Contacts of the helix formed by residues 302 - 320 (chain A) in PDB entry 1TQ6
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 LEU 302 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A PHE* 4.2 26.5 - - + +
301A LEU* 1.3 73.2 - - - +
303A ASP* 1.3 57.0 + - - +
304A SER* 3.9 15.9 - - - +
305A ASP* 2.7 40.8 + - - +
306A LEU* 2.8 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU 4.0 0.4 + - - -
302A LEU* 1.3 68.3 - - - +
304A SER* 1.3 58.2 + - - +
305A ASP 2.8 10.1 + - - -
306A LEU* 3.9 21.8 - - - +
307A GLU* 3.1 32.2 + - + +
310A LYS* 5.5 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.0 15.8 - - - +
303A ASP* 1.3 78.0 - - - +
305A ASP* 1.3 62.9 + - - +
307A GLU* 4.5 4.9 - - - +
308A THR* 3.1 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A THR* 6.0 0.5 - - - +
300A PHE 4.5 1.7 - - - +
301A LEU* 3.9 25.1 - - + +
302A LEU* 2.7 39.6 + - - +
304A SER* 1.3 86.4 + - - +
306A LEU* 1.3 63.0 + - - +
307A GLU 3.0 2.8 + - - -
308A THR* 3.1 8.0 + - - -
309A LEU* 2.9 26.9 + - - +
387A ILE* 4.4 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 3.4 31.2 - - + +
302A LEU 2.8 34.8 + - - +
303A ASP* 3.2 20.8 + - - +
305A ASP* 1.3 74.9 - - - +
307A GLU* 1.3 57.3 + - - +
309A LEU* 3.5 8.8 + - - +
310A LYS* 2.8 53.4 + - - +
351A PHE* 4.5 1.4 - - + -
359A ILE* 4.1 33.2 - - + -
360A GLN* 3.5 17.3 - - - +
363A LEU* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASP* 3.1 19.6 + - + +
304A SER* 4.7 4.9 - - - +
305A ASP 3.0 0.6 - - - -
306A LEU* 1.3 73.3 - - - +
308A THR* 1.3 58.8 + - - +
309A LEU 3.0 1.3 - - - -
310A LYS* 2.6 61.9 + - - +
311A LYS* 2.8 45.1 + - - +
314A LYS* 5.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A SER 3.1 18.2 + - - -
305A ASP* 3.1 9.4 + - - -
307A GLU* 1.3 76.4 - - - +
309A LEU* 1.3 56.2 + - - +
311A LYS* 3.4 16.5 + - + +
312A SER* 2.8 33.4 + - - +
387A ILE* 3.8 23.8 - - + -
388A PHE* 6.2 0.4 - - + -
391A LYS* 4.4 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 4.1 17.0 - - + -
305A ASP 2.9 20.1 + - - +
306A LEU* 3.7 5.4 - - - +
308A THR* 1.3 76.9 - - - +
310A LYS* 1.3 59.4 + - - +
311A LYS 3.3 0.2 - - - -
312A SER* 3.8 2.8 - - - -
313A MET* 3.1 26.9 + - - +
351A PHE* 3.9 6.9 - - + -
363A LEU* 4.1 7.4 - - + -
387A ILE* 3.4 41.5 - - + +
390A LEU* 3.3 39.3 - - + -
391A LYS* 4.2 10.5 - - + -
394A PHE* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASP* 5.5 2.8 + - - +
306A LEU* 2.8 46.0 + - - +
307A GLU* 2.6 46.2 + - - +
309A LEU* 1.3 70.7 - - - +
311A LYS* 1.3 63.8 + - + +
313A MET* 3.4 2.6 + - - +
314A LYS* 3.1 43.6 + - - +
351A PHE* 3.7 37.9 - - + -
359A ILE* 5.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 2.8 48.2 + - - +
308A THR* 3.6 13.5 + - - +
310A LYS* 1.3 74.9 - - + +
312A SER* 1.3 66.4 + - - +
314A LYS* 3.2 15.2 + - + +
315A PHE* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A THR* 2.8 24.4 + - - +
309A LEU* 3.8 9.0 - - - -
310A LYS 3.3 0.2 - - - -
311A LYS* 1.3 76.5 - - - +
313A MET* 1.3 57.0 + - - +
315A PHE* 3.2 7.3 + - - +
