Contacts of the helix formed by residues 454 - 469 (chain B) in PDB entry 5D3O
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 454 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B ASN* 3.0 25.6 + - - +
451B ARG* 3.3 18.3 - - - +
453B LEU* 1.3 74.4 - - - +
455B PRO* 1.3 73.4 - - - +
456B GLU* 3.6 14.6 + - - +
457B ALA* 2.9 27.4 + - - +
458B VAL* 3.0 19.2 + - - +
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Residues in contact with PRO 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A HIS* 4.1 18.2 - - + +
541A PHE* 4.7 3.6 - - - -
542A ALA* 4.0 35.2 - - + +
442B GLY* 4.1 18.4 - - - +
444B PHE* 6.3 2.0 - - + -
451B ARG* 4.6 8.1 - - + +
453B LEU 3.5 4.7 - - - +
454B SER* 1.3 85.6 - - - +
456B GLU* 1.3 52.7 + - - +
458B VAL* 3.1 5.0 + - + +
459B ARG* 2.7 45.1 + - - +
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Residues in contact with GLU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B VAL* 3.9 7.9 - - + +
306B GLY* 3.8 9.9 - - - -
307B THR* 3.3 43.0 + - - +
308B GLU 5.4 0.2 + - - -
454B SER* 3.0 10.3 + - - +
455B PRO* 1.3 80.2 - - - +
457B ALA* 1.3 62.4 + - - +
459B ARG* 3.4 27.2 + - - +
460B ASN* 3.0 30.1 + - - +
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Residues in contact with ALA 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B TYR* 5.0 0.3 - - - -
299B ALA* 3.3 33.6 - - + +
302B VAL* 3.6 13.6 - - + +
303B ASN* 3.6 15.3 - - + +
453B LEU* 4.5 3.1 - - + -
454B SER* 2.9 24.2 + - - +
456B GLU* 1.3 76.2 - - - +
458B VAL* 1.3 63.8 + - - +
460B ASN* 4.0 1.3 - - - +
461B THR* 3.0 29.7 + - - -
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Residues in contact with VAL 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A TYR 5.0 0.9 - - - +
299B ALA* 5.8 0.2 - - - -
439B LEU* 3.3 48.0 - - + +
442B GLY* 4.0 7.2 - - - +
443B GLY* 3.7 31.0 - - - +
453B LEU* 3.8 11.9 - - + -
454B SER 3.0 18.2 + - - +
455B PRO* 3.7 5.2 - - + +
457B ALA* 1.3 75.2 - - - +
459B ARG* 1.3 65.7 + - - +
461B THR* 3.3 4.0 + - - -
462B LEU* 2.9 30.5 + - + +
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Residues in contact with ARG 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A PHE 5.4 0.6 + - - -
533A HIS* 3.5 38.1 - - + +
535A TYR* 3.5 24.7 - - - +
536A ASP* 3.0 26.5 + - - +
544A LYS* 3.8 22.0 - - - +
455B PRO* 2.7 24.6 + - - +
456B GLU* 3.6 32.8 + - - +
458B VAL* 1.3 74.3 - - - +
460B ASN* 1.3 72.0 + - - +
462B LEU* 3.3 1.9 + - - +
463B SER* 2.9 26.5 + - - +
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Residues in contact with ASN 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A PHE* 3.4 26.5 - - + +
298B TYR* 3.4 24.7 + - + +
302B VAL* 3.8 10.1 - - + +
307B THR* 2.5 39.6 + - - +
456B GLU* 3.0 20.0 + - - +
457B ALA* 4.0 3.1 - - - +
459B ARG* 1.3 87.6 + - - +
461B THR* 1.3 62.6 + - - +
463B SER* 3.2 5.7 + - - -
464B LEU* 3.1 25.6 + - - +
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Residues in contact with THR 461 (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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295B PRO* 3.5 33.8 + - + +
298B TYR* 3.2 24.0 - - + -
299B ALA* 3.5 16.1 - - + +
338B MET* 4.5 0.9 - - - +
439B LEU* 4.3 17.7 - - + -
457B ALA 3.0 19.9 + - - -
458B VAL* 3.8 4.9 - - - -
460B ASN* 1.3 77.2 - - - +
462B LEU* 1.3 57.5 + - - +
464B LEU* 3.4 1.0 + - - +
465B MET* 2.9 43.3 + - - +
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A TYR* 3.8 39.4 - - + +
439B LEU* 3.6 29.4 - - + +
458B VAL* 2.9 25.2 + - + +
459B ARG 3.9 1.6 - - - +
461B THR* 1.3 76.3 - - + +
463B SER* 1.3 64.0 + - - +
465B MET* 3.4 13.2 + - - +
466B HIS* 3.1 22.5 + - - +
