - - +
429A ILE* 3.0 10.1 + - + +
430A ASN* 2.9 39.4 + - - +
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Residues in contact with LYS 427 (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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413A THR* 3.2 27.0 + - + +
414A ILE 3.3 23.5 + - - -
415A LEU* 3.5 19.7 - - + +
416A GLU 4.6 7.3 + - - -
423A GLU* 2.7 14.8 + - - +
424A THR* 3.1 17.7 - - - +
426A GLU* 1.3 77.9 - - - +
428A MET* 1.3 63.2 + - - +
430A ASN* 3.0 13.4 + - - +
431A ILE* 3.2 15.1 + - + +
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Residues in contact with MET 428 (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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415A LEU* 3.5 20.6 - - + -
419A PHE* 3.8 31.2 - - + +
424A THR* 2.7 17.9 + - + +
425A ILE* 3.3 18.6 - - + +
427A LYS* 1.3 70.8 - - - +
429A ILE* 1.3 64.6 + - - +
431A ILE* 3.0 24.8 + - - +
432A ILE* 3.0 16.3 + - - +
445A ALA* 3.7 39.0 - - + +
448A LEU* 3.9 16.4 - - + -
449A LEU* 3.9 16.4 - - - -
452A LEU* 4.0 17.0 - - + +
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Residues in contact with ILE 429 (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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425A ILE* 2.7 36.6 + - + +
426A GLU* 3.0 11.9 + - + +
428A MET* 1.3 72.7 - - - +
430A ASN* 1.3 69.7 + - - +
432A ILE* 2.9 12.2 + - - +
433A LYS* 2.9 38.5 + - + +
439A LEU* 4.6 15.7 - - + -
443A PRO* 4.2 20.9 - - + -
448A LEU* 3.9 19.7 - - + -
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Residues in contact with ASN 430 (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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426A GLU* 2.9 43.4 + - - +
427A LYS* 3.7 8.2 - - - +
429A ILE* 1.3 79.7 - - - +
431A ILE* 1.3 67.0 + - - +
433A LYS* 3.0 25.3 + - - +
434A GLU* 3.0 18.2 + - - +
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Residues in contact with ILE 431 (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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411A THR* 3.1 39.0 - - + +
413A THR* 3.6 25.1 - - + -
415A LEU* 4.0 14.6 - - + -
427A LYS* 3.2 10.8 + - + +
428A MET* 3.0 22.0 + - - +
430A ASN* 1.3 76.3 - - - +
432A ILE* 1.3 62.9 + - - +
434A GLU* 5.3 0.7 - - - -
435A HIS* 2.7 42.2 + - + +
437A ILE* 4.8 0.3 - - - +
452A LEU* 3.5 24.9 - - + -
456A PHE* 4.1 4.9 - - + -
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Residues in contact with ILE 432 (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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428A MET 3.0 16.7 + - - +
429A ILE* 2.9 12.8 + - - +
431A ILE* 1.3 77.1 - - - +
433A LYS* 1.3 58.0 + - - +
436A LYS 3.4 2.3 + - - -
437A ILE* 3.0 49.1 + - + +
439A LEU* 3.3 35.2 - - + +
440A PRO* 4.0 13.9 - - + -
448A LEU* 3.5 45.1 - - + +
451A GLN* 4.4 8.3 - - + -
452A LEU* 4.1 15.7 - - + -
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Residues in contact with LYS 433 (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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429A ILE* 2.9 28.1 + - + +
430A ASN* 3.0 18.6 + - - +
432A ILE* 1.3 75.8 - - - +
434A GLU* 1.3 60.7 + - - +
436A LYS* 2.9 21.2 + - - +
437A ILE 5.1 2.0 - - - -
439A LEU* 3.6 31.9 - - + -
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Residues in contact with GLU 434 (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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430A ASN 3.0 15.1 + - - +
431A ILE* 5.3 0.2 - - - -
433A LYS* 1.3 77.5 - - - +
435A HIS* 1.3 77.8 + - + +
436A LYS* 3.1 3.0 + - - +
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Residues in contact with HIS 435 (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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410A VAL* 5.4 2.4 + - - +
411A THR* 4.4 13.5 + - - -
431A ILE* 2.7 42.8 + - + +
433A LYS 3.2 0.4 - - - -
434A GLU* 1.3 93.0 - - + +
436A LYS* 1.3 69.5 + - - +
437A ILE* 3.3 20.8 + - + +
455A HIS* 4.7 12.0 + - - +
456A PHE* 3.9 24.7 - + + -
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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