Contacts of the helix formed by residues 422 - 440 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420G ASP 3.8 7.0 + - - +
421G ASN* 1.3 88.6 + - - +
423G ILE* 1.3 60.1 + - - +
424G VAL 3.1 0.4 - - - -
425G LEU* 3.0 37.8 + - + +
426G TYR 3.5 1.9 + - - -
521G ILE* 3.7 27.3 - - + +
523G SER* 5.0 2.9 - - - -
528G THR* 3.1 26.7 + - - +
529G SER 3.8 14.4 + - - -
530G ALA* 3.2 32.8 - - + +
532G PHE* 4.2 1.3 - - + -
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Residues in contact with ILE 423 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411G GLU* 6.3 0.2 - - + -
412G ILE* 4.5 30.1 - - + +
415G SER* 3.8 11.2 - - - -
416G MET* 3.3 25.6 - - + -
421G ASN* 2.5 32.2 + - - +
422G GLU* 1.3 71.0 - - - +
424G VAL* 1.3 69.5 + - - +
426G TYR* 2.9 41.9 + - + +
427G LEU* 3.1 6.8 + - + +
532G PHE* 3.4 37.5 - - + -
533G GLN* 6.1 0.7 - - - +
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Residues in contact with VAL 424 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416G MET* 4.0 24.2 - - + -
419G PRO 3.3 25.8 - - - +
420G ASP 4.4 0.9 - - - -
421G ASN 2.6 36.0 + - - +
423G ILE* 1.3 71.4 - - - +
425G LEU* 1.3 55.2 + - + +
427G LEU* 2.9 12.3 + - - +
428G MET* 2.8 31.8 + - + +
474G VAL* 4.1 19.5 - - + -
478G TYR* 3.7 41.3 - - + -
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Residues in contact with LEU 425 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G VAL* 3.9 29.6 - - + -
421G ASN 5.5 0.2 - - - -
422G GLU* 3.0 24.9 - - - +
424G VAL* 1.3 83.0 - - + +
426G TYR* 1.3 60.2 + - - +
428G MET* 3.4 7.3 - - - +
429G LEU* 2.9 28.8 + - - +
478G TYR* 3.9 24.9 - - + -
482G PHE* 3.9 21.8 - - + -
521G ILE* 4.0 15.7 - - + -
523G SER* 3.8 31.0 - - - +
525G MET* 5.4 6.5 - - - -
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Residues in contact with TYR 426 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G TYR* 4.1 33.0 - + - -
401G GLU* 2.8 37.2 + - + +
402G TYR* 3.8 5.9 - - - -
412G ILE* 4.8 14.8 - - + -
422G GLU 3.5 1.4 + - - -
423G ILE* 2.9 30.6 + - + +
425G LEU* 1.3 77.1 - - - +
427G LEU* 1.3 75.9 - - + +
429G LEU* 2.9 21.2 + - + +
430G ARG* 3.0 54.1 + - + +
464G PHE* 5.2 1.8 - + - -
519G THR* 4.6 5.2 - - + -
521G ILE* 3.6 21.9 - - + +
533G GLN* 5.4 3.1 - - - -
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Residues in contact with LEU 427 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412G ILE* 4.1 23.6 - - + -
416G MET* 3.8 39.0 - - + -
423G ILE* 3.6 12.3 - - + +
424G VAL* 2.9 6.7 + - - +
426G TYR* 1.3 86.3 - - + +
428G MET* 1.3 54.1 + - + +
430G ARG* 2.8 12.3 + - - +
431G ALA* 2.7 34.9 + - - +
461G LEU* 4.6 10.8 - - + -
464G PHE* 3.4 30.4 - - + -
465G LEU* 4.0 9.6 - - + -
470G LEU* 4.3 3.4 - - + -
472G VAL* 4.6 8.7 - - + -
474G VAL* 4.6 7.0 - - + -
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Residues in contact with MET 428 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424G VAL* 2.8 23.7 + - + +
425G LEU* 3.4 9.2 - - - +
426G TYR 3.2 0.2 - - - -
427G LEU* 1.3 72.8 - - - +
429G LEU* 1.3 50.9 + - - +
431G ALA* 2.9 11.8 - - + +
432G VAL* 2.6 40.9 + - + +
457G LEU* 4.0 25.4 - - + -
461G LEU* 4.2 14.1 - - + -
474G VAL* 4.1 22.4 - - - -
478G TYR* 3.7 32.3 - - + +
479G VAL* 4.3 4.9 - - + -
482G PHE* 3.4 32.8 - - + -
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Residues in contact with LEU 429 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G ARG* 4.3 21.5 + - - +
156G TYR* 4.0 26.5 - - + -
159G VAL* 4.7 9.9 - - + -
161G TYR* 3.6 46.2 - - + -
425G LEU 2.9 17.9 + - - +
426G TYR* 2.9 11.9 + - + +
428G MET* 1.3 75.3 - - - +
430G ARG* 1.3 57.3 + - + +
432G VAL* 2.9 7.0 + - + +
433G ASP* 2.6 40.0 + - - +
482G PHE* 3.6 22.7 - - + -
521G ILE* 6.0 0.7 - - + -
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Residues in contact with ARG 430 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G GLU* 2.7 26.7 + - - -
401G GLU 5.2 1.2 + - - -
402G TYR* 3.5 35.0 + - - +
426G TYR* 3.0 63.6 + - + +
427G LEU 2.8 7.1 + - - +
429G LEU* 1.3 77.1 - - - +
431G ALA* 1.3 57.5 + - - +
433G ASP* 3.3 7.1 + - - +
434G ARG* 2.8 30.0 + - - +
464G PHE* 3.7 39.8 - - + -
468G TYR* 3.3 28.7 + - - -
