Contacts of the helix formed by residues 422 - 440 (chain E) in PDB entry 1R4N
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 GLU 422 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420E ASP 3.8 7.0 + - - +
421E ASN* 1.3 86.0 + - - +
423E ILE* 1.3 61.3 + - - +
424E VAL 3.0 0.4 - - - -
425E LEU* 3.0 37.9 + - + +
426E TYR 3.5 1.9 + - - -
521E ILE* 3.7 28.2 - - + +
523E SER* 5.0 2.8 - - - -
528E THR* 3.1 28.5 + - - +
529E SER 3.7 14.5 + - - -
530E ALA* 3.2 33.4 - - + +
532E PHE* 4.2 1.1 - - + -
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Residues in contact with ILE 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411E GLU* 6.3 0.4 - - + -
412E ILE* 4.5 31.6 - - + +
415E SER* 3.8 11.0 - - - -
416E MET* 3.4 25.6 - - + -
421E ASN* 2.5 33.1 + - - +
422E GLU* 1.3 69.8 - - - +
424E VAL* 1.3 68.7 + - - +
426E TYR* 2.9 36.9 + - + +
427E LEU* 3.1 12.5 + - + +
532E PHE* 3.4 36.7 - - + -
533E GLN* 6.1 0.7 - - - +
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Residues in contact with VAL 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416E MET* 4.0 23.6 - - + -
419E PRO 3.3 26.0 - - - +
420E ASP 4.4 0.7 - - - -
421E ASN 2.6 36.2 + - - +
423E ILE* 1.3 71.2 - - - +
425E LEU* 1.3 55.1 + - + +
427E LEU* 2.9 11.7 + - - +
428E MET* 2.8 33.2 + - + +
474E VAL* 4.1 20.0 - - + -
478E TYR* 3.7 40.8 - - + -
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Residues in contact with LEU 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E VAL* 3.9 31.0 - - + -
421E ASN 5.5 0.2 - - - -
422E GLU* 3.0 24.5 - - - +
424E VAL* 1.3 82.7 - - + +
426E TYR* 1.3 60.8 + - - +
428E MET* 3.4 7.6 - - - +
429E LEU* 3.0 28.8 + - - +
478E TYR* 3.9 25.4 - - + -
482E PHE* 3.9 20.9 - - + -
521E ILE* 4.0 14.6 - - + -
523E SER* 3.8 30.5 - - - +
525E MET* 5.5 6.1 - - - -
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Residues in contact with TYR 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E TYR* 4.1 32.5 - + - -
401E GLU* 2.7 37.4 + - + +
402E TYR* 3.8 6.0 - - - -
412E ILE* 4.8 15.3 - - + -
422E GLU 3.5 1.0 + - - -
423E ILE* 2.9 31.9 + - + +
425E LEU* 1.3 78.1 - - - +
427E LEU* 1.3 76.2 + - + +
429E LEU* 2.9 20.0 + - + +
430E ARG* 3.0 54.2 + - + +
464E PHE* 5.2 2.0 - + - -
519E THR* 4.6 5.4 - - + -
521E ILE* 3.6 22.5 - - + +
533E GLN* 5.4 2.7 - - - -
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Residues in contact with LEU 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412E ILE* 4.2 22.9 - - + -
416E MET* 3.8 37.9 - - + -
423E ILE* 3.6 12.1 - - + +
424E VAL* 2.9 6.4 + - - +
426E TYR* 1.3 86.0 - - + +
428E MET* 1.3 53.7 + - + +
430E ARG* 2.8 10.7 + - - +
431E ALA* 2.7 34.9 + - - +
461E LEU* 4.6 11.0 - - + -
464E PHE* 3.4 31.5 - - + -
465E LEU* 3.9 9.9 - - + -
470E LEU* 4.3 3.4 - - + -
472E VAL* 4.5 9.0 - - + -
474E VAL* 4.6 7.9 - - + -
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Residues in contact with MET 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424E VAL* 2.8 23.1 + - + +
425E LEU* 3.4 3.6 - - - +
427E LEU* 1.3 73.0 - - - +
429E LEU* 1.3 50.9 + - - +
431E ALA* 2.9 11.8 - - + +
432E VAL* 2.7 40.5 + - + +
457E LEU* 4.0 24.9 - - + -
461E LEU* 4.2 14.8 - - + -
474E VAL* 4.1 21.8 - - - -
478E TYR* 3.6 33.7 - - + +
479E VAL* 4.3 4.5 - - + -
482E PHE* 3.4 38.1 - - + -
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Residues in contact with LEU 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E ARG* 4.3 22.2 - - - +
156E TYR* 4.0 26.5 - - + -
159E VAL* 4.7 10.8 - - + -
161E TYR* 3.5 45.8 - - + -
425E LEU 3.0 17.2 + - - +
426E TYR* 2.9 11.9 + - + +
428E MET* 1.3 76.1 - - - +
430E ARG* 1.3 57.1 + - + +
432E VAL* 3.0 7.4 + - + +
433E ASP* 2.6 39.6 + - - +
482E PHE* 3.6 22.4 - - + -
521E ILE* 6.1 0.9 - - + -
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Residues in contact with ARG 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E GLU* 2.7 26.9 + - - -
401E GLU 5.3 1.4 + - - -
402E TYR* 3.5 34.4 + - - +
426E TYR* 3.0 59.6 + - + +
427E LEU* 2.8 7.0 + - - +
429E LEU* 1.3 76.2 - - - +
431E ALA* 1.3 58.0 - - - +
433E ASP* 3.3 6.7 + - - +
434E ARG* 2.9 29.5 + - - +
464E PHE* 3.6 40.2 - - + -
468E TYR* 3.3 29.7 + - - -
