Contacts of the helix formed by residues 397 - 410 (chain B) in PDB entry 4REA
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 397 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396B PHE* 1.3 77.8 - - - +
398B GLU* 1.3 67.4 + - - +
399B GLN* 2.8 24.8 + - - +
400B GLU* 3.1 30.4 + - - +
401B LYS* 3.0 20.3 + - - +
599B ARG* 3.2 37.8 + - - +
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Residues in contact with GLU 398 (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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396B PHE 4.7 3.3 - - - +
397B ASP* 1.3 76.3 + - - +
399B GLN* 1.3 60.5 + - - +
401B LYS* 3.3 31.3 + - - +
402B GLY* 2.8 26.9 + - - -
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Residues in contact with GLN 399 (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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397B ASP* 2.8 13.8 + - - +
398B GLU* 1.3 74.0 - - - +
400B GLU* 1.3 61.6 + - - +
402B GLY* 3.3 3.8 + - - +
403B ILE* 3.0 52.1 + - + +
406B LYS* 4.4 6.0 + - - +
541B PRO* 6.1 0.4 - - - +
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Residues in contact with GLU 400 (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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396B PHE* 3.7 6.9 - - + +
397B ASP* 3.1 41.2 + - - +
399B GLN* 1.3 80.0 - - + +
401B LYS* 1.3 64.7 + - - +
403B ILE* 3.0 28.4 + - + +
404B VAL* 3.4 3.8 + - - +
540B GLY 4.8 2.1 - - - +
544B VAL* 3.4 33.1 - - + +
547B ARG* 2.6 40.5 + - - -
599B ARG* 4.2 5.2 + - - -
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Residues in contact with LYS 401 (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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390B GLU 5.2 0.8 + - - -
393B MET* 3.1 54.7 + - - +
394B LEU* 5.0 6.1 - - - +
396B PHE* 4.4 14.3 + - + +
397B ASP 3.0 13.9 + - - +
398B GLU* 3.3 32.4 + - - +
400B GLU* 1.3 73.7 - - - +
402B GLY* 1.3 58.7 + - - +
404B VAL* 3.0 25.5 + - - +
405B THR* 3.1 15.4 + - - -
544B VAL* 5.8 0.2 - - - -
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Residues in contact with GLY 402 (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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398B GLU 2.8 14.1 + - - -
399B GLN* 3.5 5.8 - - - -
400B GLU 3.2 0.4 - - - -
401B LYS* 1.3 76.0 - - - +
403B ILE* 1.3 57.4 + - - +
405B THR* 3.4 9.6 + - - -
406B LYS* 2.9 45.8 + - - +
409B GLN* 3.5 0.2 - - - +
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Residues in contact with ILE 403 (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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399B GLN* 3.0 38.6 + - + +
400B GLU* 3.0 17.5 + - + +
402B GLY* 1.3 76.3 - - - +
404B VAL* 1.3 67.0 + - + +
406B LYS* 3.2 17.3 + - - +
407B PHE 3.0 17.8 + - - -
454B GLY 5.7 0.7 - - - +
455B PHE* 3.3 31.7 - - + -
540B GLY 4.9 0.4 - - - -
541B PRO* 3.7 42.0 - - + +
544B VAL* 4.5 7.0 - - + -
545B PHE* 3.8 11.0 - - + -
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Residues in contact with VAL 404 (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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383B LEU* 3.7 23.8 - - + -
387B LEU* 4.1 13.5 - - + -
400B GLU 3.4 6.0 + - - +
401B LYS* 3.0 11.2 + - - +
403B ILE* 1.3 76.2 - - - +
405B THR* 1.3 66.9 + - - +
407B PHE* 3.1 8.0 + - - +
408B TYR* 3.0 38.2 + - + -
544B VAL* 4.8 4.9 - - + -
545B PHE* 3.8 17.3 - - + -
548B ILE* 3.6 30.7 - - + -
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Residues in contact with THR 405 (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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401B LYS 3.1 15.0 + - - -
402B GLY* 3.6 12.0 - - - -
404B VAL* 1.3 75.7 - - - +
406B LYS* 1.3 46.6 - - - +
408B TYR* 3.0 11.2 + - + +
409B GLN* 1.7 50.4 + - + +
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Residues in contact with LYS 406 (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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399B GLN* 4.4 7.5 + - - +
402B GLY* 2.9 41.3 + - - +
403B ILE* 3.6 20.8 - - - +
404B VAL 3.2 0.2 - - - -
405B THR* 1.3 46.5 - - - +
407B PHE* 1.3 50.4 + - - +
409B GLN* 1.0 166.9 + - + +
410B LEU* 2.8 20.6 + - - +
453B ALA* 4.0 32.4 - - + +
455B PHE* 4.2 8.0 - - + -
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Residues in contact with PHE 407 (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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376B LEU* 4.6 0.9 - - + -
379B PHE* 3.3 35.2 - + - -
380B LEU* 4.4 12.6 - - + -
383B LEU* 3.9 20.4 - - + -
403B ILE 3.0 7.5 + - - +
404B VAL 3.3 7.2 - - - +
406B LYS* 1.3 71.5 - - - +
408B TYR* 1.3 63.6 + + - +
409B GLN* 2.0 6.1 - - - +
410B LEU* 2.8 31.5 + - + +
415B GLN* 3.8 27.5 - - + +
418B TYR* 3.5 38.8 - + + -
419B VAL* 4.1 11.2 - - + -
455B PHE* 3.4 32.0 - + + -
545B PHE* 3.8 10.5 - + + -
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Residues in contact with TYR 408 (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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380B LEU* 3.5 39.9 + - + +
383B LEU* 2.8 47.3 - - + +
384B LYS* 4.2 2.8 + - - -
387B LEU* 4.7 15.7 - - + -
404B VAL* 3.0 29.3 + - + -
405B THR* 3.5 11.0 - - + +
407B PHE* 1.3 80.1 - + - +
409B GLN* 1.3 60.5 + - - +
410B LEU 3.4 5.9 + - - +
415B GLN* 3.9 18.5 + - - +
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Residues in contact with GLN 409 (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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405B THR* 1.7 34.2 + - + +
406B LYS* 1.0 146.7 + - + +
407B PHE 2.0 2.8 - - - +
408B TYR* 1.3 69.2 - - - +
410B LEU* 1.3 62.2 + - - +
411B SER* 3.7 1.0 + - - -
449B GLU* 4.6 1.4 - - - +
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Residues in contact with LEU 410 (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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406B LYS 2.8 10.5 + - - +
407B PHE* 2.8 20.8 + - + +
408B TYR 3.7 3.5 - - - +
409B GLN* 1.3 80.3 - - - +
411B SER* 1.3 73.5 + - - +
414B GLY* 2.2 51.1 - - - +
415B GLN* 2.3 31.4 - - + +
449B GLU* 2.3 60.8 - - + +
450B LEU* 4.0 18.2 - - + -
455B PHE* 5.1 2.7 - - + -
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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