Contacts of the helix formed by residues 465 - 484 (chain B) in PDB entry 6MZL
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 SER 465 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ILE* 1.3 72.9 - - - +
466B MET* 1.3 57.3 + - - +
467B GLU* 2.8 29.5 + - - +
468B PHE* 2.9 37.6 + - - +
469B MET* 2.9 27.4 + - - +
513B LYS* 5.7 0.8 - - - +
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Residues in contact with MET 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B TYR* 4.6 1.1 - - - +
380B LEU* 4.6 11.9 - - + -
383B LYS* 3.8 27.6 - - + +
461B GLU* 4.4 15.3 - - + +
464B ILE 3.6 2.4 + - - +
465B SER* 1.3 68.4 + - - +
467B GLU* 1.3 63.3 + - + +
469B MET* 3.0 23.5 + - - +
470B LEU* 2.9 32.4 + - + +
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Residues in contact with GLU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B SER* 2.8 14.2 + - - +
466B MET* 1.3 73.8 - - + +
468B PHE* 1.3 67.2 + - + +
470B LEU* 3.2 19.5 + - + +
471B GLN* 2.9 32.7 + - - +
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Residues in contact with PHE 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A GLU* 2.9 45.8 - - + -
877A ARG* 5.4 2.9 - - - -
464B ILE* 3.6 21.1 - - + -
465B SER* 2.9 32.9 + - - +
467B GLU* 1.3 81.0 - - + +
469B MET* 1.3 59.8 + - - +
471B GLN* 3.1 34.2 - - - +
472B VAL* 2.8 33.3 + - + +
510B VAL* 3.9 13.4 - - + +
511B SER* 4.3 22.2 - - - -
513B LYS* 5.4 5.8 - - - -
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Residues in contact with MET 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B TYR* 3.6 34.5 - - + +
457B MET* 3.9 15.3 - - + +
460B ILE* 4.5 11.9 - - + -
461B GLU* 3.6 38.6 - - + +
464B ILE* 4.1 8.3 - - + +
465B SER 2.9 11.4 + - - +
466B MET* 3.0 21.1 + - - +
468B PHE* 1.3 75.0 - - - +
470B LEU* 1.3 65.2 + - + +
472B VAL* 3.3 5.5 + - - +
473B PHE* 3.0 53.4 + - + -
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Residues in contact with LEU 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A ILE* 4.2 33.7 - - + -
293B GLU 5.4 0.2 - - - +
294B ILE* 3.3 49.5 - - + +
295B LEU* 6.1 0.2 - - - -
380B LEU* 6.1 2.9 - - + -
466B MET* 2.9 19.0 + - + +
467B GLU* 3.2 19.7 + - + +
469B MET* 1.3 76.6 - - + +
471B GLN* 1.3 56.6 + - + +
473B PHE* 3.9 5.8 - - + +
474B ASN* 2.9 32.4 + - - +
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Residues in contact with GLN 471 (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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590A GLN* 5.0 16.1 - - - +
467B GLU* 2.9 18.3 + - - +
468B PHE* 3.1 43.3 - - - +
470B LEU* 1.3 76.2 - - + +
472B VAL* 1.3 63.0 + - - +
474B ASN* 3.8 4.1 - - - +
475B LYS* 3.0 39.1 + - - +
510B VAL* 3.3 19.6 - - + +
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Residues in contact with VAL 472 (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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464B ILE* 6.2 2.5 - - + -
468B PHE* 2.8 24.4 + - + +
469B MET* 3.7 7.0 - - - +
471B GLN* 1.3 71.1 - - - +
473B PHE* 1.3 69.8 + - + +
475B LYS* 3.1 8.7 + - - +
476B LEU* 2.9 36.1 + - + +
503B PHE* 3.8 30.5 - - + -
506B SER* 4.6 7.5 + - - +
507B ILE* 4.4 20.0 - - + -
510B VAL* 3.7 28.5 - - + -
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Residues in contact with PHE 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ILE* 5.0 6.3 - - + -
295B LEU* 4.1 20.0 - - + -
355B PHE* 5.8 2.0 - + + -
373B ILE* 3.5 45.5 - - + -
376B TYR* 4.8 10.3 - + - -
377B ILE* 4.5 17.5 - - + -
380B LEU* 5.8 2.0 - - + -
457B MET* 5.8 2.2 - - - -
469B MET* 3.0 49.1 + - + +
470B LEU* 4.1 7.0 - - + +
472B VAL* 1.3 86.7 - - + +
474B ASN* 1.3 58.0 + - - +
476B LEU* 3.2 21.1 + - + +
477B LEU* 2.9 38.2 + - + +
503B PHE* 4.8 3.1 - + - -
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Residues in contact with ASN 474 (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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661A GLU* 4.3 17.7 + - - +
294B ILE 6.0 0.2 - - - +
295B LEU* 3.7 24.0 + - - +
296B THR* 4.1 22.6 + - - +
297B CYS* 4.5 6.6 - - - -
470B LEU 2.9 20.3 + - - +
471B GLN* 3.8 4.7 - - - +
473B PHE* 1.3 74.5 - - - +
475B LYS* 1.3 59.9 + - + +
477B LEU* 4.9 1.8 - - - -
478B SER* 2.8 34.1 + - - -
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Residues in contact with LYS 475 (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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471B GLN* 3.0 27.2 + - - +
