Contacts of the helix formed by residues 313 - 324 (chain A) in PDB entry 1TW2
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 313 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ASP 3.1 17.0 - - - +
288A HIS* 3.8 24.0 - - + +
291A SER* 4.4 6.7 - - - -
296A PHE* 4.5 4.7 - - + -
312A ARG* 1.3 77.2 - - - +
314A ARG* 1.3 66.3 + - - +
315A GLU* 3.5 15.7 + - - +
316A LYS* 3.0 36.5 + - - +
317A TRP* 3.0 22.1 + - - -
69B ARG* 4.1 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASP* 2.6 43.9 + - - -
286A ASP* 3.1 18.8 + - - +
287A LEU* 3.8 39.9 - - + +
313A THR* 1.3 71.3 - - - +
315A GLU* 1.3 66.1 + - - +
317A TRP* 3.1 19.8 + - - +
318A ASP* 3.4 15.1 + - - +
328A VAL* 5.4 3.6 - - - -
331A VAL* 3.6 43.6 + - - +
333A GLN* 4.4 13.1 - - - +
346A LEU* 5.1 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.1 11.0 - - - +
288A HIS* 3.2 37.9 + - + +
289A GLU* 4.7 6.1 - - - +
313A THR* 3.5 11.5 + - - +
314A ARG* 1.3 82.5 + - + +
316A LYS* 1.3 64.0 + - + +
317A TRP 3.2 0.7 + - - -
318A ASP* 3.3 24.4 + - - +
319A GLY* 3.7 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A HIS* 5.5 5.6 - - - -
311A LEU 5.3 3.6 + - - +
312A ARG* 4.1 20.9 - - + -
313A THR* 3.0 41.1 + - - +
315A GLU* 1.3 77.1 - - + +
317A TRP* 1.3 61.2 + - - +
318A ASP 3.4 0.2 - - - -
319A GLY* 3.4 3.9 + - - +
320A LEU* 3.4 27.0 + - + +
65B LEU* 5.3 7.8 - - - +
69B ARG* 3.8 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 3.6 41.7 - - + -
266A LEU* 4.8 4.5 - - + -
281A ILE* 3.8 25.1 - - + -
283A GLU* 3.5 21.1 - - - -
284A ARG 4.5 2.5 + - - -
285A ASP* 3.5 21.4 - - + +
312A ARG* 3.3 40.2 + - + +
313A THR 3.0 21.7 + - - -
314A ARG* 3.1 9.8 + - - +
316A LYS* 1.3 74.8 - - - +
318A ASP* 1.3 59.1 + - - +
320A LEU* 3.5 23.4 + - + +
321A ALA* 2.9 31.1 + - - +
328A VAL* 4.0 9.4 - - + +
346A LEU* 3.7 30.0 - - + +
348A LEU* 5.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ARG* 3.4 16.2 + - - +
315A GLU* 3.3 15.2 + - - +
317A TRP* 1.3 77.9 - - - +
319A GLY* 1.3 61.2 + - - +
321A ALA* 3.4 6.6 + - - +
322A ALA* 3.1 25.6 + - - +
328A VAL* 3.8 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLU 3.7 4.8 + - - -
316A LYS* 3.4 8.1 + - - -
317A TRP 3.3 0.8 - - - -
318A ASP* 1.3 78.2 - - - +
320A LEU* 1.3 58.1 + - - +
322A ALA* 3.4 5.4 + - - +
323A SER* 2.9 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASP* 3.9 28.9 - - + +
262A ALA* 4.3 15.5 - - + -
263A VAL* 4.2 17.1 - - + +
266A LEU* 3.9 11.4 - - + +
312A ARG* 3.3 40.4 - - - +
316A LYS* 3.4 14.5 + - + +
317A TRP* 3.9 24.2 - - + +
319A GLY* 1.3 72.8 - - - +
321A ALA* 1.3 67.5 + - - +
322A ALA 3.4 0.2 + - - -
323A SER* 3.5 8.8 + - - +
324A ALA* 3.4 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 4.5 3.7 - - - +
317A TRP* 2.9 19.3 + - - +
318A ASP* 3.5 5.8 - - - +
320A LEU* 1.3 77.3 - - - +
322A ALA* 1.3 56.7 + - - +
324A ALA* 3.1 13.0 + - - -
325A GLY 3.2 0.2 + - - -
326A LEU* 2.9 45.0 + - - +
327A VAL* 4.4 0.4 - - - -
328A VAL* 3.9 21.5 - - + +
348A LEU* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASP 3.1 17.7 + - - +
319A GLY* 3.9 4.7 - - - +
320A LEU 3.2 0.2 - - - -
321A ALA* 1.3 71.1 - - - +
323A SER* 1.3 59.2 + - - +
324A ALA 2.9 4.5 - - - -
325A GLY* 2.9 19.3 + - - +
326A LEU 3.5 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A VAL* 3.7 30.3 - - - +
267A THR* 4.5 1.4 + - - -
319A GLY 2.9 18.7 + - - -
320A LEU* 3.7 7.9 - - - +
322A ALA* 1.3 74.5 - - - +
324A ALA* 1.3 56.7 + - - +
325A GLY 4.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A VAL* 4.2 4.3 - - + +
266A LEU* 3.7 25.4 - - + -
267A THR* 3.7 25.5 + - - +
270A ALA* 4.2 12.6 - - - +
320A LEU 3.4 8.4 + - - +
321A ALA 3.1 9.3 + - - +
322A ALA 2.9 0.8 - - - -
323A SER* 1.3 78.8 - - - +
325A GLY* 1.3 61.6 + - - +
326A LEU* 3.8 13.4 - - + +
----------------------------------------------------------
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