Contacts of the helix formed by residues 325 - 346 (chain G) in PDB entry 2I2X
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 THR 325 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E GLU* 5.4 0.2 - - - -
315G VAL* 3.2 27.1 - - + +
316G GLU 2.9 26.1 + - - +
317G TYR* 3.4 20.0 - - + -
318G HIS* 3.0 17.3 + - - +
320G GLU* 4.2 22.8 + - - +
323G GLY 3.6 1.0 + - - -
324G THR* 1.3 70.7 - - - +
326G VAL* 1.3 80.4 + - + +
328G CYS* 3.2 8.9 + - - +
329G TRP* 2.9 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 326 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ILE* 3.8 9.2 - - + +
44G ASN 4.3 5.6 - - - +
45G TYR* 3.6 37.5 - - + -
65G ILE* 4.0 12.8 - - + +
68G ASP* 4.1 2.7 - - + -
69G VAL* 3.9 23.9 - - + +
315G VAL* 4.6 3.4 - - + -
317G TYR* 4.0 14.8 - - + -
324G THR* 3.2 22.4 - - + -
325G THR* 1.3 89.7 - - + +
327G GLN* 1.3 53.5 + - - +
330G SER* 2.8 38.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 327 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ASP* 3.0 52.2 + - + +
69G VAL* 5.5 0.2 - - - +
71G GLU* 4.8 7.5 - - - +
72G ARG* 3.8 44.2 + - + +
323G GLY* 3.9 4.5 - - - -
324G THR* 2.7 44.3 + - + +
326G VAL* 1.3 70.7 - - - +
328G CYS* 1.3 63.6 + - - +
330G SER* 3.2 5.9 + - - -
331G GLU* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 328 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E THR* 2.7 59.1 + - - +
293E CYS* 4.1 4.9 - - - +
329E TRP* 4.5 3.8 - - + -
72G ARG* 5.0 2.5 - - - +
320G GLU* 3.9 22.2 - - - -
322G GLY 4.2 4.5 - - - -
323G GLY 3.8 17.7 - - - -
324G THR 3.1 18.2 + - - -
325G THR* 3.2 5.1 + - - +
327G GLN* 1.3 77.1 - - - +
329G TRP* 1.3 70.0 + - + +
331G GLU* 3.6 0.6 + - - -
332G THR* 3.0 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 329 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E GLU* 5.9 3.9 - - + -
328E CYS* 4.6 3.8 - - + -
329E TRP* 3.4 52.5 - + - +
332E THR* 4.4 5.8 - - + -
43G ILE* 4.2 3.8 - - + -
290G THR* 3.7 40.1 - - + +
292G THR* 3.5 25.1 - - - -
293G CYS* 3.5 35.6 - - + +
312G ASN* 4.0 19.3 - - + +
315G VAL* 4.1 8.3 - - + +
320G GLU* 5.9 3.2 + - - +
325G THR* 2.9 39.9 + - - +
327G GLN 3.2 0.2 - - - -
328G CYS* 1.3 80.4 - - + +
330G SER* 1.3 60.7 + - - +
332G THR* 3.3 3.9 + - - -
333G LEU* 2.8 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 330 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G PRO* 4.5 1.9 - - - +
43G ILE* 3.9 24.3 - - - +
69G VAL* 4.4 12.3 - - - +
72G ARG* 4.2 4.9 - - - +
73G MET* 4.1 21.0 - - - +
81G ILE* 5.2 2.5 - - - -
326G VAL 2.8 24.4 + - - -
327G GLN* 3.2 9.2 + - - -
329G TRP* 1.3 77.1 - - - +
331G GLU* 1.3 54.8 + - - +
333G LEU* 3.4 7.7 + - - +
334G ALA* 2.8 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E LYS* 5.7 0.3 - - - -
292E THR* 3.4 22.6 - - + +
296E SER* 3.0 17.0 + - - -
297E ASP* 3.1 32.4 + - - +
72G ARG* 2.8 39.1 + - + +
73G MET* 5.2 0.2 - - - -
76G VAL* 4.1 6.1 - - - -
78G PHE* 3.7 14.3 - - + -
327G GLN 3.1 17.0 + - - +
328G CYS 3.7 4.5 - - - +
330G SER* 1.3 74.8 + - - +
332G THR* 1.3 58.9 + - - +
