Contacts of the helix formed by residues 298 - 308 (chain A) in PDB entry 2QJK
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 PHE 298 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SMA 3.6 63.4 - - + +
105A PHE* 4.7 0.4 - + - -
140A MET* 3.7 45.5 - - + -
143A ALA* 4.6 1.8 - - + -
144A PHE* 4.5 10.3 - + + -
162A ILE* 5.4 0.7 - - + -
294A PRO* 4.3 10.8 - - + -
295A GLU* 2.4 52.4 + - - +
297A TYR* 1.3 101.9 - + - +
299A LEU* 1.3 63.3 + - - +
300A PRO* 3.3 4.9 - - - -
301A PHE* 2.9 20.7 + + - +
302A TYR* 3.0 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL* 3.7 28.3 - - + -
294A PRO* 3.8 19.1 - - + +
295A GLU 3.3 0.6 + - - -
296A TRP* 3.1 30.5 + - + +
298A PHE* 1.3 74.6 - - - +
300A PRO* 1.3 60.4 - - + +
302A TYR* 2.8 8.8 + - + +
303A ALA* 2.6 34.5 + - - +
377A LEU 4.5 0.9 - - - -
378A THR* 3.6 33.9 - - + +
381A GLY* 4.0 13.7 - - - +
382A ALA* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 5.5 0.7 - - + -
296A TRP 3.7 7.4 - - - +
297A TYR 4.5 4.0 - - - +
298A PHE* 3.3 3.8 - - - +
299A LEU* 1.3 94.8 - - + +
301A PHE* 1.3 76.8 + - + +
303A ALA* 3.0 10.7 + - - +
304A ILE* 3.1 13.6 + - - +
374A PHE* 4.0 31.2 - - + +
377A LEU* 3.6 25.4 - - + +
378A THR* 3.4 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SMA 3.8 23.8 - - + -
109A TYR* 4.0 9.0 - + - -
136A TYR* 3.1 32.8 - + - -
140A MET* 4.8 4.5 - - - -
297A TYR 5.0 2.5 - - - -
298A PHE 2.9 12.0 + - - +
300A PRO* 1.3 86.7 - - + +
302A TYR* 1.3 60.4 + - - +
304A ILE* 3.7 7.9 - - + +
305A LEU 3.2 16.3 + - - -
336A MET* 3.4 25.6 - - + +
339A ALA* 4.5 17.5 - - + -
340A ILE* 3.2 42.2 - - + -
343A MET* 4.8 9.2 - - + -
374A PHE* 4.7 13.0 - + - -
400A TRP* 5.1 9.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SMA 3.3 64.4 - + + +
292A ILE 4.8 4.9 + - - -
293A VAL* 5.4 0.2 - - + -
294A PRO* 3.7 23.9 - - + +
298A PHE 3.0 10.3 + - - +
299A LEU* 2.8 12.9 + - + +
301A PHE* 1.3 76.2 - - - +
303A ALA* 1.3 71.5 + - - +
305A LEU* 3.1 4.9 + - - +
306A ARG* 3.0 46.8 + - - +
381A GLY* 3.2 34.3 - - - -
150F PRO 4.5 3.5 + - - -
151F CYS 2.7 19.1 + - - -
152F HIS* 3.5 15.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU 2.6 10.7 + - - +
300A PRO 3.2 9.4 - - - +
302A TYR* 1.3 79.8 - - - +
304A ILE* 1.3 65.3 + - - +
306A ARG* 2.9 20.4 + - - +
307A ALA* 3.0 13.0 + - - +
377A LEU* 3.4 36.6 - - + +
380A VAL* 4.1 10.1 - - + -
381A GLY* 4.2 6.3 - - - +
393A SER* 4.7 7.5 - - - -
397A SER* 5.0 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
300A PRO 3.1 6.0 + - - +
301A PHE* 3.7 15.0 - - + +
303A ALA* 1.3 77.8 - - - +
305A LEU* 1.3 66.6 + - - +
307A ALA* 3.0 17.2 + - - +
308A PHE* 3.4 14.0 - - + -
335A ALA* 4.0 33.9 - - + +
336A MET* 4.1 4.0 - - - +
339A ALA* 3.7 23.3 - - + -
377A LEU* 3.5 32.9 - - + +
397A SER* 3.7 24.0 - - - +
400A TRP* 4.5 13.9 - - + -
401A PHE* 4.6 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SMA 4.6 5.6 - - + -
165A LEU* 4.0 22.0 - - + -
301A PHE 3.2 10.2 + - - +
302A TYR* 3.1 11.0 + - - +
304A ILE* 1.3 80.5 - - - +
306A ARG* 1.3 63.4 + - - +
307A ALA 3.5 0.3 + - - -
308A PHE 3.8 8.5 + - - +
329A LYS 5.3 0.4 - - - +
332A GLY* 3.5 46.2 - - - +
333A VAL* 3.7 12.3 - - + +
336A MET* 4.1 16.8 - - + -
131F HIS* 4.0 17.4 - - + +
132F LEU* 4.2 2.9 - - + -
152F HIS* 3.7 31.0 - - + +
166F PRO* 5.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 3.0 45.7 + - + +
303A ALA* 2.9 18.7 + - - +
305A LEU* 1.3 73.6 - - - +
307A ALA* 1.3 66.3 + - - +
308A PHE* 3.2 3.6 - - - -
309A THR* 3.9 15.1 - - - +
380A VAL* 2.7 24.2 + - - +
381A GLY* 3.2 11.9 + - - -
383A GLN 2.6 30.6 + - - -
384A GLN* 4.1 14.9 + - - +
385A THR* 4.2 26.6 + - - +
389A TYR* 6.0 0.2 - - - +
393A SER* 6.1 3.3 - - - -
131F HIS* 6.0 0.4 - - - -
151F CYS 5.3 0.2 + - - -
152F HIS* 4.0 33.4 - - + +
153F GLY 5.9 0.2 - - - +
166F PRO* 5.9 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA 3.0 7.8 + - - +
304A ILE 3.0 12.8 + - - +
306A ARG* 1.3 79.3 - - - +
308A PHE* 1.3 62.8 + - + +
309A THR* 3.1 13.2 + - - +
312A VAL* 3.7 10.4 - - - +
390A ASP* 5.2 3.3 - - - +
393A SER* 3.6 25.8 - - - +
394A LEU* 4.2 21.1 - - + +
397A SER* 3.8 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 3.4 25.6 - - + -
305A LEU 3.8 11.8 + - - +
306A ARG 3.2 2.1 - - - +
307A ALA* 1.3 73.8 - - + +
309A THR* 1.3 61.7 + - - +
312A VAL* 4.0 17.3 - - + -
314A VAL* 5.6 4.5 - - + -
315A VAL* 4.1 3.8 - - + -
328A ALA* 4.2 13.8 - - - +
331A PHE* 3.3 38.6 - + + -
332A GLY* 4.5 4.1 - - - -
335A ALA* 3.4 32.5 - - + -
394A LEU* 3.8 23.8 - - + -
397A SER* 4.1 20.0 - - - -
398A ALA* 5.6 0.7 - - - -
401A PHE* 5.3 7.0 - + - -
166F PRO* 4.2 9.0 - - - +
----------------------------------------------------------
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