Contacts of the helix formed by residues 306 - 321 (chain A) in PDB entry 5K9S
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 GLU 306 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PRO* 4.4 19.4 - - + +
304A ALA* 3.5 9.2 - - - +
305A THR* 1.3 89.8 + - - +
307A LEU* 1.3 67.7 + - - +
308A PRO* 4.0 10.5 - - + -
309A ILE* 2.9 41.3 + - + +
310A VAL* 3.1 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A THR 3.4 6.0 + - - +
306A GLU* 1.3 71.0 - - - +
308A PRO* 1.3 68.1 - - + +
310A VAL* 4.4 9.2 - - + +
311A THR* 2.8 44.0 + - - +
346A ASN* 4.8 7.9 - - - +
348A LYS* 3.8 32.1 - - + +
351A ILE* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ALA* 3.4 18.1 - - + +
273A TRP* 4.4 3.3 + - - -
306A GLU* 3.3 12.3 - - + -
307A LEU* 1.3 94.5 - - + +
309A ILE* 1.3 57.8 + - + +
311A THR* 4.7 2.2 - - - +
312A PRO* 3.1 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PRO* 3.8 31.2 - - + +
268A LEU* 4.0 20.6 - - + -
269A ALA* 4.2 9.0 - - + +
272A CYS* 4.5 3.8 - - - -
301A LEU* 3.5 44.6 - - + +
304A ALA* 4.1 7.4 - - + -
306A GLU* 2.9 37.0 + - + +
308A PRO* 1.3 81.8 - - + +
310A VAL* 1.3 65.2 + - - +
311A THR 3.3 0.4 - - - -
312A PRO* 3.2 7.4 - - - +
313A ALA* 3.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU 3.9 11.0 - - - +
302A LEU* 3.6 20.4 - - + +
304A ALA* 3.3 27.8 - - + +
305A THR 5.0 0.7 - - - -
306A GLU 3.1 13.7 + - - +
307A LEU* 3.2 10.7 + - + +
309A ILE* 1.3 76.7 - - - +
311A THR* 1.3 58.9 + - - +
313A ALA* 3.8 1.5 - - - +
314A LEU* 2.8 31.7 + - + +
343A LEU* 3.8 29.2 - - + -
346A ASN* 5.7 2.9 - - - +
351A ILE* 4.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A TRP* 4.3 18.8 - - + -
307A LEU* 2.8 24.2 + - - +
308A PRO* 4.9 1.8 - - - -
310A VAL* 1.3 77.3 - - - +
312A PRO* 1.3 67.3 - - + +
314A LEU* 3.3 2.8 + - - +
315A ARG* 2.9 35.4 + - - +
348A LYS* 5.2 3.2 - - - +
350A ASN* 4.1 20.9 + - - +
351A ILE* 3.7 20.3 - - + +
354A GLU* 5.7 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ALA 3.9 4.5 - - - +
272A CYS* 3.5 22.7 - - + +
273A TRP* 3.5 45.8 - - + +
276A SER* 3.8 3.8 - - - -
308A PRO 3.1 26.2 - - - +
309A ILE* 3.2 14.6 - - - +
311A THR* 1.3 94.0 - - + +
313A ALA* 1.3 54.3 + - - +
315A ARG* 3.3 8.5 + - + +
316A ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A CYS* 3.9 18.5 - - - +
298A LEU* 4.0 23.9 - - + +
301A LEU 4.1 4.0 - - - +
302A LEU* 4.0 15.9 - - - +
309A ILE 3.1 19.7 + - - +
310A VAL 3.8 2.2 - - - +
312A PRO* 1.3 77.5 - - - +
314A LEU* 1.3 58.7 + - - +
316A ALA* 3.1 6.6 + - - +
317A ILE* 2.9 32.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
302A LEU* 3.4 22.6 - - + +
310A VAL* 2.8 22.0 + - + +
311A THR 3.7 2.7 - - - +
313A ALA* 1.3 71.3 - - - +
315A ARG* 1.3 58.9 + - - +
317A ILE* 4.5 3.1 - - + -
