Contacts of the helix formed by residues 417 - 433 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B LYS* 2.6 27.1 + - - -
415B THR* 2.9 22.5 + - - +
416B ASN* 1.3 76.7 - - - +
418B THR* 1.3 65.5 + - - +
419B GLU* 4.2 4.5 - - - +
420B SER* 2.9 31.1 + - - -
421B ASP* 3.2 19.8 + - - +
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Residues in contact with THR 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ASP* 1.3 77.4 - - - +
419B GLU* 1.3 65.6 + - - +
421B ASP* 3.2 9.4 + - - +
422B ILE* 3.0 35.2 + - - +
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Residues in contact with GLU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 3.4 57.0 - - + +
274B LYS* 4.0 21.7 + - + +
417B ASP* 3.3 7.0 + - - +
418B THR* 1.3 86.7 + - - +
420B SER* 1.3 61.6 + - - +
422B ILE* 3.3 3.5 + - - +
423B ASN* 3.0 23.6 + - - +
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Residues in contact with SER 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LYS* 3.2 19.5 - - - +
275B PRO* 4.9 0.2 - - - +
277B LEU* 4.3 4.0 - - - +
402B PRO* 5.9 0.7 - - - +
414B VAL* 3.1 30.0 - - - +
415B THR* 3.2 13.0 + - - -
416B ASN* 5.3 0.7 - - - -
417B ASP* 2.9 28.9 + - - -
419B GLU* 1.3 73.2 - - - +
421B ASP* 1.3 56.5 + - - +
423B ASN* 3.4 7.9 + - - +
424B TYR* 3.1 28.8 + - - +
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Residues in contact with ASP 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ASN* 5.3 0.7 - - - +
417B ASP 3.2 10.0 + - - +
418B THR* 3.2 13.7 + - - +
420B SER* 1.3 77.3 - - - +
422B ILE* 1.3 62.6 + - + +
424B TYR* 3.6 5.1 + - - +
425B LEU* 3.0 35.4 + - - +
526B HIS* 2.8 36.9 + - - -
527B GLN* 3.0 23.6 + - - +
576B LEU* 3.1 23.7 - - + +
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Residues in contact with ILE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B PRO* 3.9 17.5 - - + -
271B PHE* 3.9 12.8 - - + -
418B THR* 3.0 20.5 + - - +
419B GLU 3.7 6.5 - - - +
421B ASP* 1.3 76.4 - - + +
423B ASN* 1.3 56.2 + - - +
425B LEU* 4.5 1.3 - - + +
426B LEU* 2.7 32.7 + - - +
576B LEU* 3.8 38.1 - - + +
577B VAL* 4.1 9.8 - - + +
580B TRP* 3.8 45.3 - - + +
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Residues in contact with ASN 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B TYR* 3.5 13.7 + - - +
269B VAL* 3.7 13.7 - - - +
270B PRO* 3.4 15.7 - - - +
271B PHE* 3.0 48.0 + - - -
274B LYS* 3.6 22.0 - - - +
275B PRO 5.1 3.2 + - - -
277B LEU* 3.7 8.5 - - + +
419B GLU 3.0 13.5 + - - +
420B SER* 3.6 9.6 - - - +
421B ASP 3.4 0.2 - - - -
422B ILE* 1.3 75.3 - - - +
424B TYR* 1.3 58.8 + - - +
426B LEU* 3.6 2.1 - - - +
427B LYS* 2.8 30.5 + - - +
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Residues in contact with TYR 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 3.3 19.9 - - + +
353B MET* 6.3 0.2 - - + -
397B LEU 3.8 6.8 + - - -
400B SER* 3.2 39.1 - - - -
401B THR* 3.6 12.3 + - - +
402B PRO* 3.8 24.0 - - + -
420B SER 3.1 14.1 + - - +
421B ASP* 3.8 5.2 - - - +
423B ASN* 1.3 79.0 - - - +
425B LEU* 1.3 65.8 + - + +
427B LYS* 3.2 9.2 + - + +
428B MET* 2.9 52.0 + - + +
526B HIS* 3.5 31.6 - + + -
527B GLN* 6.2 0.4 - - + -
573B TYR* 3.4 21.0 + + - -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B ASP 3.0 21.5 + - - +
422B ILE* 4.1 1.3 - - + +
424B TYR* 1.3 79.1 - - + +
426B LEU* 1.3 60.4 + - - +
428B MET* 3.3 2.5 + - - +
429B ALA* 2.9 28.8 + - - +
526B HIS* 3.6 39.0 - - + +
573B TYR* 3.5 44.0 - - + +
574B PHE* 3.8 9.0 - - + +
576B LEU* 3.8 30.7 - - + -
577B VAL* 3.6 23.3 - - + +
