Contacts of the helix formed by residues 362 - 373 (chain B) in PDB entry 4U1D
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 THR 362 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 4.2 3.8 - - - +
338B ASP* 3.1 21.5 - - - +
360B LYS 5.3 1.3 - - - +
361B PRO* 1.3 78.3 - - + +
363B ARG* 1.3 61.9 + - - +
364B LYS* 3.2 10.0 + - - +
365B GLU* 2.9 44.2 + - + +
366B MET* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 4.1 9.1 - - - +
332B ALA 3.7 9.7 + - - +
333B ILE* 2.7 38.4 + - - +
335B THR* 3.1 45.6 + - + -
336B GLN 3.5 11.0 - - - +
337B LEU* 3.2 28.4 - - - +
338B ASP* 3.0 20.7 + - - +
339B GLU* 5.0 2.0 + - + -
362B THR* 1.3 69.6 - - - +
364B LYS* 1.3 65.6 + - + +
366B MET* 3.4 3.4 + - - +
367B LEU* 2.9 38.7 + - - +
392B GLU* 2.8 35.4 + - - -
427B VAL* 4.3 2.2 - - - +
431B ARG* 3.3 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ASP* 4.8 0.4 + - - +
362B THR* 3.2 7.5 + - - +
363B ARG* 1.3 85.8 - - + +
365B GLU* 1.3 65.0 + - + +
367B LEU* 3.3 8.5 + - - +
368B GLN* 2.9 29.3 + - + +
392B GLU* 6.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LYS 4.7 0.5 - - - +
361B PRO* 3.2 27.7 - - + +
362B THR* 2.9 38.5 + - + +
364B LYS* 1.3 78.3 - - + +
366B MET* 1.3 57.8 + - - +
368B GLN* 3.1 8.3 + - - +
369B SER* 2.9 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 3.6 27.6 - - + +
300B THR* 4.1 30.1 - - + -
301B THR* 3.4 24.7 - - - +
304B LYS* 3.5 26.9 - - - -
332B ALA* 4.4 9.9 - - + -
335B THR* 5.9 0.4 - - - +
357B LEU* 5.5 0.4 - - + -
361B PRO* 3.9 26.4 - - + +
362B THR 3.1 12.7 + - - +
363B ARG* 3.7 4.9 - - - +
364B LYS 3.4 0.2 - - - -
365B GLU* 1.3 77.9 - - - +
367B LEU* 1.3 62.4 + - - +
369B SER* 2.6 22.3 + - - -
370B ILE* 3.0 15.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B PHE* 3.6 26.9 - - + -
332B ALA* 3.6 28.7 - - + +
333B ILE* 3.8 13.9 - - + -
363B ARG* 2.9 45.5 + - - +
364B LYS* 3.7 6.5 - - - +
366B MET* 1.3 77.5 - - - +
368B GLN* 1.3 57.7 + - - +
370B ILE* 3.2 4.8 + - - +
371B ILE* 3.0 34.0 + - - +
388B TYR* 3.6 29.8 - - + +
392B GLU* 4.2 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LYS* 2.9 18.4 + - + +
365B GLU* 3.3 11.4 - - - +
367B LEU* 1.3 74.2 - - - +
369B SER* 1.3 57.0 + - - +
370B ILE 3.0 4.0 - - - -
371B ILE* 3.0 16.3 + - - +
372B GLU* 2.9 76.2 + - - +
388B TYR* 5.1 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LYS* 2.9 28.8 + - - -
365B GLU 2.9 12.1 + - - -
366B MET* 2.6 22.8 + - - -
368B GLN* 1.3 75.5 - - - +
370B ILE* 1.3 58.6 + - - +
372B GLU* 4.3 8.9 - - - +
373B ASP* 3.4 21.7 + - - +
376B ILE* 5.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B THR* 3.9 8.5 - - + -
304B LYS* 4.1 16.6 - - + -
328B ILE* 3.7 23.3 - - + +
329B PHE* 3.6 26.9 - - + -
332B ALA* 3.5 32.8 - - + -
366B MET* 3.0 14.5 + - + +
367B LEU* 3.6 6.7 - - - +
368B GLN 3.0 0.8 - - - -
369B SER* 1.3 79.1 - - - +
371B ILE* 1.3 64.4 + - - +
372B GLU 3.3 0.4 + - - -
373B ASP* 3.5 19.0 - - - +
376B ILE* 4.1 24.4 - - + +
377B TYR* 3.5 10.7 + - + +
380B VAL* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B PHE* 3.8 15.9 - - + -
367B LEU 3.0 19.8 + - - +
368B GLN* 3.0 18.1 + - - +
370B ILE* 1.3 79.4 - - - +
372B GLU* 1.3 61.2 + - + +
373B ASP 3.6 0.2 + - - -
374B GLU* 3.6 12.6 - - - +
377B TYR* 3.6 36.1 - - + +
388B TYR* 3.3 48.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLN* 2.9 52.9 + - - +
369B SER* 4.8 5.7 - - - +
371B ILE* 1.3 74.8 - - + +
373B ASP* 1.3 60.8 + - - +
374B GLU* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B SER 3.4 20.0 + - - +
370B ILE 3.5 7.6 + - - +
371B ILE 3.4 0.8 - - - -
372B GLU* 1.3 74.3 - - - +
374B GLU* 1.3 59.6 + - - +
375B SER* 2.9 27.8 + - - -
376B ILE* 3.1 24.1 + - + +
377B TYR* 2.9 24.7 + - - +
----------------------------------------------------------
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