Contacts of the helix formed by residues 453 - 472 (chain B) in PDB entry 5SY1
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 PRO 453 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASN* 5.4 6.5 - - + +
121A GLU* 4.5 20.4 - - + +
122A PHE* 4.0 33.1 - - + -
125A ILE* 3.8 9.4 - - + +
451B LEU* 3.7 3.1 - - - +
452B TRP* 1.4 120.4 - - + +
454B PHE* 1.3 64.3 + - - +
455B TRP 3.5 0.4 - - - -
456B LEU* 3.4 20.3 + - + +
457B THR* 3.8 5.7 - - - +
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Residues in contact with PHE 454 (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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121A GLU* 5.2 8.2 - - + +
124A MET* 5.0 7.9 - - + -
125A ILE* 3.7 28.2 - - + +
128A LEU* 5.3 9.9 - - + -
451B LEU* 3.0 33.2 + - + +
453B PRO* 1.3 80.7 - - + +
455B TRP* 1.3 85.9 + + - +
457B THR* 2.9 26.9 + - - -
458B LEU* 3.9 16.2 + - + +
502B MET* 4.5 24.9 - - + -
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Residues in contact with TRP 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ILE* 6.2 2.0 - - + -
448B ILE* 3.8 42.6 - - + -
451B LEU* 3.3 30.4 + - + +
452B TRP* 4.6 2.7 + - - +
453B PRO 3.5 0.2 - - - -
454B PHE* 1.3 102.7 - + - +
456B LEU* 1.3 62.5 + - - +
457B THR 3.3 0.2 - - - -
458B LEU* 3.9 21.8 + - + +
459B VAL* 3.3 24.3 + - - +
506B VAL* 5.8 3.2 - - - +
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Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B TRP 4.3 9.1 + - - +
453B PRO* 3.4 17.3 + - + +
454B PHE 3.1 1.6 - - - -
455B TRP* 1.3 79.0 - - - +
457B THR* 1.3 60.1 + - + +
459B VAL* 3.0 13.3 + - + +
460B LEU* 2.8 61.3 + - + +
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Residues in contact with THR 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 5.4 6.5 - - + -
125A ILE* 3.6 34.0 - - + +
128A LEU* 5.7 3.1 - - - +
453B PRO 3.8 14.1 - - - +
454B PHE* 2.9 15.8 + - - -
455B TRP 3.3 0.2 - - - -
456B LEU* 1.3 78.2 - - + +
458B LEU* 1.3 69.5 + - - +
460B LEU* 3.8 10.8 - - + +
461B ALA* 3.1 27.7 + - - +
499B VAL* 4.7 4.4 - - - +
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Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 6.3 1.3 - - + -
454B PHE* 3.9 20.4 + - + +
455B TRP* 3.9 31.3 + - + +
456B LEU 3.3 0.4 - - - -
457B THR* 1.3 81.3 + - - +
459B VAL* 1.3 62.1 + - + +
462B ALA* 3.3 22.2 + - - +
499B VAL* 4.4 8.1 - - + +
502B MET* 3.8 36.3 - - + +
503B ILE* 3.7 30.7 - - + +
506B VAL* 4.2 17.0 - - + -
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Residues in contact with VAL 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B TRP 3.3 16.1 + - - +
456B LEU* 3.0 14.7 + - + +
458B LEU* 1.3 78.5 - - + +
460B LEU* 1.3 61.4 + - + +
462B ALA* 3.1 4.8 + - - +
463B LEU* 2.5 42.9 + - + +
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Residues in contact with LEU 460 (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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456B LEU* 2.8 55.8 + - + +
457B THR* 4.4 9.0 - - + +
459B VAL* 1.3 79.0 - - + +
461B ALA* 1.3 58.5 + - - +
463B LEU* 3.4 15.7 - - + +
464B ILE* 2.8 28.6 + - - +
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Residues in contact with ALA 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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457B THR 3.1 19.0 + - - +
458B LEU 4.8 0.7 - - - +
460B LEU* 1.3 74.3 - - - +
462B ALA* 1.3 61.7 + - - +
464B ILE* 3.2 12.0 + - - +
465B GLN* 3.1 34.0 + - - +
496B LEU* 4.3 15.5 - - + -
499B VAL* 3.7 26.0 - - + -
503B ILE* 4.9 2.7 - - + -
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Residues in contact with ALA 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B LEU 3.3 19.0 + - - +
459B VAL* 3.1 5.0 + - - +
461B ALA* 1.3 75.6 - - - +
463B LEU* 1.3 64.0 + - - +
465B GLN* 4.5 10.1 - - - +
466B HIS* 3.2 34.4 + - + +
503B ILE* 4.2 15.8 - - + +
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Residues in contact with LEU 463 (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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459B VAL* 2.5 25.7 + - + +
