Contacts of the helix formed by residues 294 - 301 (chain D) in PDB entry 1T5A
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 ARG 294 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ARG* 2.7 43.6 + - + +
343B ALA 4.2 0.6 - - - +
346B SER* 3.6 10.1 + - - -
292D VAL* 2.9 23.4 + - + +
293D ALA* 1.3 69.2 - - - +
295D GLY* 1.3 54.1 + - - +
297D LEU* 4.0 8.1 - - - -
298D GLY* 2.6 31.0 + - - -
306D VAL* 4.1 17.9 - - + +
310D GLN* 3.0 25.4 + - - +
326D CYS* 3.6 16.6 - - - -
327D ALA 2.8 21.3 + - - +
328D THR 3.1 18.5 + - - -
330D MET* 3.6 11.1 - - - +
347D ASP* 2.4 47.3 + - - -
533D OXL 3.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ARG* 2.8 30.7 + - - -
178D ASP* 4.5 9.2 - - - -
294D ARG* 1.3 72.9 - - - +
296D ASP* 1.3 59.9 + - - -
298D GLY 3.2 1.7 + - - -
299D ILE* 3.4 7.1 - - - +
328D THR* 3.2 21.3 - - - +
533D OXL 2.9 18.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ASN* 3.4 21.1 + - - +
244D PHE* 3.5 20.5 - - + -
272D GLU* 2.4 45.3 - - + +
293D ALA 3.7 0.2 + - - -
295D GLY* 1.3 71.2 - - - +
297D LEU* 1.3 62.3 + - - +
299D ILE* 3.1 8.7 + - - +
300D GLU* 2.8 31.9 + - - +
533D OXL 2.4 18.1 + - - +
604D MG 2.6 10.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ILE 4.1 9.4 - - - +
272D GLU 3.3 23.9 + - - +
273D ASN 3.8 17.7 - - - +
277D VAL* 3.9 14.4 - - + -
292D VAL* 4.3 12.1 - - + -
293D ALA 3.3 15.9 + - - +
294D ARG* 3.2 4.4 + - - +
296D ASP* 1.3 79.1 - - - +
298D GLY* 1.3 57.6 + - - +
299D ILE 3.1 0.2 + - - -
300D GLU* 4.3 0.2 - - - -
301D ILE* 2.9 52.2 + - + +
306D VAL* 4.4 13.5 - - + -
309D ALA* 4.1 12.8 - - + -
313D MET* 4.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ARG* 3.4 26.1 + - - -
294D ARG 2.6 14.3 + - - -
295D GLY 3.2 0.2 + - - -
296D ASP 3.2 0.2 - - - -
297D LEU* 1.3 73.8 - - - +
299D ILE* 1.3 63.2 + - - +
301D ILE 3.2 10.9 - - - +
303D ALA* 4.0 13.8 + - - +
306D VAL* 3.8 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ARG* 5.9 3.6 - - + -
342B ARG* 3.4 18.8 - - - +
175D TYR* 3.9 27.4 - - + -
178D ASP* 3.6 10.5 - - - +
179D GLY* 3.4 32.8 - - - +
210D ASN* 3.3 39.0 - - + +
212D PRO* 3.6 13.9 - - - +
295D GLY 3.4 15.3 - - - +
296D ASP* 3.6 5.4 - - - +
297D LEU 3.0 0.8 - - - -
298D GLY* 1.3 79.9 - - - +
300D GLU* 1.3 65.9 + - - +
301D ILE* 3.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ASN* 2.7 32.8 + - - -
211D LEU 3.9 9.4 - - - +
212D PRO* 4.1 21.9 - - + +
213D GLY 4.8 3.3 + - - -
214D ALA 5.4 1.6 - - - +
244D PHE* 5.0 2.1 - - - -
272D GLU 3.5 10.4 - - - +
273D ASN* 3.5 30.7 - - + +
274D HIS* 4.0 9.8 + - + +
296D ASP 2.8 13.9 + - - +
297D LEU* 3.9 2.5 - - - +
299D ILE* 1.3 80.0 - - - +
301D ILE* 1.3 64.1 + - + +
302D PRO* 4.9 0.3 - - - +
707D GOL 2.7 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.9 28.0 - - + -
274D HIS* 4.1 38.6 - - + +
297D LEU* 2.9 38.4 + - + +
298D GLY 3.2 17.2 - - - +
299D ILE 4.1 3.0 - - - -
300D GLU* 1.3 81.7 - - + +
302D PRO* 1.3 79.5 - - + +
305D LYS* 4.0 29.2 - - + +
306D VAL* 4.4 5.2 - - + +
309D ALA* 4.6 2.2 - - + -
----------------------------------------------------------
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