Contacts of the helix formed by residues 412 - 430 (chain A) in PDB entry 2IO0
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 ASN 412 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLY 5.3 0.2 - - - -
401A ASP* 3.0 26.4 + - - +
404A THR* 3.2 27.9 + - + +
410A TRP 3.6 0.8 + - - -
411A LEU* 1.3 77.3 - - - +
413A ASP* 1.3 67.7 + - - +
414A GLU* 3.0 15.7 + - - +
415A VAL* 3.2 14.3 + - - +
416A ILE* 3.3 20.8 + - - +
479A TRP* 4.0 2.2 - - - -
59B ARG* 4.1 9.5 - - - +
89B GLN* 5.5 3.8 - - + +
90B GLN 3.3 14.1 - - - +
91B THR* 4.3 13.7 - - + +
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Residues in contact with ASP 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ASN* 1.3 72.0 - - - +
414A GLU* 1.3 64.9 + - - +
415A VAL 3.3 0.2 - - - -
416A ILE* 3.8 2.1 - - - +
417A ASN* 2.7 38.2 + - - +
440A THR* 3.6 8.1 - - - +
441A PHE* 3.2 19.4 - - - -
479A TRP* 3.9 11.4 - - + -
59B ARG* 2.7 44.3 + - - -
89B GLN* 4.0 0.2 - - - +
90B GLN* 2.9 48.0 + - + +
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Residues in contact with GLU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 3.3 28.7 - - - +
396A ARG 4.0 17.3 + - - +
397A ILE* 3.6 18.4 - - + +
401A ASP* 3.7 24.5 - - - +
412A ASN* 3.0 6.1 + - - +
413A ASP* 1.3 74.2 - - - +
415A VAL* 1.3 66.5 + - - +
417A ASN* 3.8 3.0 + - - +
418A PHE* 2.9 26.9 + - - +
59B ARG* 3.7 34.5 + - - +
61B ARG* 3.6 14.7 + - - -
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ILE* 4.7 5.8 - - + -
401A ASP* 3.3 35.4 - - + +
402A ILE* 4.3 6.5 - - - -
404A THR* 3.5 10.1 - - - +
405A LEU* 3.9 21.1 - - + -
411A LEU* 3.7 26.5 - - + -
412A ASN* 3.2 12.0 + - - +
414A GLU* 1.3 77.5 - - - +
416A ILE* 1.3 64.7 + - - +
418A PHE* 3.7 4.1 - - - +
419A TYR* 3.1 22.7 + - - +
579A MET* 4.3 4.3 - - - -
583A ILE* 4.3 15.4 - - + +
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Residues in contact with ILE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU* 4.0 15.3 - - + -
412A ASN 3.3 15.2 + - - +
413A ASP* 4.0 4.0 - - - +
415A VAL* 1.3 78.8 - - - +
417A ASN* 1.3 58.3 + - - +
418A PHE 3.3 0.2 + - - -
419A TYR* 3.6 4.9 - - - +
420A MET* 2.9 52.4 + - + +
440A THR* 3.8 19.7 - - + -
472A PRO* 4.4 4.9 - - + -
479A TRP* 3.4 45.8 - - + +
549A GLY* 4.1 15.5 - - - +
552A THR* 5.0 4.0 - - + -
553A CYS* 4.3 4.7 - - - -
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Residues in contact with ASN 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 3.7 19.5 - - + -
413A ASP* 2.7 37.7 + - - +
414A GLU* 4.0 1.7 - - - +
416A ILE* 1.3 72.6 - - - +
418A PHE* 1.3 62.6 + - - +
420A MET* 3.6 6.1 + - - +
421A ASN* 2.8 32.3 + - - +
437A VAL* 5.9 0.2 - - - +
438A PHE 4.3 1.7 - - - +
439A SER* 3.5 12.5 + - - -
440A THR* 2.9 47.6 + - - +
441A PHE* 4.4 6.9 - - - -
472A PRO* 5.3 0.5 - - - +
61B ARG* 4.7 7.1 - - - +
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Residues in contact with PHE 418 (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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390A SER* 3.5 21.1 - - - -
392A ALA* 3.7 31.9 - - + -
393A PHE* 3.8 13.0 - + - -
395A LEU* 3.5 19.0 - - + +
397A ILE* 3.4 29.6 - - + -
414A GLU 2.9 17.9 + - - +
415A VAL* 3.7 4.5 - - - +
417A ASN* 1.3 76.3 - - - +
419A TYR* 1.3 63.8 + - - +
421A ASN* 3.0 15.8 + - - +
422A LEU* 3.1 29.3 + - + +
583A ILE* 3.5 34.1 - - + -
586A GLN* 3.6 19.5 - - + -
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Residues in contact with TYR 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A VAL 3.1 14.7 + - - +
416A ILE 3.6 3.4 - - - +
418A PHE* 1.3 80.2 - - - +
420A MET* 1.3 66.8 + - + +
422A LEU* 2.8 25.8 + - + +
423A LEU* 3.0 31.2 + - + +
553A CYS* 3.5 45.5 - - + -
554A LYS* 3.2 27.0 + - - +
557A ASP* 3.7 12.6 - - - +
579A MET* 3.8 31.9 - - + -
582A GLU* 3.8 12.4 + - + -
583A ILE* 5.2 3.1 - - + +
588A LEU* 3.7 30.2 - - + +
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Residues in contact with MET 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 2.9 40.8 + - + +
417A ASN* 3.9 7.0 - - - +
419A TYR* 1.3 73.2 - - + +
421A ASN* 1.3 62.7 + - - +
423A LEU* 3.3 11.4 + - - +
424A VAL* 3.3 22.9 + - - +
437A VAL* 3.1 37.7 - - + +
470A LEU* 4.2 12.8 - - - -
