Contacts of the helix formed by residues 413 - 420 (chain B) in PDB entry 3R29
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 413 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A GLU* 5.4 8.1 + - - -
397A TYR* 3.8 16.9 + - - -
401A GLU* 5.3 4.7 - - - -
412B PRO* 1.3 81.5 - - - +
414B ARG* 1.3 66.7 + - - +
415B PHE* 3.1 4.7 - - - -
416B ALA* 2.9 10.2 + - - +
417B LYS* 2.9 22.6 + - - +
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Residues in contact with ARG 414 (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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360B MET* 3.1 40.6 + - + +
361B GLN* 3.7 13.3 + - - +
362B MET* 4.1 1.4 - - - +
366B GLU* 2.4 43.8 + - - +
404B CYS* 4.5 11.0 - - + -
408B TYR* 3.5 51.1 + - + -
411B GLN* 3.5 49.3 + - - +
412B PRO 3.7 0.2 - - - -
413B GLY* 1.3 75.5 - - - +
415B PHE* 1.3 65.5 + - - +
417B LYS* 3.0 12.8 + - - +
418B LEU* 2.9 26.5 + - + +
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Residues in contact with PHE 415 (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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401A GLU* 5.1 1.8 - - - +
415A PHE* 4.7 16.4 - + - -
416A ALA* 4.1 13.5 - - + -
397B TYR* 3.7 36.8 - + + -
400B LEU* 3.8 26.9 - - + -
401B GLU* 3.8 48.0 - - + +
404B CYS* 4.4 13.5 - - + +
405B LYS* 6.3 0.9 - - + +
412B PRO 5.2 2.7 - - - +
413B GLY* 4.1 3.3 - - - -
414B ARG* 1.3 79.0 - - - +
416B ALA* 1.3 60.2 + - - +
418B LEU* 2.9 31.6 + - - +
419B LEU* 3.1 32.1 + - + +
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Residues in contact with ALA 416 (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 TYR* 3.5 33.0 - - + -
415A PHE* 3.7 13.5 - - + -
419A LEU* 3.6 25.6 - - + -
413B GLY* 2.9 8.9 + - - +
415B PHE* 1.3 74.4 - - - +
417B LYS* 1.3 67.0 + - - +
418B LEU 2.9 2.0 - - - -
419B LEU* 3.2 3.8 + - - +
420B LEU* 3.0 29.2 + - - +
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Residues in contact with LYS 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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390A GLU* 4.4 22.8 - - - +
394A GLU* 4.8 12.4 + - - +
397A TYR* 3.6 19.5 + - - +
356B LYS 6.0 0.2 - - - -
359B ASP* 5.8 2.0 - - - -
360B MET* 3.8 39.9 - - + +
411B GLN* 5.4 6.3 - - - +
413B GLY 2.9 11.1 + - - +
414B ARG* 3.3 16.4 - - - +
416B ALA* 1.3 79.1 - - - +
418B LEU* 1.3 63.0 + - - +
420B LEU* 3.2 11.4 + - - +
421B ARG* 3.8 11.6 + - - +
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Residues in contact with LEU 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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360B MET* 3.7 29.2 - - + -
362B MET* 4.3 13.9 - - + -
366B GLU* 3.9 32.8 - - + +
370B LEU* 3.8 26.3 - - + +
400B LEU* 4.1 16.8 - - + -
404B CYS* 3.6 31.9 - - - -
414B ARG* 2.9 16.9 + - + +
415B PHE* 2.9 13.2 + - - +
417B LYS* 1.3 77.3 - - - +
419B LEU* 1.3 60.7 + - + +
421B ARG* 3.2 19.7 + - - +
422B LEU 4.3 0.5 + - - -
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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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416A ALA* 4.0 22.2 - - + +
419A LEU* 4.0 33.6 - - + +
420A LEU* 4.5 13.0 - - + +
423A PRO* 5.5 0.3 - - - +
370B LEU* 4.4 10.5 - - + -
373B ILE* 4.8 12.1 - - + -
397B TYR* 4.9 0.9 - - + -
400B LEU* 4.8 2.7 - - + -
415B PHE* 3.1 45.8 + - + +
416B ALA 3.2 4.9 + - - +
418B LEU* 1.3 76.1 - - - +
420B LEU* 1.3 59.2 + - - +
421B ARG 3.0 0.4 - - - -
422B LEU* 3.0 45.4 + - + +
423B PRO* 3.5 3.8 - - - +
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Residues in contact with LEU 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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373A ILE* 3.8 13.7 - - + -
393A ARG* 3.8 23.6 + - - +
397A TYR* 3.3 42.0 - - + -
419A LEU* 4.1 19.7 - - + +
422A LEU* 3.6 30.7 - - + -
416B ALA 3.0 19.4 + - - +
417B LYS* 3.2 6.0 + - - +
418B LEU 3.1 1.0 - - - -
419B LEU* 1.3 79.6 - - - +
421B ARG* 1.3 77.7 + - - +
422B LEU 3.4 0.4 - - - -
423B PRO* 3.3 18.3 - - + +
424B ALA 4.5 1.9 + - - -
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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