Contacts of the helix formed by residues 335 - 352 (chain J) in PDB entry 5TJ4
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 GLN 335 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J GLN* 5.0 1.6 - - - +
169J PHE* 3.7 24.9 - - + -
178J ILE* 3.9 21.7 - - + +
333J ILE* 3.2 13.3 - - + +
334J PRO* 1.3 94.8 - - - +
336J MET* 1.3 59.3 + - - +
337J SER 3.2 0.4 - - - -
338J ALA* 2.9 21.4 + - - +
339J PHE 3.0 9.9 + - - -
1221J SER* 3.4 39.2 + - - +
1224J LEU* 3.9 28.2 + - + +
1225J ASP* 3.9 9.9 - - - +
1227J HIS* 5.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 336 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J ASP* 4.1 13.5 - - + +
168J ALA* 3.7 16.8 - - + -
169J PHE* 3.5 34.0 - - + -
258J PHE* 4.7 1.3 - - + -
330J MET* 3.8 24.9 - - - -
331J PRO* 3.3 51.8 - - + +
333J ILE* 3.3 15.2 + - + +
334J PRO 3.1 0.8 - - - -
335J GLN* 1.3 77.0 - - - +
337J SER* 1.3 63.0 + - - +
339J PHE* 3.2 15.4 + - + +
340J TRP* 2.9 35.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J ARG* 4.6 24.9 + - - +
69J GLY* 5.5 4.7 - - - -
334J PRO* 3.4 14.7 + - - +
335J GLN 3.2 0.2 - - - -
336J MET* 1.3 77.8 - - - +
338J ALA* 1.3 63.1 + - - +
340J TRP* 3.3 2.9 + - - +
341J TYR* 2.9 45.9 + - - -
1224J LEU* 5.5 6.5 - - - +
1365J VAL* 5.3 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334J PRO 4.5 0.2 + - - -
335J GLN 2.9 11.9 + - - +
337J SER* 1.3 78.8 - - - +
339J PHE* 1.3 65.3 + - - +
341J TYR* 3.4 2.4 + - - +
342J ALA* 3.1 25.1 + - - +
368J ALA* 3.9 3.1 - - - +
1220J MET* 3.7 36.1 - - + -
1221J SER* 3.6 22.0 - - - +
1224J LEU* 4.3 8.4 - - + +
1361J GLN* 4.3 2.9 + - - -
1365J VAL* 5.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 339 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158J TRP* 3.6 29.4 - + - -
168J ALA* 3.5 36.1 - - + -
169J PHE* 4.0 16.6 - - + -
181J VAL* 4.7 5.4 - - + -
183J VAL* 3.8 15.9 - - + -
258J PHE* 3.8 14.8 - + - -
335J GLN 3.0 10.9 + - - +
336J MET* 3.5 16.2 - - - +
338J ALA* 1.3 76.8 - - - +
340J TRP* 1.3 101.0 + + - +
342J ALA* 3.3 2.3 + - - +
343J VAL* 3.1 43.1 + - + +
368J ALA* 4.3 12.0 - - + +
1221J SER* 4.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 340 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J ASP* 3.1 13.6 + - - -
66J ARG* 4.5 7.2 - - - +
154J PRO* 3.6 27.8 - - + +
155J TYR* 3.8 32.8 - + - -
158J TRP* 4.7 7.0 - + + -
258J PHE* 3.6 28.7 - + + -
330J MET* 2.8 43.3 - - + +
336J MET* 2.9 33.4 + - + +
337J SER* 3.8 2.7 - - - +
339J PHE* 1.3 91.8 - + - +
341J TYR* 1.3 59.0 + - - +
343J VAL* 3.3 3.9 + - + +
344J ARG* 2.9 38.8 + - - +
2T GLC 3.8 32.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 341 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J GLU* 3.4 38.0 - - - +
66J ARG* 3.9 26.7 + - - -
337J SER* 2.9 39.9 + - - +
338J ALA* 4.0 4.5 - - - +
340J TRP* 1.3 75.8 - - - +
342J ALA* 1.3 63.6 + - - +
344J ARG* 3.4 19.5 + - - +
345J THR* 3.2 26.6 + - - -
1220J MET* 4.9 2.5 - - + -
1361J GLN* 4.5 16.2 - - + +
1364J SER* 3.6 33.5 + - - -
1365J VAL* 4.5 17.5 - - + +
1367J GLU* 5.7 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 342 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338J ALA 3.1 18.4 + - - +
339J PHE 3.5 4.5 - - - +
341J TYR* 1.3 78.8 - - - +
343J VAL* 1.3 62.6 + - + +
345J THR* 3.6 3.8 - - - -
346J ALA* 3.1 21.5 + - - +
364J ALA* 3.5 36.8 - - + +
368J ALA* 3.8 8.1 - - + -
1361J GLN* 3.6 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 343 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J PRO* 3.7 21.1 - - + -
