Contacts of the helix formed by residues 320 - 339 (chain G) in PDB entry 1XFB
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 ASN 320 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G ALA 3.3 19.5 - - - +
314G TRP* 3.3 24.1 - - - +
315G ARG* 4.4 4.5 - - - +
317G GLN* 3.2 19.6 + - - +
319G ASP* 1.3 90.1 + - - +
321G ALA* 1.3 64.4 + - - +
322G GLY 3.4 0.7 - - - -
323G ALA* 3.1 13.6 + - + +
324G ALA* 2.8 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G VAL* 3.6 13.2 - - + +
314G TRP* 4.2 12.3 - - + +
317G GLN 3.4 4.8 + - - +
318G ARG* 3.2 22.0 - - + +
319G ASP 2.9 2.9 + - - +
320G ASN* 1.3 76.6 - - - +
322G GLY* 1.3 58.2 + - - +
324G ALA* 3.1 5.0 + - - +
325G THR* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 322 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319G ASP 3.8 5.6 + - - -
320G ASN 3.4 0.6 - - - -
321G ALA* 1.3 80.0 - - - +
323G ALA* 1.3 57.8 + - - +
325G THR* 3.3 9.2 + - - -
326G GLU* 3.0 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G ALA* 4.4 11.2 - - + -
319G ASP 4.8 1.0 + - - +
320G ASN* 3.1 17.3 + - + +
322G GLY* 1.3 72.9 - - - +
324G ALA* 1.3 65.8 + - - +
326G GLU* 3.0 10.2 + - - +
327G GLU* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G VAL* 3.3 17.9 - - + -
310G ALA* 3.2 33.0 - - - +
313G ALA* 3.8 7.1 - - - +
314G TRP* 3.5 16.2 - - + +
320G ASN 2.8 12.8 + - - +
321G ALA 3.3 10.1 - - - +
323G ALA* 1.3 77.0 - - - +
325G THR* 1.3 62.7 + - - +
327G GLU* 3.0 14.2 + - - +
328G PHE* 3.1 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 325 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G VAL* 2.8 33.1 + - - +
65G SER* 3.8 9.1 + - - +
66G ALA* 3.6 31.2 - - + +
321G ALA 2.9 16.4 + - - -
322G GLY* 3.5 11.6 - - - -
323G ALA 3.2 0.2 - - - -
324G ALA* 1.3 76.5 - - - +
326G GLU* 1.3 58.5 + - - +
328G PHE* 3.4 6.3 + - + +
329G ILE* 3.0 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 326 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ARG* 2.5 43.9 + - - -
322G GLY 3.0 19.2 + - - +
323G ALA* 3.0 11.6 + - - +
325G THR* 1.3 76.5 - - - +
327G GLU* 1.3 71.0 + - - +
328G PHE 3.1 0.2 + - - -
329G ILE* 3.2 7.9 + - - +
330G LYS* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309G SER* 3.1 39.1 - - - +
310G ALA* 3.5 15.3 - - - +
313G ALA* 4.7 6.5 - - + +
323G ALA* 2.9 15.4 + - - +
324G ALA* 3.0 10.5 + - - +
326G GLU* 1.3 78.7 - - - +
328G PHE* 1.3 61.2 + - - +
330G LYS* 3.4 29.1 + - - +
331G ARG* 3.2 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 328 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G LEU* 3.7 38.8 - - + -
62G VAL 5.0 1.1 - - - -
63G LEU* 3.4 47.1 - - + -
66G ALA* 3.9 17.3 - - + -
70G VAL* 4.0 19.1 - - + -
74G ILE* 4.7 4.5 - - + -
306G LEU* 3.6 30.5 - - + -
310G ALA* 3.8 12.9 - - + +
324G ALA 3.1 10.2 + - - +
325G THR* 3.5 8.7 - - - +
326G GLU 3.1 0.6 - - - -
327G GLU* 1.3 72.7 - - - +
329G ILE* 1.3 71.8 + - - +
330G LYS 2.9 1.8 + - - -
331G ARG* 2.9 4.0 + - - +
332G ALA* 2.8 34.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G ALA* 3.7 31.9 - - + -
67G ASP* 3.8 18.4 - - - +
69G ARG* 3.6 61.9 - - + +
70G VAL* 4.8 5.4 - - + +
325G THR* 3.0 23.7 + - + +
326G GLU* 3.7 6.7 - - - +
328G PHE* 1.3 76.0 - - + +
330G LYS* 1.3 62.7 + - - +
332G ALA* 3.6 7.9 - - + +
333G GLU* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 330 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ARG* 5.6 0.8 - - - +