335G TYR* 3.0 52.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 332 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E LYS* 2.7 33.9 + - + +
290E THR* 4.6 9.9 - - + +
292E THR* 2.8 17.8 + - - -
329E TRP* 4.2 6.9 - - + -
332E THR* 4.9 7.4 - - + -
290G THR* 3.7 26.5 - - + +
328G CYS 3.0 4.4 + - - -
329G TRP* 3.7 9.6 - - + -
331G GLU* 1.3 75.0 - - - +
333G LEU* 1.3 66.6 + - - +
335G TYR* 3.3 5.3 + - - +
336G ASP* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G PRO* 3.7 13.7 - - + -
42G GLU 3.7 20.6 - - - +
43G ILE* 4.2 12.6 - - + +
290G THR* 3.5 24.0 - - + +
310G TRP* 3.6 26.0 - - + +
311G SER 3.5 24.5 - - - +
312G ASN* 3.6 24.9 - - + +
329G TRP 2.8 20.7 + - - +
330G SER* 3.7 4.9 - - - +
332G THR* 1.3 76.1 - - - +
334G ALA* 1.3 57.7 + - - +
336G ASP* 3.2 4.9 + - - +
337G CYS* 3.1 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 334 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G PRO* 3.8 12.3 - - + -
73G MET* 3.5 13.5 - - + -
78G PHE* 3.4 43.5 - - + -
330G SER 2.8 18.9 + - - +
333G LEU* 1.3 73.8 - - - +
335G TYR* 1.3 60.5 + - - +
337G CYS* 3.5 4.6 + - - +
338G ALA* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 335 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E LYS* 3.5 33.4 - - + -
297E ASP 2.7 20.6 + - - -
298E VAL 3.2 18.0 + - - -
300E GLY* 3.3 22.7 - - - -
301E ASN* 2.9 33.0 - - - +
360E ASP* 3.4 23.8 - - - -
363E ARG* 3.8 10.9 - - - -
76G VAL* 3.3 12.6 - - + +
78G PHE* 3.6 15.7 - + - -
331G GLU* 3.0 48.2 + - + +
332G THR 3.7 1.6 - - - +
333G LEU 3.2 0.2 - - - -
334G ALA* 1.3 76.6 - - - +
336G ASP* 1.3 66.2 + - - +
338G ALA* 3.0 3.2 + - + +
339G LEU* 3.0 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 336 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E LYS* 2.5 44.2 + - - +
289G LYS* 3.9 13.3 - - - -
290G THR* 2.6 28.9 + - - -
304G MET* 4.7 4.6 - - - +
310G TRP* 2.8 28.4 + - + +
332G THR* 3.0 17.8 + - - +
333G LEU 3.5 4.3 - - - +
335G TYR* 1.3 74.5 - - - +
337G CYS* 1.3 61.7 + - - +
339G LEU* 3.2 7.2 + - - +
340G MET* 3.1 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 337 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G THR* 3.1 31.4 + - - +
40G ILE 3.5 9.6 - - - -
41G PRO* 3.5 30.3 - - + -
310G TRP* 3.8 20.0 - - - -
333G LEU 3.1 18.1 + - - +
334G ALA 3.8 8.1 - - - +
336G ASP* 1.3 73.2 - - - +
338G ALA* 1.3 55.0 + - - +
340G MET* 3.1 3.8 + - - -
341G ASN* 2.6 43.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
301E ASN* 4.1 1.3 - - - +
359E SER* 3.6 15.3 - - - +
363E ARG* 3.9 19.5 - - - +
12F VAL* 4.6 11.2 - - + +
78G PHE* 4.8 2.9 - - + -
334G ALA 3.0 14.0 + - - +
335G TYR* 3.0 14.4 + - + +
337G CYS* 1.3 73.6 - - - +
339G LEU* 1.3 62.9 + - - +
341G ASN* 3.8 7.2 - - - +
342G THR* 2.8 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E LYS* 4.2 15.7 - - - +
301E ASN* 3.7 15.7 + - + +
304E MET* 4.8 6.7 - - + -
339E LEU* 4.6 21.3 - - + -
352E LEU* 4.6 9.2 - - + -
355E LEU* 4.0 12.3 - - + +
356E MET* 3.7 41.7 - - + +
359E SER* 4.3 1.8 - - - -
289G LYS* 5.8 1.3 - - - +
335G TYR 3.0 11.5 + - - +
