Contacts of the helix formed by residues 417 - 433 (chain A) in PDB entry 5AM8
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 ASP 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A LYS* 3.8 17.2 + - - -
415A THR* 2.9 32.6 + - + +
416A ASN* 1.3 75.4 - - - +
418A THR* 1.3 64.8 + - - +
419A GLU* 3.6 18.8 + - - +
420A SER* 3.2 23.8 + - - -
421A ASP* 3.2 23.4 + - - +
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Residues in contact with THR 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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417A ASP* 1.3 77.4 + - - +
419A GLU* 1.3 66.8 + - - +
421A ASP* 3.4 9.4 + - - +
422A ILE* 3.0 36.7 + - - +
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Residues in contact with GLU 419 (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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271A PHE* 3.4 58.7 - - + +
273A ASP* 5.3 0.7 - - - +
274A LYS* 3.6 23.6 + - - -
417A ASP* 3.3 11.5 + - - +
418A THR* 1.3 83.8 - - - +
420A SER* 1.3 58.3 + - - +
422A ILE* 3.4 1.2 + - - -
423A ASN* 3.1 24.4 + - - -
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Residues in contact with SER 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 3.7 21.2 - - - +
275A PRO* 4.7 2.9 - - - +
277A LEU* 4.6 2.1 - - - +
402A PRO* 6.0 0.5 - - - +
414A VAL* 4.4 12.9 - - - +
415A THR 3.4 22.3 + - - -
417A ASP* 3.2 22.2 + - - -
419A GLU* 1.3 76.4 - - - +
421A ASP* 1.3 65.0 + - - +
423A ASN* 3.2 10.3 + - - +
424A TYR* 3.0 24.7 + - - +
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Residues in contact with ASP 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ASN* 4.3 4.7 - - - +
417A ASP 3.2 17.1 + - - +
418A THR* 3.4 12.4 - - - +
420A SER* 1.3 76.8 - - - +
422A ILE* 1.3 64.3 + - + +
424A TYR* 3.4 5.1 + - - +
425A LEU* 3.0 30.7 + - - +
524A PRO* 5.7 0.9 - - - +
526A HIS* 3.1 31.0 + - - +
527A GLN* 3.1 26.5 + - - +
576A LEU* 3.9 16.3 - - + +
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Residues in contact with ILE 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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270A PRO* 4.1 13.9 - - + -
271A PHE* 4.1 7.2 - - + -
418A THR* 3.0 24.3 + - - +
419A GLU* 3.7 6.5 - - - +
420A SER 3.3 0.2 - - - -
421A ASP* 1.3 77.2 - - + +
423A ASN* 1.3 58.0 + - - +
425A LEU* 4.8 2.2 - - + -
426A LEU* 2.9 29.3 + - + +
576A LEU* 3.9 39.5 - - + +
577A VAL* 4.0 7.5 - - + +
580A TRP* 3.8 49.6 - - + -
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Residues in contact with ASN 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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265A TYR* 3.3 27.0 + - - +
269A VAL* 3.8 6.7 - - - +
270A PRO* 3.4 25.4 - - - +
271A PHE* 3.2 34.2 + - - +
274A LYS* 3.6 21.4 - - - +
275A PRO 4.9 4.8 + - - -
277A LEU* 4.0 6.3 - - + -
419A GLU 3.1 12.2 + - - +
420A SER* 3.2 10.4 + - - +
422A ILE* 1.3 78.6 - - - +
424A TYR* 1.3 55.7 + - - +
426A LEU* 3.6 5.9 - - - +
427A LYS* 3.0 23.7 + - - +
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Residues in contact with TYR 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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277A LEU* 3.3 23.1 - - + -
353A MET* 6.1 1.3 - - + -
397A LEU 3.6 5.5 + - - -
400A SER* 2.7 44.0 + - - -
401A THR* 3.3 14.0 + - - +
402A PRO* 3.8 26.0 - - + -
420A SER 3.0 14.1 + - - +
421A ASP* 3.9 4.5 - - - +
423A ASN* 1.3 74.4 - - - +
425A LEU* 1.3 71.2 + - + +
427A LYS* 3.0 11.0 + - + +
428A MET* 2.9 44.9 + - + +
526A HIS* 3.5 28.0 - + - -
527A GLN* 6.2 0.4 - - + -
573A TYR* 3.4 19.8 + - - -
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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
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421A ASP 3.0 21.7 + - - +
422A ILE* 4.2 0.7 - - - +
424A TYR* 1.3 80.6 - - + +
426A LEU* 1.3 57.1 + - - +
428A MET* 4.3 2.0 - - - -
429A ALA* 2.8 29.1 + - - +
526A HIS* 3.6 49.1 - - + +
573A TYR* 3.6 34.8 - - + +
574A PHE* 3.6 10.1 - - + +
576A LEU* 4.1 27.8 - - + +
577A VAL* 3.8 22.9 - - + +
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Residues in contact with LEU 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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225A LEU* 3.9 24.7 - - + -