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Residues in contact with LEU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B LEU* 4.0 16.6 - - + -
228B PHE* 3.9 20.0 - - + -
265B TYR* 4.3 6.1 - - + -
268B VAL* 3.7 28.7 - - + +
270B PRO* 3.4 32.1 - - + -
422B ILE 2.7 23.5 + - - +
423B ASN 3.6 3.1 - - - +
425B LEU* 1.3 74.1 - - - +
427B LYS* 1.3 63.6 + - - +
429B ALA* 3.0 5.1 + - - +
430B LEU* 3.0 29.3 + - + +
577B VAL* 3.8 9.1 - - + +
580B TRP* 5.0 0.4 - - + -
581B LEU* 4.0 22.7 - - + -
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Residues in contact with LYS 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B GLU* 4.7 18.3 - - + +
265B TYR* 3.5 33.7 - - + -
277B LEU* 3.6 37.2 - - + +
278B ASP* 4.0 20.6 - - - +
353B MET* 3.6 23.9 - - + +
423B ASN 2.8 14.4 + - - +
424B TYR* 3.4 13.9 - - + +
426B LEU* 1.3 76.0 - - - +
428B MET* 1.3 71.1 + - + +
430B LEU* 3.4 14.7 + - - +
431B GLU* 3.4 20.3 + - - +
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Residues in contact with MET 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LEU* 3.9 28.0 - - + -
400B SER* 4.0 17.7 - - - +
424B TYR* 2.9 57.6 + - + +
425B LEU* 3.8 5.2 - - - +
427B LYS* 1.3 85.8 - - - +
429B ALA* 1.3 58.6 + - - +
431B GLU* 3.2 24.6 + - - +
432B LYS* 2.8 45.0 + - + +
573B TYR* 3.7 12.8 - - + +
574B PHE* 3.8 13.9 - - + -
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Residues in contact with ALA 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 3.6 16.5 - - + +
425B LEU 2.9 14.4 + - - +
426B LEU* 3.0 12.3 + - + +
428B MET* 1.3 74.5 - - - +
430B LEU* 1.3 64.0 + - - +
433B ILE* 2.8 43.9 + - + +
434B ALA 3.1 8.0 + - - -
574B PHE* 3.6 13.4 - - + -
577B VAL* 4.7 7.2 - - + -
581B LEU* 5.3 2.9 - - + -
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B LEU* 4.1 12.3 - - + -
229B VAL* 3.9 27.1 - - + -
260B SER* 3.7 0.7 - - - -
261B TRP* 2.9 61.7 + - + +
262B GLU* 3.8 4.3 - - - +
264B ILE* 4.7 1.8 - - + -
265B TYR* 3.7 43.7 - - + +
268B VAL* 3.9 14.8 - - + -
426B LEU* 3.0 19.8 + - + +
427B LYS* 3.5 8.3 - - - +
429B ALA* 1.3 76.5 - - - +
431B GLU* 1.3 56.2 + - - +
434B ALA* 3.2 13.0 - - - +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B SER* 3.8 11.1 - - - -
262B GLU* 4.0 30.0 + - + +
354B ASP* 6.3 1.8 - - - -
357B SER* 4.1 21.2 + - - -
396B ALA* 6.0 0.7 - - - +
400B SER* 5.3 2.1 + - - -
427B LYS* 3.4 15.0 + - - +
428B MET* 3.2 26.6 + - - +
429B ALA 3.1 0.6 - - - -
430B LEU* 1.3 79.3 - - - +
432B LYS* 1.3 88.6 + - + +
435B PHE* 3.7 16.2 - - - +
505B PHE* 3.8 6.0 - - + -
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Residues in contact with LYS 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ASP* 3.5 23.4 + - - +
396B ALA* 6.1 1.6 - - - +
397B LEU* 4.0 16.2 - - - +
428B MET* 2.8 30.5 + - + +
431B GLU* 1.3 102.9 + - + +
433B ILE* 1.3 65.0 + - + +
434B ALA 3.5 0.2 - - - -
435B PHE* 3.5 14.8 + - - +
436B LEU* 3.6 13.8 - - - +
505B PHE* 3.6 26.2 - - + -
508B GLN* 2.7 28.8 + - - +
509B PHE* 4.1 19.1 - - + -
570B LEU* 5.8 1.8 - - + -
574B PHE* 3.9 15.3 - - + -
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Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 4.0 28.5 - - + +
222B TYR* 3.8 32.6 - - + +
225B LEU* 4.0 10.3 - - + -
429B ALA* 2.8 33.8 + - + +
432B LYS* 1.3 68.8 - - - +
434B ALA* 1.3 68.6 + - - +
435B PHE 3.1 1.6 - - - -
436B LEU* 3.2 31.6 + - + +
437B PRO* 3.6 5.7 - - - +
570B LEU* 4.1 10.1 - - + -
574B PHE* 3.8 32.1 - - + -
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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
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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