Contacts of the helix formed by residues 392 - 402 (chain G) in PDB entry 5UQ9
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 392 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379G ALA* 3.8 29.3 - - + +
382G ARG* 3.1 20.4 + - - +
383G ASN* 5.8 1.9 - - - +
386G LEU* 4.0 15.3 - - + +
389G LEU* 3.5 6.7 + - + +
391G LEU* 1.3 77.8 - - - +
393G ASP* 1.3 64.1 + - - +
394G PHE* 3.1 32.1 + - - +
395G PHE* 3.7 19.2 - - + -
396G LYS* 2.8 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 393 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382G ARG* 4.8 11.7 - - - +
391G LEU 3.8 1.0 + - - +
392G ASP* 1.3 75.8 + - - +
394G PHE* 1.3 50.7 + - - +
396G LYS* 3.7 25.3 + - - +
397G SER* 2.5 36.7 + - - -
303H LYS* 4.2 16.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 394 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G GLU* 6.1 2.7 - - + -
328G TYR* 4.5 10.8 - - - -
375G LYS* 3.4 63.7 - - + -
378G ASP* 6.1 2.9 - - + -
382G ARG* 3.8 12.5 - - - +
392G ASP* 3.1 14.7 + - - +
393G ASP* 1.3 77.9 - - - +
395G PHE* 1.3 58.7 + + + +
397G SER* 2.9 7.6 + - - -
398G ALA* 2.7 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 395 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328G TYR* 5.6 1.3 - - - -
332G ILE* 3.8 34.3 - - + -
372G PHE* 3.4 31.2 - + - -
375G LYS* 3.1 35.2 - - + -
376G ILE* 3.4 22.0 - - + -
379G ALA* 3.8 8.7 - - + -
389G LEU* 3.5 42.2 - - + +
390G LEU* 5.1 2.2 - - - -
392G ASP* 3.2 15.7 + - + +
394G PHE* 1.3 78.8 - + + +
396G LYS* 1.3 58.1 + - - +
398G ALA* 4.2 5.8 - - + -
399G VAL* 2.7 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 396 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390G LEU* 3.9 17.1 + - - +
391G LEU 4.8 1.3 - - - -
392G ASP 2.8 19.9 + - - +
393G ASP* 3.7 33.0 + - - +
395G PHE* 1.3 73.4 - - - +
397G SER* 1.3 64.5 + - - +
399G VAL* 4.1 5.1 - - - +
400G GLU* 3.1 28.1 + - + +
303H LYS* 3.5 42.0 - - + +
304H LEU* 3.8 19.0 - - + +
305H LYS* 6.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 397 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393G ASP 2.5 25.3 + - - -
394G PHE* 2.9 13.5 + - - -
396G LYS* 1.3 88.4 - - - +
398G ALA* 1.3 58.9 + - - +
400G GLU* 3.3 7.6 + - - +
401G ASN* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 398 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328G TYR* 4.0 27.8 - - + +
332G ILE* 4.5 3.6 - - + -
394G PHE* 2.7 34.8 + - + +
395G PHE* 3.8 7.4 - - + +
397G SER* 1.3 71.8 + - - +
399G VAL* 1.3 62.9 + - - +
401G ASN* 2.6 29.5 + - - +
402G CYS* 3.2 10.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 399 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G ALA* 4.6 6.7 - - + -
332G ILE* 3.6 37.5 - - + -
333G ILE* 4.4 9.4 - - + -
390G LEU* 4.8 5.2 - - + -
395G PHE 2.7 24.1 + - - +
396G LYS* 4.1 5.4 - - - +
398G ALA* 1.3 72.5 - - - +
400G GLU* 1.3 62.5 + - - +
402G CYS* 3.0 9.2 + - - +
403G GLN* 3.0 22.2 + - + -
406G TRP* 4.7 14.1 - - + -
430G TYR* 4.2 35.4 - - + +
304H LEU* 6.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 400 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396G LYS* 3.1 23.9 + - + +
397G SER* 3.5 9.6 - - - +
398G ALA 3.2 0.4 - - - -
399G VAL* 1.3 78.5 - - - +
401G ASN* 1.3 62.0 + - - +
403G GLN* 3.3 25.2 + - + +
404G ASP 4.8 0.5 + - - -
430G TYR* 5.7 3.6 - - - +
305H LYS* 3.4 47.2 + - + +
306H GLY 5.7 0.9 - - - +
308H GLN* 5.4 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 401 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G GLU* 5.2 5.0 + - - -
325G LYS* 2.1 36.9 + - - +
328G TYR* 5.0 2.6 - - - -
397G SER 3.0 13.2 + - - +
398G ALA* 2.6 31.7 + - - +
399G VAL 3.3 0.4 - - - -
400G GLU* 1.3 80.0 + - - +
402G CYS* 1.3 69.6 + - - +
403G GLN 4.0 0.2 + - - -
404G ASP* 5.2 1.8 + - - +
405G SER* 5.6 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 402 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G GLU* 6.1 0.4 - - - -
324G ARG* 6.2 0.4 - - - -
325G LYS* 3.4 47.0 - - + +
328G TYR* 3.6 25.1 - - - -
329G ALA* 4.0 9.2 - - + -
398G ALA 3.2 7.0 - - - +
399G VAL 3.0 8.7 + - - +
401G ASN* 1.3 104.5 - - - +
403G GLN* 1.3 61.4 + - - +
404G ASP 3.5 2.2 - - - -
405G SER 3.8 2.2 + - - +
406G TRP* 3.1 25.2 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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