326G GLU* 2.8 19.4 + - - +
327G GLU* 3.4 32.5 + - - +
328G PHE 2.9 0.2 + - - -
329G ILE* 1.3 76.9 - - - +
331G ARG* 1.3 66.7 + - + +
333G GLU* 3.0 11.8 + - - +
334G VAL* 2.8 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 331 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G GLU* 2.8 68.2 + - - +
278G GLU* 2.5 30.3 + - - -
281G SER* 3.0 17.4 + - - -
305G ALA 3.6 3.9 + - - +
306G LEU* 3.7 20.2 - - + +
309G SER* 4.0 3.6 - - - +
327G GLU 3.2 16.4 - - - +
328G PHE 2.9 4.4 + - - +
330G LYS* 1.3 80.6 - - + +
332G ALA* 1.3 64.3 + - - +
334G VAL* 3.2 32.1 - - - +
335G ASN* 2.9 38.8 + - - +
343G TYR* 4.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G VAL* 4.4 2.7 - - + -
73G CYS* 3.1 24.8 - - - +
74G ILE* 4.0 14.4 - - + -
300G PHE* 4.4 3.0 - - - -
306G LEU* 3.6 12.2 - - + +
328G PHE* 2.8 40.3 + - + +
329G ILE* 3.6 9.2 - - - +
331G ARG* 1.3 72.1 - - - +
333G GLU* 1.3 58.0 + - - +
335G ASN* 4.0 2.0 - - - +
336G GLY 3.0 20.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ARG* 3.2 27.6 + - - +
72G LYS* 2.7 42.4 + - - +
73G CYS* 3.7 14.0 - - - +
329G ILE* 2.9 31.4 + - + +
330G LYS* 3.0 7.3 + - - +
332G ALA* 1.3 76.0 - - - +
334G VAL* 1.3 66.0 + - - +
336G GLY* 3.0 11.1 + - - -
337G LEU* 3.0 17.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G SER* 3.7 14.6 - - - +
330G LYS* 2.8 25.1 + - + +
331G ARG* 3.1 43.3 - - - +
333G GLU* 1.3 73.0 - - - +
335G ASN* 1.3 57.6 + - - +
337G LEU* 2.9 13.4 + - - +
338G ALA* 2.8 23.9 + - - +
343G TYR* 3.3 42.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 335 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G SER* 2.7 32.6 + - - -
284G LEU* 4.0 1.8 - - + +
300G PHE* 3.5 28.5 - - + -
302G TYR* 3.5 24.4 + - - -
305G ALA 4.0 0.8 + - - -
306G LEU* 3.7 16.2 - - - +
331G ARG* 2.9 41.4 + - - +
332G ALA 4.1 0.7 - - - +
334G VAL* 1.3 73.0 - - - +
336G GLY* 1.3 60.5 + - - +
338G ALA* 3.7 6.3 - - - +
339G ALA* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G GLY* 3.2 30.1 - - - -
73G CYS* 3.7 7.2 - - - -
300G PHE* 4.1 6.7 - - - -
332G ALA 3.0 13.2 + - - -
333G GLU 3.0 8.7 + - - -
335G ASN* 1.3 77.7 - - - +
337G LEU* 1.3 60.2 + - - +
339G ALA* 3.6 2.3 - - - +
340G GLN* 3.1 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333G GLU* 3.0 14.7 + - + +
334G VAL* 2.9 10.9 + - - +
336G GLY* 1.3 76.6 - - - +
338G ALA* 1.3 53.3 + - - +
339G ALA 2.9 4.7 - - - -
340G GLN* 2.7 32.1 + - - +
342G LYS* 3.2 51.9 + - + +
343G TYR* 3.8 21.5 - - + -
344G GLU 5.5 0.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
281G SER* 3.3 29.8 - - - +
284G LEU* 3.6 9.7 - - + +
285G ASN* 3.2 30.1 - - + +
288G ASN* 2.9 16.6 + - - -
334G VAL 2.8 12.9 + - - +
335G ASN* 3.7 12.3 - - - +
337G LEU* 1.3 76.0 - - - +
339G ALA* 1.3 56.8 + - - +
340G GLN 2.9 3.0 + - - -
341G GLY 3.1 6.8 + - - -
343G TYR* 3.7 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G GLY* 4.3 10.8 + - - -
284G LEU* 4.1 4.2 - - - +
288G ASN* 3.2 24.3 + - - +
298G LEU 4.2 2.9 + - - +
299G THR* 3.8 32.4 - - + +
300G PHE* 4.4 5.6 - - + -
335G ASN 2.8 16.5 + - - +
336G GLY* 3.6 11.9 - - - +
337G LEU 2.9 0.4 - - - -
338G ALA* 1.3 76.0 - - - +
340G GLN* 1.3 60.8 + - - +
----------------------------------------------------------
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