Contacts of the helix formed by residues 328 - 339 (chain B) in PDB entry 4U7B
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 LYS 328 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B TYR* 3.9 19.4 - - + +
286B HIS* 3.4 20.0 + - - +
324B ARG* 3.1 34.6 + - + +
325B GLY 3.7 9.0 - - - +
326B ILE 3.1 0.8 - - - -
327B HIS* 1.3 75.9 - - - +
329B LEU* 1.3 65.9 + - - +
330B PRO* 3.1 5.1 - - - -
331B GLU* 3.3 29.0 + - - +
332B ARG* 3.2 28.7 + - + +
4C G 3.0 50.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 5.1 4.7 - - + -
152B ILE* 5.3 4.9 - - + -
247B LEU* 4.9 9.4 - - + -
280B LEU* 3.4 28.0 - - - +
282B PRO* 3.4 24.7 - - + -
285B TYR* 3.5 17.2 + - + +
326B ILE* 3.1 34.8 + - + +
328B LYS* 1.3 77.9 - - - +
330B PRO* 1.3 69.8 - - + +
332B ARG* 3.3 5.3 + - + +
333B TRP* 2.9 65.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.7 4.0 - - + +
143B TYR* 3.6 46.0 - - + +
149B LEU* 4.1 11.9 - - + -
326B ILE 4.2 1.3 - - - +
327B HIS* 3.3 17.7 - - + +
328B LYS 3.2 5.6 - - - -
329B LEU* 1.3 94.0 - - + +
331B GLU* 1.3 56.6 + - - +
333B TRP* 3.1 17.2 + - + +
334B GLU* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B HIS 4.5 3.8 - - - +
328B LYS* 3.3 36.6 + - - +
330B PRO* 1.3 80.6 - - - +
332B ARG* 1.3 72.1 + - + +
334B GLU* 3.2 17.1 + - - +
335B LYS* 3.1 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ASP* 3.0 36.4 + - - +
280B LEU* 4.1 9.9 - - + -
285B TYR* 3.4 53.7 - - + +
328B LYS* 3.2 23.7 + - + +
329B LEU* 3.6 9.2 - - + +
330B PRO 3.2 0.4 - - - -
331B GLU* 1.3 82.7 + - + +
333B TRP* 1.3 59.2 + - - +
335B LYS* 3.3 6.0 + - + +
336B CYS* 2.8 29.3 + - - +
344B PHE* 3.5 30.3 - - + -
345B GLU* 5.8 2.3 + - - -
4C G 4.0 22.6 - - - -
55D G 4.0 6.3 - - - +
56D A 5.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B CYS* 3.8 27.8 - - + +
139B LEU* 3.7 47.7 - - + +
140B LEU* 3.7 20.9 - - + -
143B TYR* 4.3 9.6 - + + -
148B PHE* 3.9 24.2 - + - -
149B LEU* 4.3 11.0 - - + -
247B LEU* 5.9 2.0 - - + -
271B LEU* 5.0 5.6 - - + -
280B LEU* 3.7 23.6 + - + +
329B LEU* 2.9 57.5 + - + +
330B PRO* 3.1 17.0 + - + +
332B ARG* 1.3 74.7 - - - +
334B GLU* 1.3 56.9 + - - +
336B CYS* 3.5 5.1 - - - +
337B VAL* 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.8 19.5 - - + +
144B LYS* 4.4 14.1 + - - +
330B PRO* 2.9 18.0 + - - +
331B GLU* 3.2 19.3 + - - +
333B TRP* 1.3 76.6 - - - +
335B LYS* 1.3 56.7 + - + +
337B VAL* 3.2 9.4 - - - +
338B ALA* 3.1 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLU* 3.1 35.0 + - - +
332B ARG* 3.7 6.9 - - - +
334B GLU* 1.3 76.6 - - + +
336B CYS* 1.3 56.4 + - - +
337B VAL 3.2 0.4 - - - -
338B ALA* 4.1 5.6 - - - -
339B SER* 2.7 41.6 + - - +
344B PHE* 3.7 39.1 - - + -
345B GLU* 4.7 11.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ARG* 3.5 28.5 - - - +
133B LYS* 4.3 1.3 - - - -
136B CYS* 2.1 50.0 - - - -
280B LEU* 4.2 8.3 - - + -
332B ARG 2.8 17.5 + - - +
333B TRP 3.2 1.8 + - - +
335B LYS* 1.3 77.7 - - - +
337B VAL* 1.3 59.8 + - - +
339B SER* 3.7 3.3 + - - -
341B GLY* 3.1 25.6 + - - -
342B LYS 4.8 3.1 - - - -
344B PHE* 3.6 17.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LYS* 4.1 17.3 - - + +
136B CYS* 4.8 2.7 - - + -
137B GLU* 3.5 41.7 - - + +
140B LEU* 4.5 11.7 - - + -
333B TRP 3.0 17.6 + - - +
334B GLU* 3.2 19.3 - - + +
336B CYS* 1.3 77.4 - - - +
338B ALA* 1.3 66.3 + - - +
340B ASP* 2.6 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLU 3.1 17.4 + - - +
335B LYS* 3.7 7.0 - - - +
337B VAL* 1.3 83.8 - - + +
339B SER* 1.3 58.2 + - - +
340B ASP* 3.1 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LYS* 2.7 22.6 + - - +
336B CYS 4.0 1.3 - - - -
338B ALA* 1.3 74.6 - - - +
340B ASP* 1.3 69.3 + - - +
341B GLY 3.2 1.0 + - - -
342B LYS* 3.3 45.8 + - - +
343B TYR 4.4 3.6 - - - -
344B PHE* 3.6 17.3 - - - +
----------------------------------------------------------
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