484B PRO* 3.6 25.3 - - + +
496B VAL* 3.8 27.6 - - + -
498B PRO* 4.4 9.0 - - + -
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Residues in contact with SER 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ALA 5.3 1.1 - - - -
479A PHE* 3.9 28.5 + - - -
533A HIS* 3.4 27.9 + - - -
535A TYR* 3.8 9.9 - - - -
459B ARG* 2.9 17.2 + - - +
460B ASN* 3.2 8.9 + - - -
462B LEU* 1.3 75.7 - - - +
464B LEU* 1.3 59.6 + - - +
466B HIS* 3.0 24.6 + - - +
467B SER* 3.3 9.3 + - - -
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Residues in contact with LEU 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A PHE* 3.8 17.0 - - + -
298B TYR* 3.5 30.3 - - + +
311B HIS* 4.2 5.6 - - + -
315B GLY 4.5 0.4 - - - +
316B LYS* 3.1 35.2 - - - +
336B ASN* 5.0 4.0 - - + -
337B PRO* 3.6 29.2 - - + -
338B MET* 3.6 21.9 - - + +
460B ASN 3.1 11.5 + - - +
463B SER* 1.3 73.9 - - - +
465B MET* 1.3 64.8 + - - +
467B SER* 3.8 9.6 - - - +
468B CYS* 3.0 28.1 + - - +
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Residues in contact with MET 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PRO* 3.9 24.2 - - + -
338B MET* 4.5 5.6 - - + -
439B LEU* 4.4 6.3 - - - -
461B THR* 2.9 37.7 + - - +
462B LEU* 3.8 17.7 - - - +
464B LEU* 1.3 76.9 - - - +
466B HIS* 1.3 65.1 + - - +
469B GLY* 3.1 23.6 + - - +
470B MET* 5.7 1.6 - - - +
477B PHE* 6.2 0.3 - - - -
484B PRO* 3.8 11.4 - - + +
485B ALA* 3.3 46.7 + - - +
486B LYS* 3.7 10.1 - - + +
494B LEU* 4.0 16.4 - - + +
496B VAL* 4.7 6.1 - - + -
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Residues in contact with HIS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A HIS* 3.8 34.7 + + - -
534A ASN* 5.5 0.2 - - - -
535A TYR* 2.8 29.1 + + + +
462B LEU 3.1 12.3 + - - +
463B SER 3.0 12.4 + - - +
465B MET* 1.3 80.4 - - - +
467B SER* 1.3 66.5 + - - +
469B GLY 4.8 0.9 + - - -
474B SER* 4.2 6.1 - - - +
477B PHE* 5.6 3.5 - - - -
478B ALA* 3.8 44.1 - - + +
482B GLY* 4.3 20.7 - - - -
483B LEU 4.5 6.2 + - - +
484B PRO* 4.3 7.6 - - + +
534B ASN* 5.0 5.4 - - + -
535B TYR* 5.3 6.6 - + - -
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Residues in contact with SER 467 (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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316B LYS 4.7 1.4 + - - -
318B PRO* 3.8 24.0 - - - +
463B SER 3.3 10.7 + - - -
464B LEU* 3.7 11.4 + - - +
466B HIS* 1.3 87.7 - - - +
468B CYS* 1.3 81.3 + - - +
469B GLY 3.9 0.2 - - - -
474B SER* 3.2 18.5 - - - -
475B GLY 5.1 0.2 + - - -
478B ALA* 5.7 1.3 - - - -
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Residues in contact with CYS 468 (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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317B GLU* 4.1 2.0 - - - -
318B PRO* 3.6 22.9 - - + -
336B ASN* 3.6 37.7 - - - +
338B MET* 3.2 21.5 - - + +
339B VAL* 5.5 3.9 - - + +
464B LEU* 3.0 16.0 + - - +
467B SER* 1.3 106.6 - - - +
469B GLY* 1.3 62.5 + - - +
470B MET 3.8 0.2 + - - -
471B TYR* 4.2 6.8 + - - -
474B SER* 3.5 9.2 - - - -
486B LYS* 4.8 1.2 + - - -
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Residues in contact with GLY 469 (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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338B MET* 4.9 0.4 - - - -
465B MET* 3.1 21.8 + - - -
466B HIS 4.8 0.2 - - - -
467B SER 3.9 0.4 - - - -
468B CYS* 1.3 79.1 - - - +
470B MET* 1.3 65.5 + - - +
471B TYR 3.5 0.9 - - - -
474B SER* 3.5 1.6 + - - -
485B ALA 3.5 10.5 - - - -
486B LYS* 3.2 32.6 + - - +
487B SER* 3.2 15.6 + - - -
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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