460B LEU* 3.4 19.7 - - + +
461B ALA 3.2 0.2 - - - -
462B ALA* 1.3 74.3 - - - +
464B ILE* 1.3 65.6 + - + +
466B HIS* 3.4 4.6 + - + -
467B VAL* 2.9 59.1 + - + +
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Residues in contact with ILE 464 (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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460B LEU 2.8 15.6 + - - +
461B ALA* 3.3 19.1 - - - +
463B LEU* 1.3 83.5 - - + +
465B GLN* 1.3 60.7 + - - +
467B VAL* 4.1 12.1 - - + +
468B ALA* 3.3 29.5 + - + +
492B LEU* 4.7 11.1 - - + +
496B LEU* 4.2 19.7 - - + -
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Residues in contact with GLN 465 (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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397A VAL* 3.7 32.3 - - + +
400A MET* 4.3 33.5 + - + +
405A TYR* 5.7 1.0 + - - -
461B ALA* 3.1 22.6 + - - +
462B ALA* 4.2 9.3 - - - +
463B LEU 3.2 0.2 - - - -
464B ILE* 1.3 77.8 - - - +
466B HIS* 1.3 63.5 + - - +
468B ALA* 5.0 0.4 - - - +
469B SER* 3.2 23.4 + - - -
473B PHE* 5.8 0.5 - - - -
492B LEU* 5.3 1.8 - - + -
496B LEU* 3.5 28.8 - - + +
500B ASN* 3.0 41.8 + - - +
503B ILE* 5.1 2.1 - - - +
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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
----------------------------------------------------------
393A ARG* 3.9 25.7 + - - +
394A PRO* 4.8 14.4 - - + -
397A VAL* 3.7 38.2 - - + +
543A ARG* 6.1 0.9 - - - -
462B ALA* 3.2 29.4 + - + +
463B LEU* 3.4 5.7 + - + +
465B GLN* 1.3 77.7 - - - +
467B VAL* 1.3 65.8 + - + +
469B SER* 3.5 1.9 + - - -
470B ARG* 3.4 23.2 + - - +
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Residues in contact with VAL 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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463B LEU* 2.9 50.1 + - + +
464B ILE* 4.6 8.7 - - + -
466B HIS* 1.3 79.9 - - + +
468B ALA* 1.3 65.3 + - - +
469B SER 3.2 0.7 + - - -
470B ARG* 3.6 1.1 + - - +
471B PHE* 3.4 44.9 + - + +
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Residues in contact with ALA 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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464B ILE* 3.3 27.8 + - + +
465B GLN 5.0 0.4 - - - +
467B VAL* 1.3 79.9 - - - +
469B SER* 1.3 58.2 + - - +
471B PHE* 5.2 0.2 - - - -
472B LEU* 3.2 41.1 + - + +
473B PHE* 3.2 25.6 - - + -
492B LEU* 4.6 8.3 - - + -
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Residues in contact with SER 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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393A ARG* 4.0 11.4 + - - +
396A LEU* 3.3 33.4 - - - +
397A VAL* 4.6 6.1 - - - -
400A MET* 5.5 2.2 - - - -
465B GLN 3.2 21.1 + - - -
466B HIS* 3.8 5.6 - - - -
467B VAL 3.1 1.2 - - - -
468B ALA* 1.3 78.1 - - - +
470B ARG* 1.3 61.7 + - - +
473B PHE* 3.3 15.1 + - - -
474B ILE* 3.0 34.1 + - - +
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Residues in contact with ARG 470 (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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393A ARG* 3.7 33.4 - - + +
466B HIS 3.4 9.7 + - - +
467B VAL* 3.6 2.2 + - - +
469B SER* 1.3 79.5 - - - +
471B PHE* 1.3 79.5 + - + +
474B ILE* 3.9 17.9 - - - +
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Residues in contact with PHE 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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467B VAL* 3.4 34.6 + - + +
468B ALA* 5.2 0.2 - - - -
469B SER 3.2 0.4 - - - -
470B ARG* 1.3 98.0 - - + +
472B LEU* 1.3 73.9 + - + +
474B ILE 5.2 1.6 - - - -
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Residues in contact with LEU 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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71A LEU* 5.1 17.7 - - + -
468B ALA* 3.2 26.5 + - + +
471B PHE* 1.3 92.9 - - + +
473B PHE* 1.3 75.7 + - + +
474B ILE 4.8 2.1 - - - +
475B ARG* 5.7 1.2 - - - +
485B ASN* 4.0 15.8 + - - +
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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