Contacts of the helix formed by residues 303 - 316 (chain A) in PDB entry 5TE0
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 ASP 303 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LYS* 4.0 8.9 - - + +
245A ILE* 3.7 7.0 - - - -
301A ARG 3.8 0.4 + - - -
302A PRO* 1.3 74.9 - - - +
304A ILE* 1.3 67.2 + - + +
305A TYR* 3.3 12.1 + - - +
306A GLN* 2.9 34.8 + - - +
307A VAL* 3.0 21.0 + - - +
323A ASN* 4.7 0.5 - - - +
325A GLN* 3.6 18.9 + - + +
327A SER* 2.6 27.8 + - - -
402A PEG 4.7 2.2 + - - +
405A GOL 3.4 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A CYS* 3.7 33.7 - - - +
162A VAL* 4.0 7.2 - - + -
163A ALA* 3.7 24.5 - - + +
166A HIS* 4.0 15.3 + - + +
167A GLN* 3.6 27.4 - - + +
245A ILE* 3.4 15.6 - - + +
248A LEU* 3.6 30.7 - - + -
303A ASP* 1.3 77.8 - - + +
305A TYR* 1.4 61.3 + - - +
307A VAL* 4.5 3.6 - - + -
308A SER* 2.9 42.5 + - - +
321A ILE* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLN* 4.2 2.9 - - - +
303A ASP* 3.2 10.8 + - - +
304A ILE* 1.4 81.3 - - - +
306A GLN* 1.4 60.4 + - + +
308A SER* 3.3 1.2 + - - -
309A TYR* 2.8 50.7 + + - +
319A CYS* 4.5 11.2 - - + -
321A ILE* 3.2 36.8 - - + -
322A PRO 3.7 16.8 - - - +
323A ASN* 3.3 48.3 + - + +
324A VAL 5.0 0.2 - - - +
325A GLN 6.0 0.2 - - - +
327A SER 4.3 2.0 - - - -
329A ILE* 3.5 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A TYR* 3.3 26.1 + - - +
302A PRO* 3.2 6.4 - - + +
303A ASP* 2.9 38.9 + - - +
305A TYR* 1.4 77.9 - - + +
307A VAL* 1.3 64.6 + - - +
309A TYR* 3.4 5.7 + - - +
310A PHE* 3.2 23.0 - - - -
327A SER* 3.5 20.9 - - - -
328A PRO* 2.7 38.8 + - - +
329A ILE* 4.4 7.2 - - + -
330A PRO* 4.8 1.0 - - - +
402A PEG 3.0 32.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PHE* 3.7 30.1 - - + -
159A CYS* 3.9 7.2 - - - -
245A ILE* 3.8 19.3 - - + -
248A LEU* 4.8 0.7 - - + -
289A LEU* 3.9 9.2 - - + +
292A TYR* 4.7 2.9 - - + -
293A MET* 3.6 37.2 - - + -
302A PRO* 3.9 9.6 - - + -
303A ASP 3.0 19.7 + - - +
304A ILE* 3.8 9.9 - - + +
306A GLN* 1.3 73.7 - - - +
308A SER* 1.3 58.9 + - - +
310A PHE* 3.2 6.1 + - - +
311A SER* 2.9 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A CYS* 3.4 23.0 - - - +
304A ILE* 2.9 24.5 + - - +
305A TYR 3.6 3.1 - - - -
307A VAL* 1.3 71.2 - - - +
309A TYR* 1.3 68.2 + - - +
311A SER* 3.5 9.2 - - - -
312A PHE* 2.9 33.5 + - - +
319A CYS* 3.8 7.2 - - - -
321A ILE* 3.5 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A TYR* 2.8 38.2 + + + +
306A GLN 3.5 10.3 - - - +
308A SER* 1.3 72.5 - - - +
310A PHE* 1.3 77.3 + + - +
312A PHE* 4.3 1.2 - - - +
313A LYS* 3.1 51.7 + - + +
319A CYS* 3.8 17.5 - - + +
329A ILE* 3.5 46.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 4.1 17.0 - - + +
292A TYR* 3.7 19.7 - + - -
306A GLN 3.2 21.5 - - - -
307A VAL 3.2 6.4 + - - +
309A TYR* 1.3 93.1 - + - +
311A SER* 1.3 60.9 + - - +
313A LYS* 3.4 14.7 + - + +
314A LEU* 3.0 29.3 + - - +
329A ILE* 3.8 12.6 - - + -
330A PRO* 3.7 34.8 - - + -
331A ALA 5.9 1.3 - - - -
332A LYS 6.1 0.2 - - - -
333A LEU* 3.6 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.9 6.2 - - - +
155A PHE* 3.8 26.9 - - - -
156A CYS* 3.5 21.3 - - - -
159A CYS* 3.8 7.6 - - - -
289A LEU* 3.9 15.4 - - - +
307A VAL 2.9 12.9 + - - -
308A SER* 3.2 16.8 + - - -
310A PHE* 1.3 73.1 - - - +
312A PHE* 1.3 65.5 + - - +
314A LEU* 3.3 4.4 + - - +
315A LEU* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A CYS* 3.6 45.1 - - + -
159A CYS* 4.4 4.0 - - + -
160A GLU* 3.8 20.4 - - + -
308A SER* 2.9 39.0 + - - +
311A SER* 1.3 83.8 + - - +
313A LYS* 1.4 56.0 + - - +
315A LEU* 3.2 5.0 + - + +
316A LYS 2.9 23.9 + - - -
317A LYS* 3.0 37.2 + - + +
318A GLU 3.6 14.1 - - - -
319A CYS* 3.7 12.6 - - + -
320A PRO* 3.5 30.3 - - + -
321A ILE* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASP* 5.1 9.3 + - - -
309A TYR* 3.1 47.9 + - + +
310A PHE* 3.6 16.7 - - + +
311A SER 3.3 0.2 - - - -
312A PHE* 1.4 75.5 - - - +
314A LEU* 1.3 56.6 + - - +
316A LYS* 3.0 23.6 + - - +
317A LYS 4.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 3.6 22.9 - - - +
152A LEU* 3.7 24.5 - - + +
283A SER* 3.8 3.4 - - - +
285A ASP* 3.6 33.0 - - + +
286A MET* 3.6 35.0 - - + +
289A LEU* 4.9 6.7 - - + -
310A PHE 3.0 17.2 + - - +
311A SER* 3.3 5.1 + - - +
313A LYS* 1.3 75.6 - - - +
315A LEU* 1.3 58.8 + - - +
316A LYS* 3.4 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASN* 3.3 34.0 + - - +
152A LEU* 3.9 32.9 - - + +
153A GLN* 4.4 11.4 - - + +
156A CYS* 3.7 26.9 - - + -
311A SER 3.0 16.4 + - - +
312A PHE* 3.2 7.8 + - + +
314A LEU* 1.3 73.4 - - - +
316A LYS* 1.4 70.0 + - - +
317A LYS* 4.5 15.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
312A PHE 2.9 3.4 + - - -
313A LYS* 3.0 18.2 + - - +
314A LEU 4.0 7.0 - - - +
315A LEU* 1.4 80.3 - - - +
317A LYS* 1.3 58.8 + - - +
----------------------------------------------------------
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