Contacts of the helix formed by residues 422 - 440 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ASP 3.8 7.0 + - - +
421A ASN* 1.3 85.1 + - - +
423A ILE* 1.3 60.1 + - - +
424A VAL 3.1 0.7 - - - -
425A LEU* 3.0 37.3 + - + +
426A TYR 3.5 2.1 + - - -
521A ILE* 3.7 29.6 - - + +
523A SER* 5.0 2.9 - - - -
528A THR* 3.1 32.6 + - - +
529A SER 3.8 9.6 + - - -
530A ALA* 3.2 31.9 - - + +
532A PHE* 4.2 1.8 - - + -
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Residues in contact with ILE 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A GLU* 6.3 0.7 - - + -
412A ILE* 4.5 30.1 - - + +
415A SER* 3.8 10.8 - - - -
416A MET* 3.3 24.7 - - + -
421A ASN* 2.5 33.3 + - - +
422A GLU* 1.3 69.9 - - - +
424A VAL* 1.3 67.8 + - - +
426A TYR* 2.8 47.3 + - + +
427A LEU* 3.1 7.6 + - + +
532A PHE* 3.4 38.1 - - + -
533A GLN* 6.2 0.2 - - - +
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Residues in contact with VAL 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A MET* 4.0 17.9 - - + -
419A PRO 3.2 26.2 - - - +
420A ASP 4.4 1.3 - - - -
421A ASN 2.7 36.2 + - - +
423A ILE* 1.3 70.5 - - - +
425A LEU* 1.3 55.9 + - + +
427A LEU* 2.9 17.8 + - - +
428A MET* 2.8 32.8 + - + +
474A VAL* 4.1 20.2 - - + -
478A TYR* 3.7 41.1 - - + -
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 3.9 31.0 - - + -
422A GLU* 3.1 24.5 - - - +
424A VAL* 1.3 77.1 - - + +
426A TYR* 1.3 59.8 + - - +
428A MET* 3.4 7.7 + - - +
429A LEU* 2.9 28.4 + - - +
478A TYR* 4.0 26.0 - - + -
482A PHE* 3.9 21.7 - - + -
521A ILE* 4.0 15.3 - - + -
523A SER* 3.8 30.5 - - - +
525A MET* 5.4 5.8 - - - -
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Residues in contact with TYR 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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161A TYR* 4.0 33.0 - + - -
401A GLU* 2.8 35.9 + - - +
402A TYR* 3.8 5.6 - - - -
412A ILE* 4.8 15.3 - - + -
422A GLU 3.5 1.4 + - - -
423A ILE* 2.8 30.8 + - + +
425A LEU* 1.3 79.3 - - - +
427A LEU* 1.3 75.9 + - + +
429A LEU* 2.9 20.3 + - + +
430A ARG* 2.9 53.3 + - + +
464A PHE* 5.2 1.8 - + - -
519A THR* 4.6 5.6 - - + -
521A ILE* 3.6 21.6 - - + +
533A GLN* 5.3 3.6 - - - -
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ILE* 4.1 22.9 - - + -
416A MET* 3.8 39.5 - - + -
423A ILE* 3.6 12.8 - - + +
424A VAL* 2.9 7.2 + - - +
426A TYR* 1.3 85.3 - - + +
428A MET* 1.3 53.7 + - - +
430A ARG* 2.9 11.9 + - - +
431A ALA* 2.7 34.9 + - - +
461A LEU* 4.6 11.0 - - + -
464A PHE* 3.4 30.8 - - + -
465A LEU* 4.0 9.2 - - + -
470A LEU* 4.3 4.0 - - + -
472A VAL* 4.5 9.6 - - + -
474A VAL* 4.6 7.2 - - + -
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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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424A VAL* 2.8 23.7 + - + +
425A LEU 3.5 3.6 - - - +
426A TYR 3.2 0.2 - - - -
427A LEU* 1.3 72.9 - - - +
429A LEU* 1.3 52.1 + - - +
431A ALA* 2.9 12.2 - - + +
432A VAL* 2.7 39.8 + - + +
457A LEU* 4.0 25.6 - - + -
461A LEU* 4.2 14.4 - - + -
474A VAL* 4.1 22.7 - - - -
478A TYR* 3.7 32.8 - - + +
479A VAL* 4.3 4.7 - - + -
482A PHE* 3.4 37.7 - - + -
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ARG* 4.3 20.6 - - - +
156A TYR* 4.0 26.9 - - + -
159A VAL* 4.7 10.3 - - + -
161A TYR* 3.6 45.8 - - + -
425A LEU 2.9 16.8 + - - +
426A TYR* 2.9 13.2 + - + +
428A MET* 1.3 71.3 - - - +
430A ARG* 1.3 60.1 + - + +
432A VAL* 2.9 5.8 + - + +
433A ASP* 2.6 39.4 + - - +
482A PHE* 3.6 22.9 - - + -
521A ILE* 6.1 0.7 - - + -
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Residues in contact with ARG 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 2.7 25.9 + - - -
401A GLU 5.3 0.8 + - - -
402A TYR* 3.5 36.8 + - - +
426A TYR* 2.9 63.1 + - + +
427A LEU* 2.9 7.1 + - - +
429A LEU* 1.3 76.7 - - - +
431A ALA* 1.3 58.1 + - - +
433A ASP* 3.3 7.6 + - - +
434A ARG* 2.8 29.7 + - - +
464A PHE* 3.7 39.1 - - + -
468A TYR* 3.3 28.7 + - - -
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Residues in contact with ALA 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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427A LEU 2.7 15.0 + - - +
428A MET* 2.9 22.4 - - + +
430A ARG* 1.3 72.1 - - - +
432A VAL* 1.3 54.8 + - - +
434A ARG* 2.7 29.8 + - - +
