Contacts of the helix formed by residues 421 - 431 (chain A) in PDB entry 5YDJ
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 LEU 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.6 50.9 - - + +
320A GLY 5.6 0.2 - - - +
321A THR* 3.8 16.4 - - + +
402A THR* 6.0 1.1 - - + -
406A LEU* 3.9 9.6 - - + -
417A GLU 3.8 15.0 - - - +
418A PRO* 3.5 25.6 - - + +
420A LYS* 1.3 70.4 - - - +
422A SER* 1.3 64.0 + - - +
423A ASP 3.4 2.0 - - - -
424A ALA* 3.7 6.8 + - + +
425A VAL* 3.6 24.9 + - - +
808A SO4 2.9 29.2 + - - +
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Residues in contact with SER 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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323A GLU* 4.9 10.1 + - - +
420A LYS* 3.5 1.3 - - - -
421A LEU* 1.3 76.9 - - - +
423A ASP* 1.3 66.2 + - - +
425A VAL* 3.5 4.1 + - - +
426A GLU* 3.2 40.5 + - - +
808A SO4 3.5 14.5 + - - -
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Residues in contact with ASP 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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415A PRO* 4.0 26.7 - - + +
420A LYS* 3.7 32.9 + - - +
421A LEU 3.4 0.4 - - - -
422A SER* 1.3 78.6 - - - +
424A ALA* 1.3 61.8 + - - +
426A GLU* 3.9 14.4 - - - +
427A CYS* 3.5 23.6 + - - +
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Residues in contact with ALA 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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319A LEU* 4.5 13.2 - - + -
405A ALA 5.9 0.4 - - - +
406A LEU* 5.0 10.8 - - + -
409A ALA* 4.5 10.3 - - + -
415A PRO 3.2 25.4 + - - +
417A GLU 5.7 0.4 - - - +
420A LYS 4.4 2.6 + - - +
421A LEU* 3.7 14.4 + - - +
422A SER 3.3 0.2 - - - -
423A ASP* 1.3 76.5 - - - +
425A VAL* 1.3 60.4 + - - +
427A CYS* 3.2 6.9 - - - -
428A LEU* 3.1 35.4 + - + +
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Residues in contact with VAL 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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206A PHE* 4.3 9.0 - - + -
317A LEU* 5.0 2.0 - - + -
319A LEU* 3.4 29.8 - - + -
321A THR* 4.6 6.3 - - - +
323A GLU* 3.8 21.3 - - + +
324A ALA* 4.0 13.7 - - + +
421A LEU 3.6 9.4 + - - +
422A SER* 3.5 6.1 + - - +
424A ALA* 1.3 73.0 - - - +
426A GLU* 1.3 56.5 + - - +
428A LEU* 3.2 7.6 + - - +
429A ARG* 2.8 68.2 + - + +
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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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323A GLU* 4.8 3.0 - - - +
422A SER* 3.2 29.2 + - - +
423A ASP* 3.9 16.3 - - - +
425A VAL* 1.3 80.2 - - - +
427A CYS* 1.3 57.0 + - - +
429A ARG* 3.5 29.1 + - - +
430A GLY* 3.2 19.8 + - - -
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Residues in contact with CYS 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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414A CYS* 2.0 51.6 - - - -
415A PRO* 3.6 9.9 - - + -
423A ASP 3.5 13.3 + - - +
424A ALA 3.2 13.0 - - - -
426A GLU* 1.3 76.9 - - - +
428A LEU* 1.3 59.9 + - - +
430A GLY* 2.8 6.2 + - - +
431A LYS* 2.8 40.8 + - - +
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Residues in contact with LEU 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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205A ARG* 2.8 19.9 + - - -
206A PHE* 3.8 12.6 - - + -
317A LEU* 3.9 24.7 - - + -
319A LEU* 4.9 3.8 - - + -
405A ALA 4.4 7.6 - - - +
408A LEU* 4.2 15.3 - - + +
409A ALA* 4.1 31.9 - - + +
412A VAL* 5.1 1.3 - - + -
414A CYS* 4.7 3.8 - - - -
424A ALA* 3.1 34.1 + - + +
425A VAL* 3.5 7.4 - - - +
427A CYS* 1.3 77.5 - - - +
429A ARG* 1.3 57.1 + - - +
431A LYS* 3.5 9.5 + - - +
436A LEU* 3.6 34.5 - - + +
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Residues in contact with ARG 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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202A GLY* 3.6 23.3 - - - +
203A PRO* 3.4 31.9 + - - +
205A ARG* 3.1 36.9 + - + +
206A PHE* 3.7 18.4 - - + -
207A ARG* 3.9 11.1 - - - +
323A GLU* 2.9 43.0 + - - +
425A VAL* 2.8 37.3 + - - +
426A GLU* 3.6 30.3 + - - +
428A LEU* 1.3 72.3 - - - +
430A GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 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 3.2 11.0 + - - -
427A CYS* 2.8 11.1 + - - -
429A ARG* 1.3 75.6 - - - +
431A LYS* 1.3 62.4 + - - -
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Residues in contact with LYS 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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205A ARG* 2.8 27.3 + - - -
412A VAL* 3.5 39.0 + - + +
413A GLY 4.4 7.9 + - - -
414A CYS* 4.2 17.9 - - - -
427A CYS* 2.8 24.1 + - - +
428A LEU* 3.8 1.8 - - - +
429A ARG 3.4 1.4 - - - -
430A GLY* 1.3 78.5 - - - +
432A ASP* 1.3 62.1 + - - +
433A PRO* 4.0 0.2 - - - +
435A VAL* 4.6 5.4 - - + -
436A LEU* 3.7 22.7 - - + -
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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