Contacts of the helix formed by residues 417 - 432 (chain A) in PDB entry 3M6L
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 PHE 417 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LEU* 5.0 3.6 - - + -
391A GLU* 4.1 21.8 - - - +
413A THR* 3.7 22.1 - - - +
414A PHE* 2.9 33.8 + + + -
416A ILE* 1.3 102.4 - - + +
418A SER* 1.3 64.4 + - - +
419A GLU 3.0 1.6 - - - +
420A TYR* 3.0 46.8 + + + +
421A LEU* 3.9 2.3 + - - +
452A THR* 4.3 7.9 - - - -
453A HIS* 3.8 29.8 - + - -
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Residues in contact with SER 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A THR* 4.5 0.2 - - - -
414A PHE 3.4 4.0 + - - -
415A PHE* 2.7 24.3 + - - -
417A PHE* 1.3 78.8 - - - +
419A GLU* 1.3 64.2 + - - +
421A LEU* 3.0 14.3 + - - +
422A LYS* 2.9 24.0 + - - +
439A PHE* 3.5 35.0 - - - -
458A GLN* 3.9 8.3 - - - +
462A PHE* 3.5 21.6 - - - -
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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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416A ILE* 3.6 18.5 - - - +
417A PHE 3.0 1.2 - - - -
418A SER* 1.3 79.0 + - - +
420A TYR* 1.3 62.1 + - + +
421A LEU 3.5 0.5 + - - -
422A LYS* 3.8 16.0 + - + +
423A PRO* 4.5 4.0 - - - +
457A GLU* 3.6 15.7 - - - +
458A GLN* 2.7 40.2 + - + +
461A THR* 5.0 4.9 + - - -
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Residues in contact with TYR 420 (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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162A GLU* 5.8 3.4 - - - -
391A GLU* 3.7 29.4 - - + +
392A HIS* 3.3 29.7 + - + +
417A PHE* 3.0 43.4 + + + +
419A GLU* 1.3 81.0 - - + +
421A LEU* 1.3 59.2 + - - +
423A PRO* 4.4 2.6 - - - +
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Residues in contact with LEU 421 (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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391A GLU* 3.4 21.8 - - + +
392A HIS* 4.0 6.3 - - - -
394A MSE 3.7 30.1 - - + -
395A ALA* 3.8 13.5 - - + -
411A SER* 5.0 1.3 - - - -
413A THR* 4.1 16.2 - - + -
417A PHE 4.2 2.0 - - - +
418A SER* 3.0 26.6 + - - +
420A TYR* 1.3 76.1 - - - +
422A LYS* 1.3 70.8 + - - +
423A PRO* 3.3 3.8 - - - -
424A ALA* 3.0 8.2 + - - +
425A ALA* 3.0 20.8 + - + -
437A PHE* 4.3 17.9 - - + -
439A PHE* 4.1 19.5 - - + -
462A PHE* 4.7 1.1 - - + -
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Residues in contact with LYS 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A SER 2.9 13.7 + - - +
419A GLU* 4.0 11.9 - - - +
420A TYR 3.7 0.2 - - - -
421A LEU* 1.3 77.0 - - - +
423A PRO* 1.4 64.8 - - + +
425A ALA* 3.2 6.9 + - + +
426A ARG* 2.9 55.0 + - - +
461A THR* 3.5 32.8 - - + -
462A PHE* 4.3 9.4 - - + -
465A MSE 3.5 44.6 - - + +
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Residues in contact with PRO 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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115A PRO* 5.6 7.8 - - + +
118A GLN* 3.9 9.8 - - - +
392A HIS* 3.6 24.7 - - + +
419A GLU 4.5 4.3 - - - +
420A TYR 4.4 3.6 - - - +
421A LEU* 3.4 6.3 - - - +
422A LYS* 1.4 93.9 - - + +
424A ALA* 1.3 58.3 + - - +
426A ARG* 3.3 16.4 + - + +
427A ILE* 3.3 17.0 + - - +
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Residues in contact with ALA 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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118A GLN* 3.4 21.8 - - - +
392A HIS* 3.8 11.0 - - - +
395A ALA* 3.6 26.7 - - + -
396A ALA 3.7 11.9 - - - +
399A ASN* 3.0 26.6 + - - +
421A LEU 3.0 4.3 + - - +
423A PRO* 1.3 74.0 - - - +
425A ALA* 1.3 65.6 + - - +
426A ARG 3.1 0.7 - - - -
427A ILE* 3.0 9.9 + - - +
428A ALA 3.1 2.3 + - - -
