Contacts of the helix formed by residues 335 - 352 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G GLN* 4.9 1.4 - - - +
169G PHE* 3.6 26.6 - - + -
178G ILE* 3.9 21.6 - - + +
333G ILE* 3.2 13.1 - - + +
334G PRO* 1.3 94.3 - - - +
336G MET* 1.3 59.2 + - - +
337G SER 3.2 0.2 - - - -
338G ALA* 2.9 22.3 + - - +
339G PHE 3.0 9.7 + - - -
1221G SER* 3.4 40.1 + - - +
1224G LEU* 3.9 28.8 + - + -
1225G ASP* 3.9 8.9 - - - +
1227G HIS* 5.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 336 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G ASP* 4.1 16.8 - - + +
168G ALA* 3.7 18.4 - - + -
169G PHE* 3.6 29.4 - - + -
258G PHE* 4.7 1.6 - - + -
330G MET* 5.0 4.3 - - - -
331G PRO* 3.3 58.3 - - + +
333G ILE* 3.3 15.4 + - + +
334G PRO 3.1 0.4 - - - -
335G GLN* 1.3 73.5 - - - +
337G SER* 1.3 64.8 + - - +
339G PHE* 3.5 17.5 - - + +
340G TRP* 2.9 47.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G ARG* 4.5 33.3 + - - +
69G GLY* 5.6 4.0 - - - -
334G PRO* 3.4 14.1 + - - +
335G GLN 3.2 0.2 - - - -
336G MET* 1.3 75.5 - - - +
338G ALA* 1.3 63.5 + - - +
340G TRP* 3.3 4.9 + - - +
341G TYR* 3.0 25.6 + - - +
1224G LEU* 5.4 7.4 - - - +
1365G VAL* 5.5 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G PRO 4.5 0.2 + - - -
335G GLN 2.9 12.5 + - - +
337G SER* 1.3 80.1 - - - +
339G PHE* 1.3 65.1 + - - +
341G TYR* 3.4 4.4 + - - +
342G ALA* 3.1 25.6 + - - +
368G ALA* 3.9 4.4 - - - +
1220G MET* 3.7 33.4 - - + -
1221G SER* 3.6 21.5 - - - +
1224G LEU* 4.3 8.2 - - + +
1361G GLN* 4.4 2.9 + - - +
1365G VAL* 5.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 339 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G TRP* 3.6 29.6 - + - -
168G ALA* 3.6 36.3 - - + -
169G PHE* 4.0 16.2 - - + -
181G VAL* 4.7 5.8 - - + -
183G VAL* 3.8 15.9 - - + -
258G PHE* 3.8 18.2 - + - -
335G GLN 3.0 9.7 + - - +
336G MET* 3.5 16.8 - - + +
338G ALA* 1.3 77.8 - - - +
340G TRP* 1.3 104.6 + + - +
342G ALA* 3.2 2.1 + - - +
343G VAL* 3.1 43.7 + - + +
368G ALA* 4.3 11.1 - - + +
1221G SER* 4.8 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 340 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G ASP* 3.1 28.1 + - - -
66G ARG* 4.6 7.2 - - - +
154G PRO* 3.6 19.6 - - + +
155G TYR* 3.8 31.6 - + - -
158G TRP* 4.7 7.0 - + + -
258G PHE* 3.6 34.5 - + + -
330G MET* 3.8 17.2 - - + -
336G MET* 2.9 39.3 + - + +
337G SER 3.8 3.6 - - - +
339G PHE* 1.3 93.0 - + - +
341G TYR* 1.3 64.5 + - - +
343G VAL* 3.3 4.5 + - + +
344G ARG* 2.9 30.0 + - - +
2Q GLC 3.5 44.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 341 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G SER 3.0 17.0 + - - +
338G ALA* 4.0 4.3 - - - +
340G TRP* 1.3 75.7 - - - +
342G ALA* 1.3 62.2 + - - +
344G ARG* 3.4 34.0 + - - +
345G THR* 3.2 38.7 + - - -
1360G ASP* 4.7 5.6 + - + +
1361G GLN* 3.0 41.5 - - + +
1364G SER* 3.2 34.8 + - - -
1365G VAL* 5.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 342 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G ALA 3.1 17.5 + - - +
339G PHE 3.5 4.3 - - - +
340G TRP 3.2 0.2 - - - -
341G TYR* 1.3 78.1 - - - +
343G VAL* 1.3 63.2 + - + +
345G THR* 3.6 4.2 - - - -
346G ALA* 3.1 22.2 + - - +
364G ALA* 3.5 35.7 - - + +
368G ALA* 3.8 9.2 - - + -
1361G GLN* 3.6 24.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 343 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G PRO* 3.7 21.3 - - + -
158G TRP* 4.4 18.6 - - + -
161G ILE* 4.9 2.9 - - + -
183G VAL* 3.9 17.5 - - + -
