Contacts of the helix formed by residues 422 - 432 (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 ASP 422 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420B HIS 3.7 2.2 + - - -
421B THR* 1.3 75.5 - - - +
423B MET* 1.3 64.5 + - - +
424B ALA* 3.5 11.8 + - - +
425B SER* 2.8 40.4 + - - -
426B VAL* 3.2 18.8 + - - +
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Residues in contact with MET 423 (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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478A TYR* 3.6 67.8 - - + +
481A GLY* 4.2 13.5 - - - +
482A LEU* 4.0 15.6 - - + +
485A ALA* 5.4 4.7 - - - -
487A LEU* 4.0 14.4 - - + -
421B THR 3.5 1.9 + - - +
422B ASP* 1.3 73.6 - - - +
424B ALA* 1.3 63.5 + - - +
426B VAL* 3.3 3.6 + - - +
427B THR* 3.1 26.0 + - - -
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Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A LEU* 4.1 26.2 - - + +
508A LEU* 5.2 0.2 - - - +
422B ASP* 3.3 9.7 + - - +
423B MET* 1.3 76.8 - - - +
425B SER* 1.4 58.1 + - - +
427B THR* 3.2 4.3 + - - -
428B LYS* 2.9 50.5 + - - +
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Residues in contact with SER 425 (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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417B LEU* 5.2 2.0 - - - +
421B THR* 4.4 9.9 - - - -
422B ASP* 2.8 33.8 + - - -
424B ALA* 1.4 73.9 - - - +
426B VAL* 1.3 60.9 + - - +
428B LYS* 3.5 12.2 + - - +
429B ALA* 3.0 27.5 + - - +
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Residues in contact with VAL 426 (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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461A TRP* 4.2 5.9 - - + -
462A LEU* 4.0 26.5 - - + -
466A VAL* 4.0 15.3 - - + -
478A TYR* 3.4 29.4 - - + +
482A LEU* 5.8 1.1 - - + -
417B LEU* 4.4 12.3 - - + -
418B SER 4.5 4.9 - - - +
421B THR* 3.7 24.2 - - + -
422B ASP 3.2 12.9 + - - +
423B MET 3.3 4.5 + - - +
425B SER* 1.3 74.5 - - - +
427B THR* 1.3 58.0 + - - +
429B ALA* 3.3 8.2 + - - +
430B MET* 2.9 26.3 + - + +
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Residues in contact with THR 427 (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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482A LEU* 3.4 24.2 - - - +
487A LEU* 3.8 25.5 - - + +
488A ILE* 4.7 2.2 - - + -
505A PHE* 3.8 27.8 - - + -
508A LEU* 4.1 11.9 - - + -
423B MET 3.1 14.6 + - - -
424B ALA* 3.2 8.5 + - - -
426B VAL* 1.3 76.1 - - - +
428B LYS* 1.3 60.2 + - - +
430B MET* 3.2 13.6 + - + +
431B ALA* 2.9 27.0 + - - +
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Residues in contact with LYS 428 (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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508A LEU* 3.5 48.5 + - + +
509A SER* 5.8 1.0 - - - +
424B ALA* 2.9 35.7 + - - +
425B SER* 3.9 9.4 + - - +
427B THR* 1.3 73.5 - - - +
429B ALA* 1.3 61.6 + - - +
431B ALA* 3.3 7.8 + - - +
432B ALA* 3.2 21.8 + - - +
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Residues in contact with ALA 429 (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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461A TRP* 4.2 5.1 - - + -
417B LEU* 4.2 26.5 - - + -
425B SER 3.0 14.7 + - - +
426B VAL* 3.4 10.1 - - - +
427B THR 3.2 0.2 - - - -
428B LYS* 1.3 74.8 - - - +
430B MET* 1.3 63.2 + - - +
432B ALA* 3.2 18.2 + - - +
435B SER* 3.3 13.3 - - - -
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Residues in contact with MET 430 (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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453A PHE* 5.1 0.2 - - + -
458A VAL* 4.1 36.6 - - + +
461A TRP* 3.7 44.1 - - + -
462A LEU* 4.6 6.3 - - - -
482A LEU* 4.4 16.4 - - + -
488A ILE* 4.5 7.4 - - + -
505A PHE* 3.7 24.7 - - + -
426B VAL* 2.9 13.3 + - + +
427B THR* 3.5 10.8 - - + +
429B ALA* 1.3 76.9 - - - +
431B ALA* 1.3 58.2 + - - +
432B ALA 4.2 0.3 - - - +
435B SER* 2.8 19.8 + - - -
437B LEU* 3.7 28.5 - - + +
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Residues in contact with ALA 431 (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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505A PHE* 3.4 35.3 - - + -
508A LEU* 3.8 18.2 - - + -
427B THR 2.9 16.6 + - - +
428B LYS* 3.7 6.1 - - - +
429B ALA 3.2 0.6 - - - -
430B MET* 1.3 75.5 - - - +
432B ALA* 1.3 63.5 + - - +
433B PRO* 3.8 2.8 - - - +
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Residues in contact with ALA 432 (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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428B LYS 3.2 9.8 + - - +
429B ALA* 3.2 18.5 + - - +
431B ALA* 1.3 79.8 - - - +
433B PRO* 1.3 80.4 - - + +
434B GLU 3.4 0.2 + - - -
435B SER* 3.1 20.4 + - - +
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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