Contacts of the helix formed by residues 395 - 408 (chain B) in PDB entry 5CTR
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 395 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B GLY 3.6 2.7 + - - -
394B VAL* 1.3 74.6 - - - +
396B HIS* 1.3 81.9 + - - +
397B GLN* 2.8 31.0 - - - +
398B VAL* 3.0 29.2 + - + +
399B ILE* 3.2 10.4 + - - +
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Residues in contact with HIS 396 (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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394B VAL 3.7 1.4 + - - -
395B ASP* 1.3 81.7 + - - +
397B GLN* 1.3 80.8 + - - +
399B ILE* 3.4 1.6 + - - +
400B SER* 3.1 39.8 + - - -
424B TYR* 3.8 10.8 - - - -
427B TYR* 3.5 30.6 + + - +
428B LEU* 4.1 18.8 - - + -
431B ARG* 4.0 29.7 + - - +
444B GLU* 4.3 14.1 + - - -
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Residues in contact with GLN 397 (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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395B ASP* 2.8 38.7 + - - +
396B HIS* 1.3 98.8 - - - +
398B VAL* 1.3 61.1 + - + +
400B SER* 3.5 7.6 + - - -
401B VAL* 3.3 20.6 + - - +
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Residues in contact with VAL 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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389B MET* 3.7 19.1 - - + -
394B VAL* 3.5 18.6 - - + -
395B ASP* 3.0 31.9 - - + +
397B GLN* 1.3 72.5 - - + +
399B ILE* 1.3 57.9 + - - +
401B VAL* 3.3 12.3 - - + +
402B THR* 2.6 36.9 + - - +
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Residues in contact with ILE 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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386B LEU* 4.0 23.3 - - + +
389B MET* 4.1 20.6 - - + +
390B GLU* 4.8 13.0 - - - +
394B VAL* 3.3 23.6 - - + +
395B ASP 3.2 11.1 + - - +
396B HIS 3.4 6.0 + - - +
398B VAL* 1.3 75.2 - - - +
400B SER* 1.3 57.8 + - - +
402B THR* 3.4 3.4 + - - -
403B PHE* 2.9 26.9 + - - +
424B TYR* 4.5 4.9 - - + -
427B TYR* 2.6 61.5 - - + +
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Residues in contact with SER 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 HIS* 3.1 26.8 + - - -
397B GLN* 3.6 11.4 - - - -
399B ILE* 1.3 75.3 - - - +
401B VAL* 1.3 59.8 + - - +
403B PHE* 3.3 4.8 + - - +
404B GLU* 2.9 37.7 + - - +
424B TYR* 2.8 27.8 + - - -
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B GLN 3.3 11.7 + - - +
398B VAL* 3.3 21.3 - - + +
400B SER* 1.3 76.2 - - - +
402B THR* 1.3 68.2 + - - +
404B GLU* 3.4 8.0 + - + +
405B LYS* 3.1 52.5 + - - +
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Residues in contact with THR 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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372B ILE* 5.4 0.2 - - + -
382B TRP* 4.2 12.4 - - + +
385B TYR* 4.1 22.6 + - + -
386B LEU* 4.0 11.0 - - + -
389B MET* 3.6 29.7 - - - +
398B VAL* 2.6 26.7 + - - +
399B ILE 3.5 5.6 - - - -
401B VAL* 1.3 77.5 - - - +
403B PHE* 1.3 65.1 + - - +
405B LYS* 3.2 23.8 + - + +
406B ALA 3.6 3.3 + - - -
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Residues in contact with PHE 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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382B TRP* 5.9 0.2 - - - -
386B LEU* 4.4 14.4 - - + -
399B ILE 2.9 16.9 + - - +
400B SER 3.4 3.6 - - - +
402B THR* 1.3 78.1 - - - +
404B GLU* 1.3 72.8 + - - +
406B ALA* 3.1 15.1 + - - +
407B LEU* 3.3 37.9 - - + +
420B ILE* 3.8 25.1 - - + -
421B TRP* 3.6 31.9 - + - -
424B TYR* 3.3 61.9 - + + -
451B ARG* 4.1 14.6 - - - -
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Residues in contact with GLU 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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400B SER* 2.9 26.7 + - - +
401B VAL* 3.5 12.3 - - + +
403B PHE* 1.3 86.6 - - - +
405B LYS* 1.3 64.2 + - + +
407B LEU* 3.5 14.1 + - + +
408B ASN* 2.8 32.3 + - - +
451B ARG* 2.6 33.8 + - - -
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Residues in contact with LYS 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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382B TRP* 4.6 10.0 - - + +
401B VAL* 3.1 33.4 + - - +
402B THR* 3.2 15.7 + - + +
403B PHE 3.1 0.4 - - - -
404B GLU* 1.3 78.1 - - + +
406B ALA* 1.3 64.7 + - - +
408B ASN* 3.2 8.9 + - - +
409B ALA* 3.0 21.0 + - - +
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Residues in contact with ALA 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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382B TRP* 3.8 29.8 - - + +
386B LEU* 6.1 0.7 - - + -
402B THR 3.6 1.8 + - - +
403B PHE* 3.1 13.0 + - - +
405B LYS* 1.3 79.8 - - - +
407B LEU* 1.3 61.4 + - - +
409B ALA* 3.1 15.6 + - - +
411B PHE* 3.2 22.4 - - - -
420B ILE* 3.7 32.8 - - + -
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Residues in contact with LEU 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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403B PHE* 3.3 42.0 - - + +
404B GLU* 3.5 15.7 + - + +
405B LYS 3.3 0.6 - - - -
406B ALA* 1.3 77.0 - - - +
408B ASN* 1.3 63.8 + - - +
411B PHE* 5.1 0.2 - - - -
417B TYR* 3.7 28.4 + - + -
420B ILE* 4.4 9.0 - - + -
421B TRP* 3.8 22.9 - - + +
451B ARG* 3.5 27.8 - - - +
455B TYR* 3.8 30.8 + - + +
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Residues in contact with ASN 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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404B GLU* 2.8 31.5 + - - +
405B LYS* 3.2 9.6 + - - +
406B ALA 3.0 0.6 - - - -
407B LEU* 1.3 82.2 - - - +
409B ALA* 1.3 64.4 + - - +
410B GLY* 3.3 3.2 + - - -
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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