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Residues in contact with ALA 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E LEU 2.7 15.2 + - - +
428E MET* 2.9 24.5 - - + +
430E ARG* 1.3 69.7 - - - +
432E VAL* 1.3 63.5 + - - +
434E ARG* 2.8 10.8 + - - +
435E PHE* 2.7 21.5 + - - +
457E LEU* 4.4 7.9 - - + -
460E CYS* 4.2 4.3 - - - +
461E LEU* 3.8 38.1 - - + +
464E PHE* 4.7 3.5 - - - -
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Residues in contact with VAL 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E ARG* 4.7 3.4 - - - +
156E TYR* 3.3 29.4 - - + +
428E MET* 2.7 21.2 + - + +
429E LEU* 3.4 9.2 - - + +
431E ALA* 1.3 70.5 - - - +
433E ASP* 1.3 52.7 + - - +
435E PHE* 2.9 11.6 + - - +
436E HIS* 2.7 33.4 + - - +
442E TYR* 3.4 21.5 - - + -
443E PRO* 3.4 17.0 - - + -
457E LEU* 4.0 8.0 - - + +
482E PHE* 3.7 30.5 - - + -
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Residues in contact with ASP 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E LEU 5.0 1.0 - - - +
132E PRO* 4.5 1.6 - - - +
133E GLU* 3.6 48.0 + - + +
154E ARG* 2.7 42.1 + - - -
402E TYR* 4.8 5.5 + - - -
429E LEU* 2.6 19.5 + - - +
430E ARG* 3.5 7.7 - - - +
432E VAL* 1.3 72.5 - - - +
434E ARG* 1.3 62.2 + - - +
436E HIS* 3.2 7.6 + - - +
437E LYS* 3.0 21.8 + - - +
442E TYR* 4.2 8.3 + - - -
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Residues in contact with ARG 434 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E GLU* 4.9 4.4 + - - +
430E ARG* 2.9 12.4 + - - +
431E ALA* 2.8 16.6 + - - +
433E ASP* 1.3 66.5 - - - +
435E PHE* 1.3 65.7 + - - +
436E HIS 2.8 3.3 + - - -
437E LYS* 3.0 7.2 + - - +
438E GLN* 2.8 35.4 + - + +
459E SER 5.4 0.2 + - - -
460E CYS* 3.2 33.6 + - + +
463E GLY* 3.4 28.0 + - - -
464E PHE* 3.4 27.6 - - + +
467E GLU* 3.5 29.3 + - - +
468E TYR* 5.9 0.2 - - - -
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Residues in contact with PHE 435 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431E ALA 2.7 14.3 + - - +
432E VAL 3.1 9.6 - - - +
434E ARG* 1.3 73.5 - - - +
436E HIS* 1.3 55.6 + - - +
438E GLN* 4.3 1.3 - - - -
439E GLN* 2.7 48.0 + - + +
441E ARG* 3.2 26.9 - - + -
442E TYR 3.6 2.0 - - - -
443E PRO* 3.5 25.8 - - + -
453E ASP* 3.1 29.4 - - + -
456E LYS* 3.8 18.6 - - + -
457E LEU* 3.6 48.0 - - + -
460E CYS* 3.9 16.5 - - - +
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Residues in contact with HIS 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B GLN* 5.5 7.6 + - - +
132E PRO* 4.5 18.7 - - + +
133E GLU 6.0 0.2 + - - -
432E VAL 2.7 14.9 + - - +
433E ASP* 3.4 10.4 + - - +
434E ARG 2.8 1.6 + - - -
435E PHE* 1.3 70.3 - - - +
437E LYS* 1.3 74.6 + - + +
438E GLN 3.0 1.7 + - - -
440E GLY* 2.7 35.6 + - - -
441E ARG* 3.6 21.8 - - - +
442E TYR* 3.2 54.7 + + + +
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Residues in contact with LYS 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E GLU* 5.8 7.4 - - + +
134E SER* 5.9 8.4 - - - -
433E ASP 3.0 8.6 + - - +
434E ARG* 3.0 9.5 + - - +
436E HIS* 1.3 89.6 + - + +
438E GLN* 1.3 62.7 + - - +
439E GLN 4.7 0.2 - - - -
440E GLY* 4.4 2.4 + - - -
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Residues in contact with GLN 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434E ARG* 2.8 28.5 + - + +
435E PHE 3.7 3.4 - - - +
436E HIS 3.0 0.4 - - - -
437E LYS* 1.3 82.5 - - - +
439E GLN* 1.3 77.2 + - + +
456E LYS* 5.1 2.2 + - - +
459E SER* 6.0 1.2 - - - -
460E CYS* 3.4 29.8 - - - -
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Residues in contact with GLN 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B TYR* 5.1 1.6 + - - -
435E PHE* 2.7 57.6 + - + +
437E LYS 4.7 0.2 - - - -
438E GLN* 1.3 95.0 + - + +
440E GLY* 1.3 58.3 + - - +
441E ARG* 3.4 27.6 + - - +
456E LYS* 3.8 29.1 + - - +
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Residues in contact with GLY 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B GLN* 3.0 20.4 - - - +
271B TYR* 4.1 21.1 + - - -
436E HIS* 2.7 33.0 + - - -
437E LYS 4.4 2.0 + - - -
439E GLN* 1.3 73.7 - - - +
441E ARG* 1.3 59.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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