316A TYR* 3.0 46.3 + - - -
391A LYS* 3.3 38.4 + - - -
394A PHE* 5.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU 3.1 19.0 + - - +
310A LYS 3.7 4.7 - - - +
311A LYS 3.3 0.2 - - - -
312A SER* 1.3 75.6 - - - +
314A LYS* 1.3 64.4 + - + +
316A TYR* 4.6 2.9 - - - -
317A ARG* 3.0 42.3 + - - +
347A SER* 4.0 17.9 - - - +
350A VAL* 3.5 36.8 - - + -
351A PHE* 3.8 17.5 - - + -
394A PHE* 3.6 39.2 - - + -
397A MET* 4.2 3.8 - - - -
398A VAL* 4.1 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 5.9 0.4 + - - -
310A LYS* 3.1 29.8 + - - +
311A LYS* 3.2 13.4 + - + +
313A MET* 1.3 77.8 - - + +
315A PHE* 1.3 63.4 + - - +
317A ARG* 3.5 7.3 + - - +
318A THR* 3.1 27.4 + - - -
323A ASP* 5.0 1.1 - - - +
324A GLU* 5.7 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASN* 5.6 2.2 - - + -
119A ILE* 4.6 14.1 - - + -
257A HIS* 5.0 8.5 - + - -
261A VAL* 5.0 10.1 - - + -
278A LEU* 4.3 19.3 - - + -
281A ARG* 5.6 5.4 - - - -
311A LYS 3.1 12.4 + - - +
312A SER* 3.5 9.4 - - - +
314A LYS* 1.3 74.2 - - - +
316A TYR* 1.3 85.0 + + - +
318A THR* 3.1 9.0 + - + -
319A VAL* 2.8 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 4.5 20.9 - - + -
281A ARG* 6.4 1.3 - - - -
282A ILE* 3.5 28.4 - - + +
285A GLU* 4.9 1.7 + - - -
312A SER* 3.0 30.3 + - - +
313A MET* 4.0 3.6 - - - +
315A PHE* 1.3 100.2 - + - +
317A ARG* 1.3 65.9 + - - +
319A VAL* 3.1 5.2 + - - -
320A PHE* 3.0 31.6 + - + -
391A LYS* 3.5 39.2 - - + +
394A PHE* 4.0 13.7 - - + -
395A LEU* 3.9 23.8 - - + -
398A VAL* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A MET* 3.0 47.9 + - - +
314A LYS* 3.8 6.7 - - - +
316A TYR* 1.3 76.5 - - - +
318A THR* 1.3 62.5 + - - +
320A PHE 3.4 0.3 + - - -
321A GLY 3.0 4.3 + - - -
322A VAL* 2.9 58.1 + - + +
323A ASP* 3.3 14.5 - - + +
324A GLU* 3.0 29.2 + - - +
327A LEU* 3.6 11.1 - - - +
342A GLU* 4.5 2.8 + - - -
347A SER* 4.0 21.6 + - - +
348A PRO* 3.2 43.6 + - - +
398A VAL* 4.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASN* 3.1 53.2 + - + +
314A LYS 3.1 18.1 + - - -
315A PHE* 3.1 8.7 + - + +
317A ARG* 1.3 78.3 - - - +
319A VAL* 1.3 64.7 + - + +
321A GLY* 3.1 12.6 + - - -
323A ASP* 3.3 26.6 + - - +
324A GLU* 5.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASN* 5.5 1.6 - - + -
119A ILE* 5.1 4.3 - - + -
261A VAL* 3.7 32.8 - - + +
265A ASN* 3.4 4.0 + - - -
274A LYS* 2.6 40.0 + - + +
278A LEU* 4.4 7.2 - - + -
315A PHE* 2.8 55.2 + - + +
316A TYR* 3.1 8.9 + - - +
318A THR* 1.3 80.8 - - + +
320A PHE* 1.3 70.9 + - + +
321A GLY 3.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASN* 3.3 21.9 + - - +
271A ILE* 3.5 39.5 - - + -
274A LYS* 3.8 22.7 - - + -
275A ARG 3.9 7.4 - - - -
278A LEU* 3.9 13.7 - - + -
316A TYR* 3.0 28.0 + - - -
317A ARG 4.3 0.4 - - - +
319A VAL* 1.3 80.0 - - + +
321A GLY* 1.3 65.0 + - - +
322A VAL* 3.4 2.8 + - + +
395A LEU* 3.9 22.4 - - + -
398A VAL* 3.4 26.7 - - + -
399A THR* 3.6 24.2 - - - -
402A ALA* 3.5 25.2 - - + +
----------------------------------------------------------
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