Contacts of the helix formed by residues 416 - 426 (chain B) in PDB entry 4PKO
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 416 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B THR* 6.2 1.6 - - - -
414B GLY 3.0 2.6 - - - -
415B GLY* 1.3 76.9 - - - +
417B VAL* 1.3 58.8 - - - +
418B ALA* 3.0 9.3 + - - -
419B LEU* 3.3 22.4 + - - +
420B ILE* 3.3 21.2 + - - +
447B MET 4.7 1.9 - - - +
450B PRO* 4.8 9.1 - - - +
451B LEU* 4.5 9.1 + - - +
454B ILE* 4.8 1.4 - - - +
495B ASP* 4.0 8.4 + - - -
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Residues in contact with VAL 417 (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 ALA* 3.2 27.1 - - + -
414B GLY 3.0 21.1 - - - +
415B GLY* 2.9 5.1 - - - +
416B GLY* 1.3 78.1 - - - +
418B ALA* 1.3 61.5 + - - +
420B ILE* 3.0 11.2 - - + +
421B ARG* 3.0 38.0 + - + +
451B LEU* 4.4 3.4 - - + -
469B VAL* 3.8 20.4 - - + -
474B GLY 5.2 1.8 - - - +
475B ASN* 4.7 3.6 - - - +
476B TYR 3.1 26.5 - - - +
477B GLY* 4.0 4.9 - - - -
488B MET* 3.9 9.6 - - + -
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Residues in contact with ALA 418 (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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131B LEU* 4.4 9.0 - - + -
134B LEU* 4.7 5.5 - - + +
412B VAL* 3.3 37.5 - - + -
413B ALA* 3.3 11.6 + - - +
416B GLY* 4.8 2.5 - - - -
417B VAL* 1.3 83.1 - - - +
419B LEU* 1.3 62.9 + - + +
421B ARG* 3.1 6.3 + - - +
422B VAL* 3.0 28.8 + - - +
495B ASP* 5.4 1.1 - - - +
500B THR* 4.7 7.9 - - + +
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Residues in contact with LEU 419 (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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91B THR* 4.7 9.0 - - + -
95B LEU* 4.4 14.1 - - + -
131B LEU* 4.8 6.1 - - + -
416B GLY* 3.3 14.8 + - - +
418B ALA* 1.3 79.1 - - + +
420B ILE* 1.3 58.1 + - - +
422B VAL* 3.1 13.1 - - + +
423B ALA* 3.0 25.8 + - - +
447B MET* 3.7 21.7 - - + +
450B PRO* 3.9 30.5 - - + -
500B THR* 3.7 35.0 - - + +
504B LEU* 4.0 28.9 - - + -
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Residues in contact with ILE 420 (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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416B GLY 3.3 5.3 + - - +
417B VAL* 3.0 40.8 - - + +
419B LEU* 1.3 78.4 - - - +
421B ARG* 1.3 65.6 + - - +
423B ALA* 3.6 8.4 - - + +
424B SER* 3.4 19.1 + - - -
447B MET 4.1 9.6 + - - +
448B GLU* 4.0 27.4 - - + -
451B LEU* 4.8 16.4 - - + -
466B ALA* 4.5 7.9 - - + +
469B VAL* 4.6 11.7 - - + -
470B LYS* 3.3 39.7 - - + +
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Residues in contact with ARG 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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134B LEU* 4.4 18.4 - - + -
417B VAL* 3.0 29.0 + - + +
418B ALA* 3.1 6.9 + - - +
420B ILE* 1.3 78.5 + - - +
422B VAL* 1.3 62.8 + - - +
423B ALA 3.1 1.3 - - - -
424B SER* 2.5 35.6 + - - -
425B LYS* 3.4 12.9 + - + +
469B VAL* 3.0 22.9 + - - +
470B LYS* 3.8 15.3 + - - +
472B GLY 2.5 33.6 + - - -
473B ASP* 4.1 7.4 + - - +
474B GLY* 3.5 26.9 + - - +
476B TYR 3.3 21.4 + - - -
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Residues in contact with VAL 422 (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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127B ALA* 4.0 24.9 - - + +
130B GLU* 3.9 21.1 - - + -
131B LEU* 3.3 31.4 - - + +
134B LEU* 4.4 12.1 - - + -
418B ALA 3.0 15.4 + - - +
419B LEU* 3.1 17.5 - - + +
421B ARG* 1.3 75.7 - - - +
423B ALA* 1.3 68.2 + - - +
425B LYS* 3.1 10.7 + - - +
426B LEU* 3.1 26.9 + - + +
447B MET* 4.2 7.4 - - - -
504B LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 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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419B LEU 3.0 14.1 + - - +
420B ILE* 3.6 13.2 - - + +
422B VAL* 1.3 81.2 - - - +
424B SER* 1.3 64.1 + - - +
426B LEU 3.4 7.8 + - - -
427B ALA* 3.6 9.7 + - - +
444B LEU* 3.9 40.4 - - + +
447B MET* 4.0 13.7 - - + -
448B GLU* 5.6 2.2 - - + +
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Residues in contact with SER 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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420B ILE 3.4 8.9 + - - -
421B ARG* 2.5 38.2 + - - -
423B ALA* 1.3 79.1 - - - +
425B LYS* 1.3 63.3 + - - +
426B LEU 3.6 0.2 + - - -
427B ALA* 3.6 16.9 - - - +
470B LYS* 6.0 1.8 - - - -
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Residues in contact with LYS 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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130B GLU* 3.6 38.4 + - + +
134B LEU* 5.0 10.8 - - + +
421B ARG* 3.7 15.9 - - + +
422B VAL* 3.1 12.3 + - - +
423B ALA 3.1 0.2 - - - -
424B SER* 1.3 84.1 + - - +
426B LEU* 1.3 61.0 + - - +
427B ALA* 3.3 3.6 + - - -
428B ASP* 4.6 5.4 + - - +
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Residues in contact with LEU 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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123B ALA* 3.5 26.2 - - - +
126B ALA* 3.9 20.9 - - + +
127B ALA* 3.6 23.8 - - + +
130B GLU* 4.2 18.8 - - + +
422B VAL 3.1 14.6 + - - +
423B ALA 3.4 0.6 + - - -
424B SER 3.4 0.4 - - - -
425B LYS* 1.3 79.1 - - - +
427B ALA* 1.3 64.1 + - - +
428B ASP 3.1 3.8 - - - -
429B LEU* 2.9 31.4 + - + +
444B LEU* 3.7 36.1 - - + +
447B MET* 4.8 0.4 - - + -
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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