318A GLY* 2.9 26.3 + - - -
340A PHE* 4.3 19.3 - - + -
343A LEU* 4.4 7.4 - - + -
351A ILE* 3.8 36.1 - - + +
354A GLU* 3.6 32.4 - - + +
355A ALA* 4.0 9.9 - - + +
358A THR* 4.2 16.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A TRP* 4.3 25.6 - - + -
276A SER* 3.8 19.3 + - - +
311A THR* 2.9 21.5 + - - +
312A PRO* 3.5 12.3 - - + +
313A ALA 3.3 0.2 - - - -
314A LEU* 1.3 77.0 - - - +
316A ALA* 1.3 61.4 + - - +
318A GLY* 3.3 1.1 + - - -
319A ASN* 3.0 33.8 + - - +
350A ASN* 5.3 4.8 + - - +
354A GLU* 3.5 25.0 + - - +
357A TRP* 5.2 0.7 - - - -
15C ARG* 3.1 41.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A CYS 4.6 0.7 - - - +
275A ILE* 4.1 17.3 - - + -
276A SER* 3.8 27.3 - - - +
279A THR* 3.9 3.7 + - - +
298A LEU* 4.1 16.2 - - + -
312A PRO 2.9 14.2 + - - +
313A ALA 3.1 7.6 + - - +
315A ARG* 1.3 73.1 - - - +
317A ILE* 1.3 67.1 + - - +
319A ASN* 3.2 3.6 + - - +
320A ILE* 3.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 4.6 3.1 - - + -
298A LEU* 3.8 33.9 - - + +
299A VAL* 4.2 17.3 - - + -
302A LEU* 4.5 19.5 - - + -
313A ALA 2.9 21.4 + - - +
314A LEU* 3.9 6.3 - - + +
316A ALA* 1.3 75.5 - - - +
318A GLY* 1.3 64.3 + - - +
320A ILE* 3.1 6.6 + - + +
321A VAL* 3.1 22.7 + - - +
331A VAL* 3.7 35.2 - - + -
336A ALA* 4.9 0.2 - - + -
340A PHE* 4.7 9.6 - - + -
358A THR* 4.4 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU 2.9 15.7 + - - -
315A ARG 3.7 1.8 - - - -
317A ILE* 1.3 79.5 - - - +
319A ASN* 1.3 62.0 + - - +
321A VAL* 3.4 15.3 - - - +
322A THR* 3.4 11.3 - - - +
357A TRP* 3.7 17.2 - - - -
358A THR* 3.4 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 2.9 31.5 + - - +
279A THR* 3.2 31.1 + - - +
280A ASP* 3.7 19.1 - - - +
286A ILE* 3.4 7.3 - - - +
315A ARG* 3.0 24.5 + - - +
316A ALA 3.2 2.0 + - - +
318A GLY* 1.3 76.2 - - - +
320A ILE* 1.3 61.9 + - - +
322A THR* 2.5 32.6 + - - +
357A TRP* 4.2 3.6 - - - -
15C ARG* 3.9 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A THR* 3.9 23.8 - - + -
286A ILE* 4.2 15.1 - - + +
289A VAL* 5.1 3.6 - - + -
290A VAL* 4.0 21.1 - - + -
295A VAL* 4.4 14.8 - - + -
298A LEU* 3.9 26.2 - - + -
316A ALA 3.0 17.8 + - - +
317A ILE* 3.1 10.3 + - + +
319A ASN* 1.3 76.0 - - - +
321A VAL* 1.3 58.0 + - - +
323A GLY* 3.1 19.6 + - - -
327A GLN* 3.9 21.8 - - + +
328A THR 4.5 0.5 + - - -
331A VAL* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 3.1 15.9 + - + +
318A GLY 3.4 14.4 - - - +
320A ILE* 1.3 73.4 - - - +
322A THR* 1.3 59.1 + - - +
323A GLY 3.2 0.9 - - - -
328A THR* 3.7 26.7 - - + -
331A VAL* 3.8 33.2 - - + -
358A THR* 3.8 30.7 - - + +
361A ASN* 3.6 15.0 - - + +
362A ILE* 4.2 10.5 - - + -
11C LYS* 3.1 24.1 + - - +
----------------------------------------------------------
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