472B VAL* 3.1 8.0 + - - +
474B ASN* 1.3 77.8 - - + +
476B LEU* 1.3 59.6 + - - +
478B SER* 2.5 23.2 + - - +
479B LEU* 3.0 24.0 + - + +
506B SER* 4.9 12.1 - - - +
509B ASN* 5.3 3.2 + - - +
510B VAL* 3.6 32.0 - - + +
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Residues in contact with LEU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PHE* 5.7 0.9 - - + -
359B ILE* 3.8 28.4 - - + +
373B ILE* 4.6 6.3 - - + -
472B VAL* 2.9 21.9 + - + +
473B PHE* 3.3 35.9 - - + +
475B LYS* 1.3 77.7 - - - +
477B LEU* 1.3 59.9 + - + +
479B LEU* 3.7 6.9 - - - +
480B ALA* 2.9 27.3 + - - +
498B VAL* 3.7 30.7 - - + +
503B PHE* 4.0 28.5 - - + -
506B SER* 5.1 8.7 - - - +
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Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.7 39.5 - - + -
297B CYS* 4.6 17.2 - - - -
354B PHE* 5.8 2.9 - - + +
355B PHE* 4.3 15.9 - - + -
358B PHE* 4.9 15.0 - - + -
359B ILE* 3.7 29.2 - - + -
473B PHE* 2.9 20.1 + - + +
474B ASN* 4.3 3.4 - - - +
476B LEU* 1.3 75.7 - - + +
478B SER* 1.3 55.1 + - - +
480B ALA* 3.9 7.6 - - + +
481B SER* 2.7 39.4 + - - -
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Residues in contact with SER 478 (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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659A GLY 5.6 3.1 - - - -
660A GLY* 5.7 1.8 - - - -
661A GLU* 5.3 17.7 - - - -
297B CYS* 5.5 2.0 - - - -
474B ASN* 2.8 23.3 + - - -
475B LYS* 2.5 26.9 + - - +
477B LEU* 1.3 77.0 - - - +
479B LEU* 1.3 60.6 + - - +
481B SER* 3.3 4.8 + - - -
482B THR* 2.4 41.3 + - - -
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Residues in contact with LEU 479 (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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657A SER 3.9 23.3 - - - +
658A GLY 4.9 2.0 - - - +
659A GLY 5.9 2.0 - - - +
475B LYS* 3.0 24.5 + - + +
476B LEU* 3.7 5.2 - - + +
478B SER* 1.3 86.0 + - - +
480B ALA* 1.3 57.2 + - - +
482B THR* 3.7 6.9 - - + +
483B ALA* 2.9 29.8 + - - +
495B GLN* 3.9 19.5 - - + +
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Residues in contact with ALA 480 (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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358B PHE* 4.5 20.4 - - + -
359B ILE* 5.3 1.1 - - + -
476B LEU 2.9 16.8 + - - +
477B LEU* 3.9 10.1 - - + +
479B LEU* 1.3 75.4 - - - +
481B SER* 1.3 59.6 + - - +
483B ALA* 2.9 5.2 + - - +
484B SER* 2.8 30.0 + - - -
495B GLN 5.0 4.0 + - - +
496B MET* 3.9 28.8 - - + +
498B VAL* 5.2 6.5 - - + -
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Residues in contact with SER 481 (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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297B CYS* 5.6 5.3 - - - -
300B PRO* 5.8 5.4 - - - -
358B PHE* 5.6 11.6 - - - -
477B LEU 2.7 25.5 + - - -
478B SER* 3.3 6.8 + - - -
480B ALA* 1.3 70.1 - - - +
482B THR* 1.3 66.4 + - - +
484B SER* 2.9 25.7 + - - +
485B SER* 3.8 5.5 + - - -
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Residues in contact with THR 482 (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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658A GLY* 4.0 31.6 - - - +
659A GLY* 3.9 20.4 + - - +
660A GLY* 4.2 5.8 + - - +
478B SER 2.4 25.2 + - - -
479B LEU* 3.7 8.4 - - + +
481B SER* 1.3 78.0 + - - +
483B ALA* 1.3 56.9 + - - +
484B SER 3.0 9.4 - - - +
486B GLN* 2.9 34.2 + - - +
489B GLN* 6.2 0.2 - - - +
495B GLN* 6.0 0.7 - - - +
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Residues in contact with ALA 483 (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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479B LEU 2.9 20.0 + - - +
480B ALA* 2.9 6.9 + - - +
482B THR* 1.3 75.2 - - - +
484B SER* 1.3 56.6 + - - +
486B GLN* 4.8 3.6 - - - -
489B GLN* 5.6 4.0 - - - +
492B MET 5.6 1.3 - - - +
493B TRP* 3.2 41.0 - - - +
495B GLN* 3.4 34.7 + - + +
496B MET* 4.5 8.9 - - + +
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Residues in contact with SER 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ILE* 5.1 5.5 - - - +
241B PRO* 3.7 24.5 - - - -
358B PHE* 5.6 4.7 - - - -
480B ALA 2.8 10.4 + - - -
481B SER* 2.9 26.9 + - - +
482B THR 3.0 14.4 - - - +
483B ALA* 1.3 78.4 - - - +
485B SER* 1.3 78.3 + - - +
486B GLN* 3.4 7.1 + - - +
493B TRP* 4.0 0.4 - - - -
496B MET* 4.0 12.1 - - - -
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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