228A PHE* 4.0 12.1 - - + -
265A TYR* 4.5 3.8 - - + -
268A VAL* 3.7 19.3 - - + +
269A VAL* 4.3 3.4 - - - -
270A PRO* 3.2 33.7 - - + -
422A ILE* 2.9 21.0 + - + +
423A ASN 3.6 3.6 - - - +
425A LEU* 1.3 73.1 - - - +
427A LYS* 1.3 67.8 + - - +
429A ALA* 3.1 2.3 + - + +
430A LEU* 2.9 32.3 + - + +
577A VAL* 3.9 12.7 - - + +
580A TRP* 5.2 1.6 - - + -
581A LEU* 4.3 18.4 - - + -
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Residues in contact with LYS 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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262A GLU* 4.6 17.0 - - + +
265A TYR* 3.7 34.7 - - + -
277A LEU* 3.4 42.8 - - + +
278A ASP* 4.0 10.5 - - - +
353A MET* 3.3 33.3 - - + +
423A ASN 3.0 13.2 + - - +
424A TYR* 3.0 14.3 + - + +
426A LEU* 1.3 77.2 - - - +
428A MET* 1.3 67.2 + - + +
430A LEU* 3.3 13.7 + - - +
431A GLU* 3.4 19.4 + - - +
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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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396A ALA 6.3 0.2 - - - -
397A LEU* 3.8 28.7 - - + -
400A SER* 3.5 27.6 - - - +
424A TYR* 2.9 43.9 + - + +
425A LEU* 3.8 6.1 - - - +
427A LYS* 1.3 80.6 - - + +
429A ALA* 1.3 60.8 + - - +
431A GLU* 3.1 23.7 + - - +
432A LYS* 2.8 49.0 + - + +
573A TYR* 3.7 10.3 - - + +
574A PHE* 3.8 14.8 - - + -
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Residues in contact with ALA 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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225A LEU* 3.5 19.0 - - + +
425A LEU 2.8 18.8 + - - +
426A LEU* 3.1 9.6 + - + +
428A MET* 1.3 74.3 - - - +
430A LEU* 1.3 66.6 + - - +
433A ILE* 2.9 38.8 + - + +
434A ALA 3.2 7.3 + - - -
574A PHE* 3.6 13.7 - - + -
577A VAL* 4.6 7.2 - - + -
581A LEU* 5.2 3.4 - - + -
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Residues in contact with LEU 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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225A LEU* 4.2 11.2 - - + -
229A VAL* 4.0 25.1 - - + -
260A SER* 3.7 0.5 - - - -
261A TRP* 2.8 63.4 + - + +
262A GLU* 3.8 3.8 - - - +
264A ILE* 4.7 1.8 - - + -
265A TYR* 3.8 43.7 - - + -
268A VAL* 4.1 12.8 - - + -
426A LEU* 2.9 24.1 + - + +
427A LYS* 3.5 8.3 - - - +
428A MET 3.3 0.2 - - - -
429A ALA* 1.3 75.6 - - - +
431A GLU* 1.3 56.9 + - - +
434A ALA* 3.2 12.5 - - - +
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Residues in contact with GLU 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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260A SER* 3.8 14.3 - - - -
262A GLU* 3.8 29.7 + - + +
354A ASP* 6.5 1.3 - - - -
357A SER* 4.2 22.8 + - - -
396A ALA* 6.0 0.9 - - - +
400A SER* 5.8 1.0 - - - -
427A LYS* 3.4 14.5 + - - +
428A MET* 3.1 26.1 + - - +
429A ALA 3.1 0.4 - - - -
430A LEU* 1.3 81.4 - - - +
432A LYS* 1.3 87.2 + - + +
434A ALA 4.9 0.2 - - - -
435A PHE* 3.8 4.8 - - - +
505A PHE* 3.7 13.9 - - + -
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Residues in contact with LYS 432 (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 ASP* 3.6 23.0 + - - +
396A ALA* 5.9 2.6 - - - +
397A LEU* 4.1 8.0 - - - +
428A MET* 2.8 41.5 + - + +
431A GLU* 1.3 98.8 + - + +
433A ILE* 1.3 63.8 + - + +
434A ALA 3.5 0.7 - - - -
435A PHE* 3.6 5.1 + - - +
436A LEU* 3.5 16.6 - - - +
505A PHE* 3.5 34.3 - - + -
508A GLN* 2.7 28.8 + - - +
509A PHE* 4.1 17.5 - - + -
570A LEU* 5.8 0.9 - - + -
574A PHE* 4.0 15.7 - - + -
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Residues in contact with ILE 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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221A LEU* 4.0 22.0 - - + +
222A TYR* 3.7 33.4 - - + +
225A LEU* 4.0 10.5 - - + -
429A ALA* 2.9 28.8 + - + +
432A LYS* 1.3 72.1 - - - +
434A ALA* 1.3 66.3 + - - +
435A PHE 3.1 1.8 - - - -
436A LEU* 3.2 32.9 + - + +
437A PRO* 3.6 5.2 - - - +
570A LEU* 3.9 28.7 - - + -
574A PHE* 3.9 20.9 - - + -
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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
------------------------------------------------------------
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