Contacts of the helix formed by residues 327 - 345 (chain A) in PDB entry 3DTC
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 SER 327 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ILE* 3.9 20.5 - - - +
319A GLU* 4.9 0.9 + - - +
325A MET 4.2 5.0 + - - -
326A PHE* 1.3 78.9 - - - +
328A LYS* 1.3 66.4 + - - +
329A GLY* 3.4 10.9 + - - -
330A SER* 2.7 28.1 + - - -
331A ASP 3.1 5.4 + - - -
390A PRO* 4.6 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A HIS* 3.1 59.2 + - + +
258A ASP* 3.1 23.8 + - - +
263A PRO* 4.3 14.6 - - - +
265A ILE* 3.7 15.3 - - + +
327A SER* 1.3 74.2 - - - +
329A GLY* 1.3 56.4 + - - +
331A ASP* 3.3 3.5 + - - +
332A VAL* 2.9 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A SER* 3.0 7.8 + - - -
328A LYS* 1.3 79.4 - - - +
330A SER* 1.3 60.9 + - - +
332A VAL* 3.2 10.6 + - - +
333A TRP 3.1 13.3 + - - -
390A PRO* 4.1 22.9 - - - -
393A ARG* 2.9 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA* 3.7 10.8 + - - +
319A GLU* 4.0 4.0 + - - -
320A VAL* 3.5 28.7 - - - +
325A MET 4.2 2.0 - - - -
326A PHE* 3.4 10.5 - - - +
327A SER* 2.7 39.7 + - - -
329A GLY* 1.3 72.6 - - - +
331A ASP* 1.3 68.5 + - - +
333A TRP* 3.1 4.5 + - - +
334A SER* 3.0 25.3 + - - -
393A ARG* 3.7 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A MET* 4.5 5.2 - - - +
257A HIS* 3.0 27.7 + - + +
265A ILE* 3.4 13.4 - - - +
266A HIS* 2.7 33.9 + - - +
267A ARG* 3.0 26.6 + - - -
269A LEU* 3.6 12.0 - - + +
327A SER 3.1 5.8 + - - +
328A LYS 3.5 8.5 - - - +
330A SER* 1.3 78.6 + - - +
332A VAL* 1.3 58.3 + - - +
334A SER* 3.3 11.2 + - - -
335A TYR* 3.0 22.0 + - - +
396A PHE* 4.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A HIS* 4.6 1.1 - - + -
328A LYS* 2.9 27.4 + - + +
329A GLY* 3.4 10.8 - - - +
330A SER 3.1 0.4 - - - -
331A ASP* 1.3 75.8 - - - +
333A TRP* 1.3 62.4 + - - +
335A TYR* 3.3 8.6 + - - +
336A GLY 3.1 16.1 + - - -
385A CYS* 3.5 25.3 - - - +
393A ARG* 4.0 16.2 - - + -
394A PRO* 3.5 28.0 - - + +
395A SER* 4.9 2.7 - - - -
396A PHE* 3.9 23.8 - - + -
399A ILE* 4.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ALA 5.0 2.0 + - - -
315A TRP 3.7 17.1 + - - -
316A MET 3.5 9.1 + - - -
317A ALA* 3.7 10.1 - - + -
318A PRO* 3.3 36.8 - - + -
329A GLY 3.1 4.6 + - - -
330A SER 3.1 9.1 + - - +
332A VAL* 1.3 73.1 - - - +
334A SER* 1.3 64.1 + - - +
336A GLY* 2.9 16.5 + - - -
337A VAL* 3.2 20.7 + - + +
361A VAL* 4.2 13.4 - - + +
385A CYS 3.6 11.0 + - - +
386A TRP* 3.4 52.2 + + + -
387A ASN 4.1 2.5 - - - -
388A PRO* 4.8 3.1 - - + -
393A ARG* 3.5 36.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG 5.5 3.5 + - - -
268A ASP* 5.8 0.2 - - - -
269A LEU* 3.4 35.2 + - - +
315A TRP* 2.9 30.1 + - - +
316A MET* 4.9 1.6 - - - -
317A ALA 5.0 0.2 + - - -
330A SER 3.0 15.2 + - - -
331A ASP* 3.4 11.9 + - - -
333A TRP* 1.3 78.0 - - - +
335A TYR* 1.3 56.3 + - - +
337A VAL* 3.1 8.7 + - - +
338A LEU* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ALA* 2.6 41.7 + - - +
249A ILE* 3.6 35.0 - - + -
250A ALA* 3.8 8.9 - - + +
269A LEU* 3.6 18.1 - - + +
331A ASP 3.0 8.9 + - - +
332A VAL 3.5 7.6 - - - +
333A TRP 3.2 0.2 - - - -
334A SER* 1.3 73.4 - - - +
336A GLY* 1.3 66.8 + - - +
338A LEU* 3.2 8.5 + - + +
339A LEU* 2.9 52.8 + - + +
381A LEU* 5.4 0.2 - - + -
385A CYS* 4.3 4.9 - - - -
396A PHE* 3.6 23.1 - + + -
399A ILE* 3.9 26.7 - - + -
403A LEU* 3.7 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A VAL 3.1 5.9 + - - -
333A TRP 2.9 10.1 + - - -
335A TYR* 1.3 78.4 - - - +