336G ASP* 3.4 10.8 - - - +
338G ALA* 1.3 75.7 - - - +
340G MET* 1.3 65.2 + - + +
342G THR* 3.2 4.7 + - - -
343G ALA* 3.2 20.6 + - - +
352G LEU* 4.1 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 340 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G PHE* 3.4 49.4 - - + -
39G THR* 3.8 14.1 - - + +
304G MET* 4.1 25.6 - - - +
307G CYS* 3.8 31.9 - - - -
310G TRP* 4.6 5.8 - - + -
336G ASP 3.1 23.2 + - - +
337G CYS* 3.1 21.7 + - - +
339G LEU* 1.3 77.5 - - + +
341G ASN* 1.3 65.6 + - - +
343G ALA* 3.1 2.1 + - - +
344G LEU* 3.0 18.9 + - - +
352G LEU* 4.1 10.5 - - + -
356G MET* 4.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 341 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LYS 5.4 4.4 + - - -
12F VAL* 4.4 21.5 + - + -
37G GLY 5.6 0.4 - - - +
38G TYR* 3.5 20.5 - - + +
39G THR* 2.7 50.7 + - - +
79G PRO* 6.0 4.0 - - - +
337G CYS* 2.6 24.5 + - - +
338G ALA* 3.3 6.3 + - - +
340G MET* 1.3 74.9 - - - +
342G THR* 1.3 63.5 + - - +
344G LEU* 3.3 7.7 + - + +
345G GLU* 2.9 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 342 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355E LEU* 3.6 30.7 - - + +
358E LEU* 3.8 18.4 - - + -
359E SER* 3.4 17.5 - - - -
4F PHE* 3.5 31.0 - - + -
12F VAL* 4.0 4.4 - - - +
338G ALA 2.8 21.8 + - - -
339G LEU 3.2 5.1 + - - -
341G ASN* 1.3 77.0 - - - +
343G ALA* 1.3 59.8 + - - +
345G GLU* 3.5 0.7 + - - +
346G THR* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355E LEU* 4.0 15.1 - - + +
19G PHE* 4.2 0.9 - - + -
339G LEU 3.2 5.5 + - - +
340G MET 3.1 8.8 + - - +
342G THR* 1.3 76.8 - - - +
344G LEU* 1.3 60.0 + - - +
346G THR* 3.4 5.6 + - - -
347G LYS 3.1 2.8 + - - -
348G ASN 2.7 34.6 + - - +
349G ASP* 3.2 21.0 + - - +
352G LEU* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G THR* 4.7 0.2 - - + -
19G PHE* 3.6 36.1 - - + +
20G GLY* 4.2 1.8 - - - -
21G VAL* 3.9 17.5 - - + -
37G GLY* 3.4 33.4 - - - +
38G TYR* 4.0 3.1 - - - +
340G MET 3.0 12.3 + - - +
341G ASN* 3.6 24.7 - - - +
343G ALA* 1.3 76.1 - - - +
345G GLU* 1.3 65.6 + - - +
347G LYS* 3.1 19.6 + - - +
349G ASP* 3.8 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 345 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F PHE* 4.0 8.5 - - + -
5F THR* 5.9 1.0 - - - +
8F SER* 3.1 46.1 + - - +
11F LYS* 3.0 41.1 + - - +
12F VAL* 3.7 21.5 - - + -
37G GLY 4.0 8.0 - - - +
38G TYR* 5.7 0.3 - - - +
341G ASN* 2.9 21.6 + - + +
342G THR 4.0 3.8 - - - +
343G ALA 3.4 0.2 - - - -
344G LEU* 1.3 78.5 - - - +
346G THR* 1.3 59.0 + - - +
347G LYS* 3.4 11.8 + - - +
12M ALA* 5.4 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 346 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355E LEU* 3.7 8.7 - - - +
358E LEU* 3.7 28.7 - - + -
2F LEU* 4.6 9.9 - - + +
3F ASP 4.2 11.7 - - - +
4F PHE* 4.2 9.0 - - + -
342G THR 2.9 21.3 + - - +
343G ALA 3.4 3.8 + - - -
344G LEU 3.1 0.6 - - - -
345G GLU* 1.3 80.2 - - - +
347G LYS* 1.3 71.5 + - - +
348G ASN* 2.9 24.8 + - - +
----------------------------------------------------------
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