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Residues in contact with ALA 431 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427G LEU 2.7 15.2 + - - +
428G MET* 2.9 26.2 - - + +
430G ARG* 1.3 71.9 - - - +
432G VAL* 1.3 51.7 + - - +
434G ARG* 2.7 28.9 + - - +
435G PHE* 2.7 14.4 + - - +
457G LEU* 4.4 6.5 - - + -
460G CYS* 4.3 3.4 - - - +
461G LEU* 3.8 36.8 - - + +
464G PHE* 4.8 3.5 - - - -
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Residues in contact with VAL 432 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G ARG* 4.7 2.7 - - - +
156G TYR* 3.3 31.2 - - + +
428G MET* 2.6 20.9 + - + +
429G LEU* 3.3 9.4 - - + +
431G ALA* 1.3 70.7 - - - +
433G ASP* 1.3 54.7 + - - +
435G PHE* 2.8 11.9 + - - +
436G HIS* 2.7 33.6 + - - +
442G TYR* 3.4 15.9 - - + -
443G PRO* 3.4 22.2 - - + -
457G LEU* 4.1 8.1 - - + -
482G PHE* 3.7 29.6 - - + -
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Residues in contact with ASP 433 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G LEU 5.0 1.0 - - - +
132G PRO* 4.5 1.8 - - - +
133G GLU* 3.7 46.7 + - + +
154G ARG* 2.7 42.8 + - - -
402G TYR* 4.8 5.4 + - - -
429G LEU* 2.6 18.7 + - - +
430G ARG* 3.5 7.1 - - - +
432G VAL* 1.3 73.8 - - - +
434G ARG* 1.3 63.2 + - - +
436G HIS* 3.1 7.8 + - - +
437G LYS* 3.0 22.3 + - - +
442G TYR* 4.2 8.3 + - - -
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Residues in contact with ARG 434 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G GLU* 4.9 4.4 + - - +
430G ARG 2.8 12.8 + - - +
431G ALA* 2.7 16.8 + - - +
433G ASP* 1.3 68.7 - - - +
435G PHE* 1.3 67.0 + - - +
436G HIS 2.8 0.9 + - - -
437G LYS* 3.0 7.5 + - + +
438G GLN* 2.8 36.9 + - + +
460G CYS* 3.2 34.1 + - + +
463G GLY* 3.4 26.7 + - - -
464G PHE* 3.4 27.1 - - + +
467G GLU* 3.5 29.7 + - - +
468G TYR* 5.8 0.4 - - - -
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Residues in contact with PHE 435 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431G ALA 2.7 14.4 + - - +
432G VAL* 3.1 10.1 - - - +
434G ARG* 1.3 72.8 - - - +
436G HIS* 1.3 56.2 + - - +
438G GLN* 4.3 1.1 - - - -
439G GLN* 2.7 46.3 + - + +
441G ARG* 3.2 27.6 - - + -
442G TYR 3.6 2.5 - - - -
443G PRO* 3.5 25.1 - - + -
453G ASP* 3.1 30.1 - - + -
456G LYS* 3.7 17.3 - - + -
457G LEU* 3.5 48.9 - - + -
460G CYS* 3.9 16.9 - - - +
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Residues in contact with HIS 436 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G PRO* 4.5 18.5 - - + +
133G GLU 6.0 0.2 + - - -
432G VAL 2.7 13.8 + - - +
433G ASP* 3.4 10.5 + - - +
434G ARG 2.8 1.0 + - - -
435G PHE* 1.3 70.6 - - - +
437G LYS* 1.3 75.5 + - + +
438G GLN 2.9 1.5 + - - -
440G GLY* 2.7 35.5 + - - -
441G ARG* 3.6 22.9 - - - +
442G TYR* 3.2 55.3 + + + +
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Residues in contact with LYS 437 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G GLU* 5.8 7.6 - - + +
134G SER* 5.8 8.8 - - - -
433G ASP 3.0 8.6 + - - +
434G ARG* 3.0 9.5 + - - +
436G HIS* 1.3 89.8 + - + +
438G GLN* 1.3 62.8 + - - +
439G GLN 4.7 0.3 - - - -
440G GLY* 4.4 2.4 + - - -
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Residues in contact with GLN 438 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434G ARG* 2.8 27.8 + - + +
435G PHE 3.7 3.6 - - - +
436G HIS 2.9 0.2 - - - -
437G LYS* 1.3 82.0 - - - +
439G GLN* 1.3 79.4 + - + +
456G LYS* 5.1 2.2 + - - +
459G SER* 6.0 1.6 - - - -
460G CYS* 3.4 29.1 - - - -
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Residues in contact with GLN 439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435G PHE* 2.7 58.9 + - + +
437G LYS 4.7 0.2 - - - -
438G GLN* 1.3 93.8 + - + +
440G GLY* 1.3 58.5 + - - +
441G ARG* 3.4 26.8 + - - +
456G LYS* 3.8 29.7 + - - +
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Residues in contact with GLY 440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436G HIS* 2.7 32.2 + - - -
437G LYS 4.4 1.5 + - - -
439G GLN* 1.3 73.9 - - - +
441G 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) + - + + + + + -
------------------------------------------------------------
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