339G PHE* 3.1 45.8 + - + +
340G TRP* 3.8 4.5 - - + +
342G ALA* 1.3 76.1 - - + +
344G ARG* 1.3 66.8 + - - +
346G ALA* 2.9 8.1 + - + -
347G VAL* 2.8 37.8 + - + +
361G LEU* 6.0 4.3 - - + -
364G ALA* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 5.5 4.0 + - - -
66G ARG* 4.4 6.7 - - - +
152G GLN 3.8 17.1 + - - +
153G GLU* 3.1 33.9 + - - -
154G PRO* 3.8 15.5 - - + +
340G TRP* 2.9 21.6 + - - +
341G TYR* 3.4 47.4 + - - +
343G VAL* 1.3 76.3 - - - +
345G THR* 1.3 62.6 + - - +
347G VAL* 3.6 3.3 + - - +
348G ILE* 3.1 37.1 + - + +
2Q GLC 3.4 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 345 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341G TYR* 3.2 29.2 + - - -
342G ALA 3.6 9.2 - - - +
343G VAL 3.2 0.2 - - - -
344G ARG* 1.3 77.6 - - - +
346G ALA* 1.3 67.3 + - - +
348G ILE* 3.1 6.3 + - - +
349G ASN* 2.8 48.8 + - - +
355G GLN* 4.8 1.8 - - - +
1357G LEU* 4.1 18.8 - - + -
1361G GLN* 4.4 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G LEU* 4.9 2.0 - - + -
342G ALA 3.1 10.8 + - - +
343G VAL* 2.9 10.6 + - - +
345G THR* 1.3 80.1 - - - +
347G VAL* 1.3 59.5 + - + +
349G ASN* 3.5 1.9 + - - -
350G ALA* 2.9 31.6 + - - +
355G GLN* 5.0 1.1 - - - -
360G ALA* 3.5 38.1 - - + +
361G LEU* 4.3 12.1 - - + +
364G ALA* 3.8 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 347 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G LEU* 3.9 16.4 - - + +
152G GLN 6.2 0.2 - - - +
154G PRO* 4.9 4.3 - - + -
157G THR* 3.9 30.3 - - + +
161G ILE* 3.9 22.0 - - + -
192G LEU* 4.3 13.0 - - + +
195G LEU* 4.4 11.2 - - + -
343G VAL* 2.8 39.4 + - + +
344G ARG* 4.0 4.5 - - - +
346G ALA* 1.3 72.7 - - + +
348G ILE* 1.3 58.3 + - + +
350G ALA* 3.3 1.7 + - - +
351G ALA* 2.9 32.3 + - + +
361G LEU* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 348 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G LEU 4.6 8.1 - - - +
152G GLN* 3.8 45.3 - - + +
344G ARG* 3.1 26.1 + - + +
345G THR* 3.1 5.9 + - - +
347G VAL* 1.3 76.7 - - + +
349G ASN* 1.3 66.2 + - - +
351G ALA* 3.7 5.0 - - - +
352G SER* 2.8 44.2 + - - +
354G ARG* 5.4 9.0 - - - +
138J GLU* 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 349 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345G THR* 2.8 37.9 + - - +
346G ALA 3.8 2.2 - - - +
348G ILE* 1.3 80.5 - - - +
350G ALA* 1.3 56.4 + - - +
352G SER* 4.6 0.4 - - - -
353G GLY 3.2 4.2 + - - -
354G ARG* 3.0 60.9 + - + +
355G GLN* 2.8 42.4 + - + +
1357G LEU* 4.0 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G LEU* 4.1 17.5 - - + -
196G VAL* 3.7 34.1 - - + +
346G ALA 2.9 17.5 + - - +
347G VAL 3.8 3.1 - - - +
349G ASN* 1.3 74.5 - - - +
351G ALA* 1.3 65.5 + - - +
353G GLY* 3.4 10.2 + - - -
355G GLN 3.6 14.3 - - - +
357G VAL* 4.3 9.5 - - + +
360G ALA* 4.3 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G LEU* 5.4 5.6 - - + -
195G LEU* 5.8 2.9 - - + -
196G VAL* 4.4 7.7 - - + +
199G ILE* 4.2 31.5 - - + +
206G ALA* 3.8 27.7 - - + +
347G VAL* 2.9 21.4 + - + +
348G ILE* 3.7 6.1 - - - +
350G ALA* 1.3 78.9 - - - +
352G SER* 1.3 60.5 + - - +
353G GLY* 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G ALA* 4.6 9.5 - - - +
348G ILE* 2.8 31.7 + - - +
349G ASN* 4.3 4.3 - - - -
351G ALA* 1.3 72.5 - - - +
353G GLY* 1.3 58.4 + - - +
354G ARG* 3.2 24.6 + - - -
138J GLU* 3.8 27.0 + - - +
141J ALA* 4.5 13.5 - - - +
142J LYS* 5.6 2.3 + - - +
----------------------------------------------------------
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