435A PHE* 2.8 14.4 + - - +
457A LEU* 4.5 5.4 - - + -
460A CYS* 4.3 3.0 - - - +
461A LEU* 3.7 38.4 - - + +
464A PHE* 4.8 4.0 - - - -
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ARG* 4.7 2.7 - - - +
156A TYR* 3.3 30.7 - - + +
428A MET* 2.7 21.5 + - + +
429A LEU* 3.4 9.2 - - + +
431A ALA* 1.3 70.7 - - - +
433A ASP* 1.3 53.1 + - - +
435A PHE* 2.9 11.3 + - - +
436A HIS* 2.7 33.6 + - - +
442A TYR* 3.4 15.7 - - + -
443A PRO* 3.4 23.6 - - + -
457A LEU* 4.1 7.8 - - + +
482A PHE* 3.6 29.4 - - + -
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Residues in contact with ASP 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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131A LEU 5.0 0.9 - - - +
132A PRO* 4.5 1.8 - - - +
133A GLU* 3.6 47.2 + - + +
154A ARG* 2.7 42.2 + - - -
402A TYR* 4.8 5.2 + - - -
429A LEU* 2.6 20.3 + - - +
430A ARG* 3.4 6.6 - - - +
432A VAL* 1.3 73.1 - - - +
434A ARG* 1.3 62.4 + - - +
436A HIS* 3.2 8.6 + - - +
437A LYS* 3.0 22.5 + - - +
442A TYR* 4.2 8.5 + - - -
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Residues in contact with ARG 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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133A GLU* 4.8 4.5 + - - +
430A ARG 2.8 11.9 + - - +
431A ALA* 2.7 16.4 + - - +
433A ASP* 1.3 68.1 - - - +
435A PHE* 1.3 66.1 + - - +
436A HIS 2.8 0.7 + - - -
437A LYS* 3.0 7.5 + - - +
438A GLN* 2.8 36.8 + - + +
460A CYS* 3.2 33.7 + - + +
463A GLY* 3.3 27.5 + - - -
464A PHE* 3.4 27.5 - - + +
467A GLU* 3.5 29.3 + - - +
468A TYR* 5.9 0.6 - - - -
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Residues in contact with PHE 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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431A ALA 2.8 13.1 + - - +
432A VAL* 3.1 9.6 - - - +
434A ARG* 1.3 73.3 - - - +
436A HIS* 1.3 55.3 + - - +
438A GLN* 4.3 1.3 - - - -
439A GLN* 2.7 48.0 + - + +
441A ARG* 3.2 28.3 - - + -
442A TYR 3.6 2.5 - - - -
443A PRO* 3.5 24.5 - - + -
453A ASP* 3.1 29.8 - - + -
456A LYS* 3.7 18.6 - - + -
457A LEU* 3.5 49.4 - - + -
460A CYS* 3.8 16.3 - - - +
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Residues in contact with HIS 436 (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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132A PRO* 4.5 18.7 - - + +
133A GLU 6.0 0.2 + - - -
432A VAL 2.7 16.0 + - - +
433A ASP* 3.4 10.9 + - - +
434A ARG 2.8 1.0 + - - -
435A PHE* 1.3 70.1 - - - +
437A LYS* 1.3 74.1 + - - +
438A GLN 3.0 1.5 + - - -
440A GLY* 2.7 36.7 + - - -
441A ARG* 3.6 22.2 - - - +
442A TYR* 3.2 54.4 + + + -
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Residues in contact with LYS 437 (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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133A GLU* 5.9 7.9 - - + +
134A SER* 5.9 8.6 - - - -
433A ASP 3.0 9.3 + - - +
434A ARG* 3.0 9.0 + - - +
436A HIS* 1.3 89.3 + - + +
438A GLN* 1.3 63.1 + - - +
440A GLY* 4.4 2.6 + - - -
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Residues in contact with GLN 438 (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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434A ARG* 2.8 28.1 + - + +
435A PHE 3.7 3.6 - - - +
437A LYS* 1.3 81.0 - - - +
439A GLN* 1.3 78.1 + - + +
456A LYS* 5.2 1.6 + - - +
459A SER* 6.0 1.6 - - - -
460A CYS* 3.4 29.5 - - - -
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Residues in contact with GLN 439 (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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435A PHE* 2.7 58.7 + - + +
437A LYS 4.7 0.2 - - - -
438A GLN* 1.3 94.0 + - + +
440A GLY* 1.3 57.8 + - - +
441A ARG* 3.4 26.8 + - - +
456A LYS* 3.8 30.5 + - - +
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Residues in contact with GLY 440 (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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436A HIS* 2.7 32.7 + - - -
437A LYS 4.4 2.0 + - - -
439A GLN* 1.3 74.6 - - - +
441A ARG* 1.3 60.7 + - - +
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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
------------------------------------------------------------
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