Contacts of the helix formed by residues 323 - 334 (chain B) in PDB entry 1TE6
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 ASN 323 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 3.3 27.7 + - - +
44B GLU* 5.0 0.6 - - - +
320B THR 2.8 17.1 + - - +
321B VAL* 3.7 9.4 - - + +
322B THR* 1.3 73.7 - - - +
324B PRO* 1.3 57.5 - - - +
325B LYS* 2.9 54.5 + - - +
326B ARG* 2.9 20.2 + - + -
327B ILE* 2.7 42.5 + - - +
346B ILE* 4.4 4.8 - - + +
355B ALA* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B THR 4.0 0.9 - - - +
323B ASN* 1.3 86.7 - - - +
325B LYS* 1.3 75.2 + - + +
327B ILE* 3.6 4.5 - - + +
328B GLU* 2.9 36.8 + - + +
346B ILE* 3.6 22.7 - - + -
351B GLU* 5.4 5.2 - - + +
354B GLN* 6.0 2.7 - - + +
355B ALA* 4.8 17.0 - - + +
358B LEU* 3.9 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ASN* 2.9 31.6 + - - +
324B PRO* 1.3 94.1 - - + +
326B ARG* 1.3 62.4 + - + +
328B GLU* 3.5 9.0 + - - +
329B ARG* 3.3 20.1 + - - +
346B ILE* 5.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 3.8 51.5 + - + -
297B GLN* 3.4 17.0 + - - +
298B ASP* 4.0 10.1 + - - -
300B TRP* 3.3 36.6 - - - +
318B ASP 4.1 4.4 + - - -
319B LEU 2.8 31.4 + - - +
320B THR* 3.4 15.7 - - - +
321B VAL* 3.8 8.7 - - + -
323B ASN* 2.9 27.4 + - + +
325B LYS* 1.3 75.2 - - + +
327B ILE* 1.3 66.9 - - - +
329B ARG* 3.3 16.8 + - - +
330B ALA* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B THR* 3.1 43.5 - - + +
322B THR 5.0 0.7 - - - -
323B ASN 2.7 36.0 + - - +
324B PRO* 3.6 6.7 - - + +
326B ARG* 1.3 76.7 - - - +
328B GLU* 1.3 56.9 + - - +
330B ALA* 3.2 6.4 + - - +
331B VAL* 2.8 41.0 + - + +
339B LEU* 4.0 19.1 - - + -
355B ALA* 5.1 4.5 - - + +
358B LEU* 3.8 27.1 - - + -
359B ALA* 4.9 7.9 - - + +
364B TRP* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B PRO* 2.9 28.0 + - + +
325B LYS* 3.6 8.7 - - - +
326B ARG 3.3 0.2 - - - -
327B ILE* 1.3 75.7 - - - +
329B ARG* 1.3 60.5 + - - +
331B VAL* 3.4 8.2 + - - +
332B GLU* 3.0 24.8 + - - +
358B LEU* 3.8 29.7 - - + +
362B ASN* 4.8 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TRP* 3.3 52.5 - - + +
325B LYS 3.3 10.1 + - - +
326B ARG* 3.7 18.2 - - - +
327B ILE 3.3 0.4 - - - -
328B GLU* 1.3 74.7 - - - +
330B ALA* 1.3 61.4 + - - +
332B GLU* 3.3 5.2 + - - +
333B GLU* 2.9 62.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TRP* 3.5 21.7 - - + -
319B LEU* 4.3 0.9 - - + -
320B THR* 4.1 10.5 - - + -
326B ARG 3.0 17.5 + - - +
327B ILE 3.6 1.1 - - - +
329B ARG* 1.3 76.4 - - - +
331B VAL* 1.3 57.0 + - - +
334B LYS* 2.9 24.3 + - - -
335B ALA* 3.0 13.6 + - + -
336B CYS* 4.2 7.4 - - - -
364B TRP* 3.5 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE* 2.8 30.4 + - + +
328B GLU* 3.6 11.0 - - - +
329B ARG 3.2 0.2 - - - -
330B ALA* 1.3 76.3 - - - +
332B GLU* 1.3 64.9 + - + +
334B LYS* 3.1 19.5 + - - +
358B LEU 5.4 0.2 - - - +
359B ALA* 5.7 0.4 - - - -
362B ASN* 3.7 43.5 - - + +
364B TRP* 3.6 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU 3.0 13.2 + - - +
329B ARG* 3.8 5.4 - - - +
331B VAL* 1.3 82.3 - - - +
333B GLU* 1.3 74.2 + - - +
334B LYS* 3.7 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TRP* 3.5 30.1 - - + +
304B SER* 2.7 34.6 + - - +
329B ARG* 2.9 53.8 + - + +
330B ALA 4.4 1.3 - - - +
332B GLU* 1.3 90.0 - - + +
334B LYS* 1.3 65.6 + - - +
335B ALA 3.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B SER* 3.6 12.4 - - - +
307B THR* 3.8 14.7 - - + +
308B ALA* 5.3 1.3 + - + -
330B ALA 2.9 8.8 + - - -
331B VAL* 3.1 12.6 + - - +
332B GLU 4.6 3.6 - - - +
333B GLU* 1.3 80.7 - - - +
335B ALA* 1.3 62.1 + - - +
336B CYS 3.3 8.2 + - - +
364B TRP* 6.0 0.4 - - - +
----------------------------------------------------------
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