437A PHE* 5.1 0.2 - - - -
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Residues in contact with ALA 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 LEU* 3.0 14.4 + - + +
422A LYS* 3.2 14.6 + - - +
424A ALA* 1.3 73.7 - - - +
426A ARG* 1.3 64.1 + - - +
428A ALA* 3.2 5.2 + - - +
429A ALA* 3.1 17.5 + - - +
437A PHE* 3.9 30.8 - - + -
462A PHE* 4.2 22.9 - - + -
465A MSE 4.1 5.2 - - + -
468A PHE* 3.7 11.4 - - + -
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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 LYS* 2.9 32.9 + - - +
423A PRO* 3.4 14.4 - - + +
424A ALA 3.1 0.4 - - - -
425A ALA* 1.3 78.9 - - - +
427A ILE* 1.3 56.8 + - + +
429A ALA* 3.3 3.4 + - + +
430A LEU* 2.8 60.1 + - + +
465A MSE 3.7 16.9 - - + +
466A PRO* 5.5 9.6 - - - +
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Residues in contact with ILE 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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111A ILE* 4.9 2.9 - - + -
112A ALA* 3.9 33.2 - - + +
113A THR 5.0 0.7 - - - +
115A PRO* 4.1 29.6 - - + -
118A GLN* 4.6 13.2 - - + +
122A ASN* 5.7 2.9 - - - +
399A ASN* 3.8 9.4 - - - +
423A PRO 3.3 12.3 + - - +
424A ALA* 3.0 9.4 + - - +
426A ARG* 1.3 74.4 - - + +
428A ALA* 1.3 67.9 + - - +
430A LEU* 3.3 20.0 + - + +
431A MSE 3.0 47.4 + - + +
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Residues in contact with ALA 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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399A ASN* 3.4 19.4 - - - +
424A ALA 3.1 8.6 + - - +
425A ALA 3.4 9.2 - - - +
427A ILE* 1.3 79.2 - - - +
429A ALA* 1.3 57.1 + - - +
432A LYS* 2.9 24.3 + - - -
433A ILE* 3.2 33.7 + - + +
435A HIS* 4.3 7.0 - - + +
437A PHE* 4.3 9.0 - - + -
492A PRO* 3.8 13.6 - - + +
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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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425A ALA 3.1 12.2 + - - +
426A ARG* 3.5 9.0 - - + +
428A ALA* 1.3 72.2 - - - +
430A LEU* 1.3 67.7 + - + +
432A LYS* 3.1 8.0 + - - +
465A MSE 4.2 7.9 - - + -
466A PRO 3.3 25.4 - - - +
467A ASN* 2.9 39.4 + - - +
468A PHE* 3.7 10.5 - - + -
492A PRO* 3.8 4.0 - - - +
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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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112A ALA* 5.5 4.0 - - + -
115A PRO* 6.2 0.7 - - + -
426A ARG* 2.8 54.9 + - + +
427A ILE* 3.7 27.4 - - + +
429A ALA* 1.3 76.3 - - + +
431A MSE 1.3 59.6 + - + +
432A LYS* 4.4 4.9 - - - +
467A ASN* 4.5 6.0 + - - +
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Residues in contact with MSE 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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104A ILE* 3.6 40.3 - - + +
111A ILE* 3.7 23.6 - - + -
112A ALA* 3.6 41.7 - - + -
399A ASN* 4.1 3.6 - - + -
403A ARG* 4.1 13.2 - - + -
427A ILE* 3.0 31.2 + - + +
428A ALA 3.8 2.7 - - - +
430A LEU* 1.3 73.5 - - - +
432A LYS* 1.3 70.0 + - - +
433A ILE* 3.5 34.5 + - + +
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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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428A ALA 2.9 8.8 + - - -
429A ALA 3.1 3.2 + - - +
430A LEU 4.4 3.1 - - - +
431A MSE 1.3 81.2 - - - +
433A ILE* 1.3 61.7 + - - +
434A LYS* 4.1 2.1 + - - +
467A ASN* 3.5 30.2 + - - +
490A ASP* 3.3 43.5 + - - +
491A ILE* 3.7 21.5 - - + -
492A PRO* 4.1 6.3 - - - -
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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
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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