337A VAL* 1.3 60.0 + - - +
339A LEU* 3.2 11.6 + - - +
340A TRP* 3.1 16.3 + - - +
382A MET* 3.8 4.9 - - - +
385A CYS* 3.7 20.4 - - - -
386A TRP* 3.5 24.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ALA 3.6 22.9 - - - +
315A TRP* 3.2 32.5 - - + +
333A TRP* 3.2 21.5 + - - +
334A SER 3.4 7.0 - - - +
336A GLY* 1.3 74.3 - - - +
338A LEU* 1.3 64.9 + - - +
340A TRP* 3.1 9.5 + - - +
341A GLU* 3.0 20.1 + - - +
348A PRO* 3.9 21.8 - - + -
368A LEU* 4.1 13.2 - - + -
386A TRP* 3.9 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.5 9.9 - - + -
249A ILE* 4.2 20.6 - - + -
269A LEU* 4.0 25.4 - - + -
270A LYS* 3.8 20.6 - - - +
271A SER* 3.3 35.2 - - - +
274A ILE* 4.1 10.8 - - + -
315A TRP* 4.7 0.2 - - - +
334A SER 3.0 11.5 + - - +
335A TYR* 3.2 13.7 + - + +
337A VAL* 1.3 76.0 - - - +
339A LEU* 1.3 64.7 + - - +
341A GLU* 2.8 23.2 + - + +
342A LEU* 2.9 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ALA* 3.6 31.6 - - + -
335A TYR* 2.9 45.4 + - + +
336A GLY* 3.3 11.0 - - - +
338A LEU* 1.3 76.5 - - - +
340A TRP* 1.3 57.3 + - - +
342A LEU* 3.4 13.1 + - + +
343A LEU* 3.0 32.4 + - - +
378A PHE* 4.0 18.9 - - + -
381A LEU* 3.9 30.7 - - + -
382A MET* 3.9 22.7 - - + +
385A CYS* 4.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLY 3.1 11.3 + - - +
337A VAL* 3.1 17.9 + - - +
339A LEU* 1.3 75.6 - - - +
341A GLU* 1.3 60.8 + - - +
343A LEU* 3.4 2.2 + - - +
344A THR* 2.9 65.6 + - + +
346A GLU* 3.4 32.3 - - + -
347A VAL 4.7 1.6 - - - -
348A PRO* 3.8 28.7 - - + -
349A PHE 5.4 0.7 - - - -
368A LEU* 3.7 23.5 - - + +
369A PRO* 2.9 43.7 + - + -
371A PRO* 4.5 3.8 - - + -
382A MET* 4.0 15.2 - - - -
386A TRP* 4.0 20.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ASN* 4.6 3.8 - - - +
232A LEU* 3.8 18.0 - - + +
271A SER* 2.4 40.7 + - - -
315A TRP* 2.9 38.5 + - - +
337A VAL 3.0 16.1 + - - +
338A LEU* 2.8 12.1 + - + +
340A TRP* 1.3 77.0 - - + +
342A LEU* 1.3 59.1 + - - +
344A THR* 4.2 0.4 - - - -
345A GLY* 2.8 29.7 + - - -
346A GLU 4.1 13.6 - - - +
347A VAL* 5.4 1.7 - - - +
348A PRO* 4.0 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.0 17.9 - - + -
232A LEU* 3.8 31.4 - - + +
236A ARG* 5.0 3.6 - - - -
237A ILE* 3.7 12.2 - - + +
242A LEU* 3.2 31.8 - - + +
245A TRP* 4.3 16.2 - - + -
246A ALA* 4.1 31.4 - - + +
249A ILE* 4.5 8.5 - - + -
338A LEU* 2.9 19.4 + - + +
339A LEU* 3.5 23.3 - - + +
340A TRP 3.2 0.2 - - - -
341A GLU* 1.3 79.5 - - - +
343A LEU* 1.3 60.2 + - - +
345A GLY* 4.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ARG* 3.2 23.9 + - - -
242A LEU* 3.3 38.1 - - + +
339A LEU 3.0 13.0 + - - +
340A TRP* 3.9 4.3 - - - +
342A LEU* 1.3 78.9 - - - +
344A THR* 1.3 64.2 + - + +
371A PRO* 4.5 7.7 - - + +
374A CYS* 4.1 21.1 - - + -
375A PRO* 5.0 7.4 - - + -
378A PHE* 3.6 26.9 - - + -
382A MET* 3.1 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ARG* 3.1 28.4 + - - +
340A TRP* 2.9 48.7 + - + +
343A LEU* 1.3 80.3 - - + +
345A GLY* 1.3 60.6 + - - +
346A GLU* 3.0 36.6 + - - +
369A PRO 5.4 0.2 - - - +
371A PRO* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 3.5 30.6 - - - +
233A SER* 3.9 13.2 - - - +
234A GLY 5.5 1.1 - - - +
236A ARG* 4.1 7.1 - - - +
341A GLU* 2.8 22.0 + - - -
342A LEU 4.3 1.9 + - - -
343A LEU 3.8 0.6 - - - -
344A THR* 1.3 71.0 - - - +
346A GLU* 1.3 63.7 + - - +
347A VAL* 5.8 0.5 - - - +
350A ARG* 5.4 0.7 + - - -
----------------------------------------------------------
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