472A PRO* 4.2 16.6 - - + -
481A LEU* 4.8 2.7 - - + -
552A THR* 4.0 20.0 - - + +
553A CYS* 4.2 13.9 - - - -
556A ALA* 3.9 31.2 - - + -
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Residues in contact with ASN 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A PHE* 3.4 47.6 - - + +
395A LEU* 4.1 4.8 - - - +
417A ASN* 2.8 28.9 + - - +
418A PHE 3.0 9.0 + - - +
420A MET* 1.3 76.7 - - - +
422A LEU* 1.3 66.2 + - - +
424A VAL* 3.2 14.1 + - - +
425A GLU* 3.2 24.8 + - - +
437A VAL* 5.7 3.0 - - - +
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Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A PHE* 4.0 18.8 - - + -
418A PHE* 3.1 32.8 + - + +
419A TYR* 2.8 22.3 + - + +
421A ASN* 1.3 73.6 - - - +
423A LEU* 1.3 58.1 + - - +
425A GLU* 3.1 7.8 + - + +
426A ARG* 2.7 31.0 + - - +
582A GLU 3.9 21.3 - - - +
583A ILE* 4.5 2.0 - - + -
586A GLN* 3.7 35.9 - - + +
587A GLN* 4.3 1.1 - - - +
588A LEU* 4.1 27.8 - - + -
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Residues in contact with LEU 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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419A TYR* 3.0 34.2 + - + +
420A MET* 3.4 18.4 - - - +
421A ASN 3.2 0.2 - - - -
422A LEU* 1.3 76.3 - - - +
424A VAL* 1.3 62.4 + - - +
426A ARG* 3.2 28.0 - - - +
427A ASN* 2.9 30.0 + - - +
435A LEU* 3.6 13.7 - - + -
470A LEU* 4.5 3.6 - - + -
556A ALA* 3.6 33.2 - - + +
557A ASP* 3.4 22.2 - - + +
560A SER* 4.7 0.2 - - - +
588A LEU* 3.6 16.4 - - + -
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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
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420A MET 3.3 14.8 + - - +
421A ASN* 3.2 15.0 + - - +
422A LEU 3.1 0.6 - - - -
423A LEU* 1.3 80.2 - - - +
425A GLU* 1.3 71.9 + - - +
427A ASN* 3.9 2.1 - - - +
428A LYS* 3.2 24.3 + - + +
435A LEU* 3.5 35.6 + - + +
436A HIS* 4.8 0.2 - - - -
437A VAL* 3.4 26.9 - - + +
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Residues in contact with GLU 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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393A PHE* 3.9 26.1 - - + -
421A ASN* 3.2 11.2 + - - +
422A LEU* 3.1 11.5 + - + +
424A VAL* 1.3 87.7 - - - +
426A ARG* 1.3 69.5 + - - +
428A LYS* 3.4 15.0 + - - +
429A LYS* 3.0 28.9 + - + +
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Residues in contact with ARG 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 LEU 2.7 20.5 + - - +
423A LEU* 3.2 16.2 + - - +
425A GLU* 1.3 75.9 - - - +
427A ASN* 1.3 93.3 + - - +
429A LYS* 2.7 12.9 + - - -
430A GLN* 3.0 35.5 + - + +
432A TYR* 4.3 6.3 - - - -
557A ASP* 2.7 28.9 + - - -
560A SER* 2.9 27.7 + - - -
561A ARG* 3.0 25.5 - - - +
587A GLN* 6.2 1.8 - - - +
588A LEU* 3.8 31.7 - - + +
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Residues in contact with ASN 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU 2.9 15.8 + - - +
424A VAL 3.9 3.6 - - - +
426A ARG* 1.3 111.1 + - - +
428A LYS* 1.3 62.6 + - - +
430A GLN 3.4 0.5 + - - -
431A GLY 3.3 2.6 + - - -
432A TYR* 2.7 46.2 + - + +
433A PRO* 2.5 30.2 + - - +
434A ALA* 5.8 0.2 - - - -
435A LEU* 3.9 15.6 - - + +
468A ILE* 5.5 0.2 - - - +
560A SER* 3.1 29.3 + - - +
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Residues in contact with LYS 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* 3.2 18.1 + - + +
425A GLU* 3.7 16.4 - - - +
426A ARG 2.8 4.4 + - - -
427A ASN* 1.3 76.7 - - - +
429A LYS* 1.3 68.8 + - + +
431A GLY* 3.3 12.1 + - - -
432A TYR 5.1 3.1 - - - -
434A ALA* 6.6 0.4 - - - +
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Residues in contact with LYS 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLU* 3.0 21.1 + - + +
426A ARG* 2.7 11.2 + - - +
428A LYS* 1.3 79.9 - - + +
430A GLN* 1.3 66.8 + - - +
431A GLY 3.3 1.4 + - - -
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Residues in contact with GLN 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 ARG* 3.0 36.1 + - + +
429A LYS* 1.3 84.3 + - - +
431A GLY* 1.3 63.3 + - - +
432A TYR* 3.0 32.7 + - + -
587A GLN* 5.4 8.1 - - - +
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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