158J TRP* 4.4 17.9 - - + -
161J ILE* 4.9 2.9 - - + -
183J VAL* 3.9 17.5 - - + -
339J PHE* 3.1 46.0 + - + +
340J TRP* 3.8 4.9 - - + +
342J ALA* 1.3 75.0 - - + +
344J ARG* 1.3 68.2 + - - +
346J ALA* 2.9 8.0 + - + +
347J VAL* 2.8 37.5 + - + +
361J LEU* 6.0 4.9 - - + -
364J ALA* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J GLU* 5.8 1.8 + - - -
45J GLU* 5.1 7.3 + - - -
66J ARG* 4.2 8.7 - - - +
152J GLN 3.6 19.0 - - - +
153J GLU* 2.2 42.4 + - - -
154J PRO* 3.6 18.8 - - + +
340J TRP* 2.9 26.4 + - - +
341J TYR* 3.5 21.5 - - - +
343J VAL* 1.3 76.8 - - - +
345J THR* 1.3 62.7 + - - +
347J VAL* 3.9 2.7 - - - +
348J ILE* 3.1 36.5 + - + +
2T GLC 3.7 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 345 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341J TYR 3.2 11.1 + - - -
342J ALA 3.6 9.2 - - - +
343J VAL 3.2 0.6 - - - -
344J ARG* 1.3 75.7 - - - +
346J ALA* 1.3 68.9 + - - +
348J ILE* 3.1 6.9 + - - +
349J ASN* 2.8 48.5 + - - +
355J GLN* 4.8 2.0 - - - +
1357J LEU* 4.1 19.5 - - + -
1361J GLN* 4.5 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192J LEU* 4.9 2.0 - - + -
342J ALA 3.1 12.0 + - - +
343J VAL* 2.9 10.6 + - - +
345J THR* 1.3 79.6 - - - +
347J VAL* 1.3 59.4 + - + +
349J ASN* 3.5 1.7 + - - -
350J ALA* 2.9 32.6 + - - +
355J GLN* 5.0 0.9 - - - -
360J ALA* 3.5 39.2 - - + +
361J LEU* 4.3 11.7 - - + +
364J ALA* 3.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 347 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J LEU* 3.9 16.4 - - + +
152J GLN 6.2 0.2 - - - +
153J GLU 6.2 0.2 - - - -
154J PRO* 5.0 4.3 - - + -
157J THR* 3.9 31.0 - - + +
161J ILE* 3.9 22.2 - - + -
192J LEU* 4.3 13.2 - - + +
195J LEU* 4.4 10.3 - - + -
343J VAL* 2.8 38.4 + - + +
344J ARG* 3.9 5.2 - - - +
346J ALA* 1.3 73.2 - - + +
348J ILE* 1.3 57.4 + - - +
350J ALA* 3.3 1.7 + - - +
351J ALA* 2.9 32.3 + - + +
361J LEU* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 348 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J LEU 4.6 8.3 - - - +
152J GLN* 3.8 33.4 - - + +
344J ARG* 3.1 25.9 + - + +
345J THR* 3.1 6.3 + - - +
347J VAL* 1.3 76.7 - - + +
349J ASN* 1.3 62.3 + - - +
351J ALA* 3.6 5.6 - - - +
352J SER* 2.8 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 349 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345J THR* 2.8 34.7 + - - +
346J ALA 3.8 2.2 - - - +
348J ILE* 1.3 88.2 - - - +
350J ALA* 1.3 56.1 + - - +
352J SER* 3.6 5.4 + - - -
353J GLY 3.2 3.3 + - - -
354J ARG* 3.0 61.5 + - + +
355J GLN* 2.8 43.8 + - + +
1357J LEU* 4.1 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192J LEU* 4.1 24.7 - - + -
196J VAL* 4.5 13.2 - - + +
346J ALA 2.9 19.0 + - - +
347J VAL 3.8 2.5 - - - +
349J ASN* 1.3 74.1 - - - +
351J ALA* 1.3 63.5 + - - +
353J GLY* 3.5 9.9 + - - -
355J GLN 3.6 14.2 - - - +
357J VAL* 4.3 17.8 - - + +
360J ALA* 4.3 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J LEU* 5.4 7.2 - - + -
192J LEU* 5.9 0.6 - - - +
195J LEU* 5.8 4.3 - - + -
196J VAL* 5.4 4.2 - - - +
199J ILE* 4.2 27.4 - - + +
206J ALA* 3.8 29.4 - - + +
347J VAL* 2.9 22.0 + - + +
348J ILE* 3.6 6.3 - - - +
350J ALA* 1.3 78.3 - - - +
352J SER* 1.3 60.9 + - - +
353J GLY* 3.2 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206J ALA* 4.4 9.6 - - - +
348J ILE* 2.8 29.8 + - - +
349J ASN* 3.5 12.0 + - - -
351J ALA* 1.3 72.6 - - - +
353J GLY* 1.3 57.5 + - - +
354J ARG* 3.2 19.5 + - - +
----------------------------------------------------------
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