Contacts of the helix formed by residues 455 - 466 (chain B) in PDB entry 5SUY
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 GLY 455 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B LEU* 1.3 69.2 - - - +
456B SER* 1.3 61.0 - - - +
458B VAL* 3.0 16.4 + - - +
459B VAL* 3.1 16.3 + - - +
497B PHE* 3.6 23.2 - - - -
499B GLU* 3.3 12.2 + - - -
501B CYS 3.0 13.5 + - - -
503B TYR* 3.6 15.4 - - - -
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Residues in contact with SER 456 (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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454B LEU* 3.7 18.0 - - - +
455B GLY* 1.3 72.9 - - - +
457B ASP* 1.3 58.4 + - - -
459B VAL* 3.4 0.3 + - - -
460B ASP* 2.9 38.1 + - - +
472B ARG* 3.9 3.6 + - - +
499B GLU* 2.9 47.0 + - - +
500B GLN* 5.1 4.7 + - - -
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Residues in contact with ASP 457 (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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437A LEU* 3.6 15.3 - - + +
438A GLU* 3.3 36.0 + - + +
440A ARG* 3.1 36.6 + - - -
453B PHE* 4.5 1.3 - - + -
454B LEU* 2.9 38.6 + - - +
456B SER* 1.3 75.9 + - - +
458B VAL* 1.3 61.5 + - - +
460B ASP* 3.8 11.4 - - - +
461B TRP* 3.2 17.0 + - - +
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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
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430A MET* 4.0 24.0 - - + +
437A LEU* 4.3 7.6 - - + -
453B PHE* 3.3 39.5 - - + -
454B LEU 3.8 4.5 - - - +
455B GLY* 3.0 11.9 + - - +
457B ASP* 1.3 75.4 - - - +
459B VAL* 1.3 65.8 + - - +
461B TRP* 3.2 3.8 + - - +
462B LEU* 3.0 40.8 + - + +
479B ALA* 4.0 14.4 - - + -
482B LEU* 4.5 6.3 - - + -
488B ILE* 4.8 11.2 - - + -
497B PHE* 5.1 1.1 - - + -
503B TYR* 5.5 0.4 - - + -
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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
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455B GLY 3.1 15.1 + - - +
456B SER 3.4 0.6 + - - +
458B VAL* 1.3 77.7 - - - +
460B ASP* 1.3 61.8 + - - +
462B LEU* 3.5 7.7 + - - +
463B TYR* 3.0 23.4 + - - +
472B ARG* 3.4 43.3 - - + +
475B ALA* 4.0 2.3 - - + +
476B ARG* 3.9 25.8 - - + +
479B ALA* 4.1 11.7 - - + -
497B PHE* 4.0 18.6 - - + -
499B GLU* 3.9 15.7 - - - +
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Residues in contact with ASP 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B SER* 2.9 24.5 + - - +
457B ASP* 3.8 12.1 - - - +
459B VAL* 1.3 75.6 - - - +
461B TRP* 1.3 57.1 + - - +
463B TYR* 3.3 5.5 + - - +
464B HIS* 3.0 31.3 + - - +
472B ARG* 3.4 22.7 + - - +
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Residues in contact with TRP 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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417A LEU* 3.7 24.7 - - + -
426A VAL* 4.2 7.2 - - + -
429A ALA* 4.3 4.9 - - + -
430A MET* 3.7 52.7 - - + -
435A SER* 2.8 28.3 + - - -
436A GLY 3.7 3.4 - - - -
437A LEU* 3.5 33.2 - - + -
457B ASP 3.2 13.9 + - - +
458B VAL 3.2 5.6 + - - +
460B ASP* 1.3 78.6 - - - +
462B LEU* 1.3 69.4 + - + +
464B HIS 3.3 0.5 + - - -
465B HIS* 2.9 70.3 + + + +
466B VAL* 4.1 18.8 - - + -
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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
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426A VAL* 3.8 29.4 - - + -
430A MET* 4.6 6.3 - - - -
458B VAL* 3.0 36.8 + - + +
459B VAL* 3.8 3.4 - - - +
461B TRP* 1.3 88.8 - - + +
463B TYR* 1.3 60.0 + - - +
466B VAL* 3.0 40.3 + - + +
469B PHE* 3.6 13.2 - - + -
475B ALA* 3.8 19.3 - - + +
478B TYR* 3.8 28.7 - - + -
479B ALA* 4.0 8.5 - - + +
482B LEU* 4.3 5.2 - - + -
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Residues in contact with TYR 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 3.0 18.1 + - - +
460B ASP* 3.3 4.9 + - - +
462B LEU* 1.3 78.2 - - - +
464B HIS* 1.3 61.6 + - - +
466B VAL 4.4 6.8 - - - +
469B PHE* 4.2 19.9 + - + -
470B PRO 4.2 4.0 + - - -
471B GLU* 3.4 36.3 - - - +
472B ARG* 3.7 35.4 + - + -
475B ALA* 4.0 12.7 - - + +
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Residues in contact with HIS 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 ASP 3.0 18.3 + - - +
463B TYR* 1.3 79.6 - - - +
465B HIS* 1.3 91.6 + + + +
466B VAL 3.9 0.2 - - - -
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Residues in contact with HIS 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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415A SER 5.2 7.4 + - - +
417A LEU* 3.7 20.9 + - + +
435A SER 4.3 7.2 + - - -
436A GLY* 5.1 5.8 - - - -
461B TRP* 2.9 76.7 + + + +
464B HIS* 1.3 110.9 + + + +
466B VAL* 1.3 59.6 + - - +
467B GLU* 4.1 1.5 + - - +
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Residues in contact with VAL 466 (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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417A LEU* 3.6 11.4 - - + -
418A SER* 3.3 34.8 - - - +
419A VAL* 3.7 4.7 - - - +
426A VAL* 4.0 28.5 - - + -
461B TRP* 4.1 9.2 - - + -
462B LEU* 3.0 24.9 + - + +
463B TYR 4.4 5.2 - - - +
464B HIS 5.6 0.2 - - - -
465B HIS* 1.3 81.3 - - - +
467B GLU* 1.3 61.8 + - - +
468B GLY 3.8 0.3 + - - -
469B PHE* 3.5 34.8 + - + +
478B TYR* 5.3 3.8 - - + -
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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
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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