Contacts of the helix formed by residues 298 - 308 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J PHE* 4.7 0.2 - + - -
140J MET* 3.7 47.1 - - + -
143J ALA* 4.7 1.6 - - + -
144J PHE* 4.5 10.3 - - + -
294J PRO* 4.3 10.8 - - + -
295J GLU* 2.4 44.4 + - - +
297J TYR* 1.3 102.7 - + - +
299J LEU* 1.3 63.8 + - - +
300J PRO* 3.4 4.9 - - - -
301J PHE* 3.0 19.9 + + - +
302J TYR* 3.1 9.9 + - - +
503J SMA 3.4 70.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293J VAL* 3.7 27.8 - - + -
294J PRO* 3.8 19.5 - - + +
295J GLU 3.3 0.6 + - - -
296J TRP* 3.1 30.0 + - + +
298J PHE* 1.3 75.8 - - - +
300J PRO* 1.3 69.9 - - + +
302J TYR* 2.8 8.9 + - + +
303J ALA* 2.7 23.6 + - - +
377J LEU 4.5 0.9 - - - -
378J THR* 3.7 32.8 - - + +
379J TRP* 5.7 0.2 - - - -
381J GLY* 3.9 14.1 - - - -
382J ALA* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 300 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J TYR* 5.1 0.9 - - + +
296J TRP 3.7 8.1 - - - +
297J TYR 4.5 3.8 - - - +
298J PHE* 3.4 3.6 - - - +
299J LEU* 1.3 90.6 - - + +
301J PHE* 1.3 79.2 + - + +
303J ALA* 3.0 13.5 + - - +
304J ILE* 3.1 13.4 + - - +
374J PHE* 4.0 30.7 - - + +
377J LEU* 3.7 35.3 - - + +
378J THR* 3.3 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 301 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J TYR* 4.0 8.1 - + - -
136J TYR* 3.1 33.0 - + - -
140J MET* 4.8 9.4 - - - -
297J TYR 5.0 2.2 - - - -
298J PHE 3.0 11.5 + - - +
300J PRO* 1.3 86.7 - - + +
302J TYR* 1.3 60.7 + - - +
304J ILE* 3.7 8.2 + - + +
305J LEU 3.2 15.4 + - - -
336J MET* 3.4 30.4 - - + +
339J ALA* 4.5 17.3 - - + -
340J ILE* 3.2 44.6 - - + -
343J MET* 4.7 9.9 - - + -
374J PHE* 4.7 12.6 - + - -
400J TRP* 5.0 10.3 - + - -
503J SMA 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 302 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150I PRO 4.3 3.8 + - - -
151I CYS 2.7 20.9 + - - -
152I HIS* 3.5 17.5 - + - -
292J ILE 4.8 3.8 + - - -
293J VAL* 5.3 0.2 - - + -
294J PRO* 3.7 26.1 - - + +
298J PHE 3.1 11.2 + - - +
299J LEU* 2.8 12.7 + - + +
301J PHE* 1.3 75.6 - - - +
303J ALA* 1.3 69.7 + - - +
305J LEU* 3.1 5.4 + - - +
306J ARG* 3.0 49.2 + - - +
381J GLY* 3.1 34.5 - - - -
503J SMA 3.3 56.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299J LEU 2.7 11.2 + - - +
300J PRO 3.2 9.6 - - - +
302J TYR* 1.3 74.7 - - - +
304J ILE* 1.3 66.2 + - - +
306J ARG* 2.9 24.5 + - - +
307J ALA* 3.0 13.5 + - - +
377J LEU* 3.3 37.5 - - + +
380J VAL* 4.1 9.9 - - + -
381J GLY* 4.2 6.1 - - - +
393J SER* 4.7 6.6 - - - -
397J SER* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300J PRO 3.1 5.9 + - - +
301J PHE* 3.8 15.3 - - + +
303J ALA* 1.3 77.1 - - - +
305J LEU* 1.3 66.2 + - - +
307J ALA* 3.0 16.7 + - - +
308J PHE* 3.4 14.2 - - + -
335J ALA* 3.9 35.2 - - + +
336J MET* 4.1 3.8 - - - +
339J ALA* 3.8 22.2 - - + -
377J LEU* 3.5 33.0 - - + -
397J SER* 3.7 23.1 - - - +
400J TRP* 4.5 13.5 - - + -
401J PHE* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131I HIS* 4.1 17.0 - - + +
132I LEU* 4.4 2.9 - - + -
152I HIS* 3.7 31.0 - - + +
166I PRO* 5.9 1.2 - - - +
165J LEU* 4.0 21.1 - - + -
301J PHE 3.2 10.6 + - - +
302J TYR 3.1 9.4 + - - +
304J ILE* 1.3 82.0 - - - +
306J ARG* 1.3 61.6 + - - +
307J ALA 3.5 0.3 + - - -
308J PHE 3.8 10.4 + - - +
329J LYS 5.4 0.4 - - - +
332J GLY* 3.5 45.6 - - - +
333J VAL* 3.8 12.6 - - + +
336J MET* 4.0 17.3 - - - -
503J SMA 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 306 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150I PRO 5.5 2.0 + - - -
151I CYS 5.1 0.2 + - - -
152I HIS* 4.2 32.6 - - + +
153I GLY 5.5 0.4 - - - +
166I PRO* 5.7 4.9 - - + +
302J TYR* 3.0 50.6 + - - +
303J ALA* 2.9 19.1 + - - +
305J LEU* 1.3 73.7 - - - +
307J ALA* 1.3 66.9 + - - +
308J PHE* 3.2 3.9 - - - -
309J THR* 3.7 14.2 - - - +
380J VAL 2.8 22.0 + - - -
381J GLY* 3.2 10.3 + - - -
383J GLN 2.3 34.7 + - - -
384J GLN* 4.0 15.5 + - - +
385J THR* 4.2 26.2 + - + +
389J TYR* 6.1 0.2 - - - +
393J SER* 6.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 307 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303J ALA 3.0 8.1 + - - +
304J ILE 3.0 12.0 + - - +
306J ARG* 1.3 79.3 - - - +
308J PHE* 1.3 62.4 + - + +
309J THR* 3.1 14.6 + - - +
312J VAL* 3.7 10.2 - - - +
390J ASP* 5.2 2.8 - - - +
393J SER* 3.5 26.2 - - - +
394J LEU* 4.2 20.8 - - + +
397J SER* 3.8 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 308 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I PRO* 4.2 8.5 - - - +
304J ILE* 3.4 25.1 - - + -
305J LEU 3.8 9.8 + - - +
306J ARG 3.2 2.7 - - - +
307J ALA* 1.3 72.5 - - + +
309J THR* 1.3 62.9 + - - +
312J VAL* 4.0 10.8 - - + -
314J VAL* 5.5 4.9 - - + -
315J VAL* 3.8 11.0 - - + -
328J ALA* 4.1 14.8 - - - +
331J PHE* 3.3 39.5 - + + -
332J GLY* 4.5 6.0 - - - +
335J ALA* 3.3 33.2 - - + -
394J LEU* 3.7 24.0 - - + -
397J SER* 4.1 20.2 - - - -
398J ALA* 6.2 0.7 - - - -
401J PHE* 5.3 7.0 - + - -
----------------------------------------------------------
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