Contacts of the helix formed by residues 420 - 429 (chain B) in PDB entry 5X61
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 LYS 420 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415B PRO* 5.0 12.1 - - - +
417B GLU* 2.8 52.2 + - + +
419B SER* 1.3 75.9 - - - +
421B LEU* 1.3 63.7 + - - +
422B SER* 3.5 4.0 - - - +
423B ASP* 3.4 45.4 - - - +
424B ALA* 4.1 3.8 + - - +
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Residues in contact with LEU 421 (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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319B LEU* 3.1 51.9 - - + +
320B GLY 5.4 0.2 - - - -
321B THR* 3.8 27.8 - - + +
402B THR* 5.6 1.1 - - + -
406B LEU* 5.1 4.3 - - + -
417B GLU 4.2 2.0 - - - +
418B PRO* 3.2 40.2 - - + +
419B SER 3.7 5.0 + - - +
420B LYS* 1.3 70.6 - - - +
422B SER* 1.3 60.3 + - - +
423B ASP 3.1 2.7 - - - -
424B ALA* 3.0 24.4 + - - +
425B VAL* 3.2 14.1 + - - +
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Residues in contact with SER 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B THR* 5.0 5.6 - - - +
323B GLU* 5.1 10.8 - - - -
420B LYS* 5.0 2.8 - - - +
421B LEU* 1.3 78.2 + - - +
423B ASP* 1.3 69.2 + - - +
424B ALA 3.3 0.2 - - - -
425B VAL* 3.4 12.1 - - - +
426B GLU* 3.2 39.8 + - - +
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Residues in contact with ASP 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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415B PRO* 3.8 17.1 - - + +
420B LYS* 3.4 49.8 + - - +
421B LEU 3.1 0.4 - - - -
422B SER* 1.3 85.4 + - - +
424B ALA* 1.3 62.8 + - - +
426B GLU* 4.0 7.9 - - - +
427B CYS* 3.3 22.5 + - - +
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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
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319B LEU* 4.8 8.1 - - + -
406B LEU* 4.5 19.1 - - + -
409B ALA* 4.6 7.6 - - + -
414B CYS* 4.7 0.7 - - - +
415B PRO* 3.3 27.3 + - - +
416B HIS* 5.0 0.4 - - - -
420B LYS 4.1 3.0 + - - +
421B LEU* 3.0 13.3 + - - +
423B ASP* 1.3 78.0 - - - +
425B VAL* 1.3 60.3 + - - +
427B CYS* 3.2 6.2 + - - +
428B LEU* 2.9 34.5 + - + +
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Residues in contact with VAL 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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206B PHE* 4.0 20.0 - - + -
317B LEU* 5.2 0.2 - - + -
319B LEU* 4.3 12.3 - - + +
321B THR* 5.1 2.7 - - - +
323B GLU* 3.8 38.6 - - + +
324B ALA* 4.4 5.2 - - + -
421B LEU 3.2 4.8 + - - +
422B SER* 3.4 25.4 - - - +
424B ALA* 1.3 77.5 - - - +
426B GLU* 1.3 61.1 + - + +
428B LEU* 3.2 11.0 + - - +
429B ARG* 2.9 48.6 + - - +
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Residues in contact with GLU 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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422B SER* 3.2 28.9 + - - +
423B ASP* 4.0 8.8 - - - +
424B ALA 3.3 0.4 - - - -
425B VAL* 1.3 81.6 - - + +
427B CYS* 1.3 62.6 + - - +
429B ARG* 3.4 38.3 + - - +
430B GLY* 3.6 7.8 + - - -
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Residues in contact with CYS 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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413B GLY 4.7 1.1 - - - -
414B CYS* 2.0 54.9 - - + -
415B PRO* 3.8 10.8 - - + -
423B ASP 3.3 12.3 + - - +
424B ALA 3.2 7.7 + - - +
426B GLU* 1.3 79.4 - - - +
428B LEU* 1.3 55.8 + - - +
430B GLY* 2.9 17.9 + - - -
431B LYS* 3.4 19.0 + - - +
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Residues in contact with LEU 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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205B ARG* 3.2 13.2 + - - -
206B PHE* 3.7 14.1 - - + -
317B LEU* 3.9 32.8 - - + -
319B LEU* 4.9 6.1 - - + -
405B ALA 4.9 3.8 - - - +
408B LEU* 4.6 5.8 - - + -
409B ALA* 4.0 25.1 - - + +
412B VAL* 3.9 19.5 - - + -
414B CYS* 4.4 3.4 - - - -
424B ALA* 2.9 26.8 + - + +
425B VAL* 3.6 8.1 - - - +
427B CYS* 1.3 75.0 - - - +
429B ARG* 1.3 61.4 + - - +
430B GLY 3.3 0.5 + - - -
431B LYS* 3.5 8.0 + - - +
436B LEU* 3.7 36.4 - - + +
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Residues in contact with ARG 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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202B GLY* 3.4 30.1 - - - +
203B PRO* 3.8 25.4 + - - +
205B ARG* 2.9 32.3 + - + +
206B PHE* 4.3 14.1 - - + -
207B ARG* 4.1 7.4 - - - +
323B GLU* 2.7 41.6 + - - +
425B VAL* 2.9 32.0 + - - +
426B GLU* 3.4 40.2 + - - +
427B CYS 3.2 0.4 - - - -
428B LEU* 1.3 76.0 - - - +
430B GLY* 1.3 57.6 + - - +
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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