Contacts of the helix formed by residues 320 - 339 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313I ALA 3.3 19.2 - - - +
314I TRP* 3.3 24.5 - - - +
315I ARG* 4.4 4.3 - - - +
317I GLN* 3.2 19.5 + - - +
319I ASP* 1.3 90.5 + - - +
321I ALA* 1.3 64.4 + - - +
322I GLY 3.4 0.7 - - - -
323I ALA* 3.1 13.6 + - + +
324I ALA* 2.8 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I VAL* 3.6 13.2 - - + +
314I TRP* 4.2 11.9 - - + +
317I GLN 3.4 4.8 + - - +
318I ARG* 3.2 22.2 - - + +
319I ASP 2.9 2.2 + - - +
320I ASN* 1.3 76.6 - - - +
322I GLY* 1.3 58.4 + - - +
324I ALA* 3.1 4.8 + - - +
325I THR* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 322 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319I ASP 3.8 5.4 + - - -
320I ASN 3.4 0.6 - - - -
321I ALA* 1.3 79.8 - - - +
323I ALA* 1.3 57.2 + - - +
325I THR* 3.3 9.3 + - - -
326I GLU* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313I ALA* 4.4 11.0 - - + -
319I ASP 4.8 1.0 + - - +
320I ASN* 3.1 17.0 + - + +
322I GLY* 1.3 73.1 - - - +
324I ALA* 1.3 65.7 + - - +
326I GLU* 3.0 10.5 + - - +
327I GLU* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I VAL* 3.3 17.7 - - + -
310I ALA* 3.2 32.4 - - - +
313I ALA* 3.8 7.1 - - - +
314I TRP* 3.5 16.4 - - + +
320I ASN 2.8 12.6 + - - +
321I ALA 3.3 10.1 - - - +
323I ALA* 1.3 77.7 - - - +
325I THR* 1.3 62.9 + - - +
327I GLU* 3.0 14.2 + - - +
328I PHE* 3.1 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 325 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I VAL* 2.8 33.3 + - - +
65I SER* 3.8 9.1 + - - +
66I ALA* 3.6 31.0 - - + +
321I ALA 2.9 16.5 + - - -
322I GLY* 3.5 11.2 - - - -
323I ALA 3.2 0.2 - - - -
324I ALA* 1.3 76.1 - - - +
326I GLU* 1.3 58.7 + - - +
328I PHE* 3.4 6.6 + - + +
329I ILE* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 326 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I ARG* 2.5 44.6 + - - -
322I GLY 3.0 19.2 + - - +
323I ALA* 3.0 11.6 + - - +
325I THR* 1.3 76.3 - - - +
327I GLU* 1.3 71.5 + - - +
328I PHE 3.1 0.2 + - - -
329I ILE* 3.2 7.8 + - - +
330I LYS* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309I SER* 3.1 38.2 - - - +
310I ALA* 3.5 14.8 - - - +
313I ALA* 4.7 6.5 - - + +
323I ALA* 2.9 15.4 + - - +
324I ALA* 3.0 10.5 + - - +
326I GLU* 1.3 79.3 - - - +
328I PHE* 1.3 61.0 + - - +
330I LYS* 3.4 29.5 + - - +
331I ARG* 3.2 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 328 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I LEU* 3.7 39.0 - - + -
62I VAL 5.0 1.1 - - - -
63I LEU* 3.4 47.3 - - + -
66I ALA* 3.9 17.7 - - + -
70I VAL* 4.0 19.3 - - + -
74I ILE* 4.7 4.3 - - + -
306I LEU* 3.6 29.8 - - + -
310I ALA* 3.8 12.5 - - + +
324I ALA 3.1 10.2 + - - +
325I THR* 3.5 8.7 - - - +
326I GLU 3.1 0.6 - - - -
327I GLU* 1.3 72.2 - - - +
329I ILE* 1.3 71.6 + - - +
330I LYS 2.9 1.8 + - - -
331I ARG* 2.9 4.0 + - - +
332I ALA* 2.8 35.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I ALA* 3.7 31.9 - - + -
67I ASP* 3.8 18.2 - - - +
69I ARG* 3.6 62.1 - - + +
70I VAL* 4.8 5.6 - - + +
325I THR* 3.0 23.7 + - + +
326I GLU* 3.7 7.0 - - - +
328I PHE* 1.3 75.8 - - + +
330I LYS* 1.3 62.5 + - - +
332I ALA* 3.6 7.9 - - + +
333I GLU* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 330 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I ARG* 5.6 0.8 - - - +
326I GLU* 2.8 19.4 + - - +
327I GLU* 3.4 33.0 + - - +
328I PHE 2.9 0.2 + - - -
329I ILE* 1.3 76.8 - - - +
331I ARG* 1.3 65.6 + - + +
333I GLU* 3.0 12.2 + - - +
334I VAL* 2.8 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 331 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I GLU* 2.8 67.4 + - - +
278I GLU* 2.5 30.3 + - - -
281I SER* 3.0 17.4 + - - -
305I ALA 3.6 3.9 + - - +
306I LEU* 3.7 20.6 - - + +
309I SER* 4.0 3.6 - - - +
327I GLU 3.2 16.6 - - - +
328I PHE 2.9 4.4 + - - +
330I LYS* 1.3 80.6 - - + +
332I ALA* 1.3 64.7 + - - +
334I VAL* 3.2 32.1 - - - +
335I ASN* 2.9 38.7 + - - +
343I TYR* 4.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I VAL* 4.4 2.7 - - + -
73I CYS* 3.1 25.0 - - - +
74I ILE* 4.0 14.4 - - + -
300I PHE* 4.4 3.0 - - - -
306I LEU* 3.6 12.0 - - + +
328I PHE* 2.8 40.7 + - + +
329I ILE* 3.6 9.2 - - - +
331I ARG* 1.3 71.7 - - - +
333I GLU* 1.3 58.1 + - - +
335I ASN* 4.0 2.0 - - - +
336I GLY 3.0 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I ARG* 3.2 27.6 + - - +
72I LYS* 2.7 42.2 + - - +
73I CYS* 3.7 13.8 - - - +
329I ILE* 2.9 31.4 + - + +
330I LYS* 3.0 7.3 + - - +
332I ALA* 1.3 75.8 - - - +
334I VAL* 1.3 65.6 + - - +
336I GLY* 3.0 11.1 + - - -
337I LEU* 3.0 17.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I SER* 3.7 14.4 - - - +
330I LYS* 2.8 24.8 + - + +
331I ARG* 3.1 43.3 - - - +
333I GLU* 1.3 73.2 - - - +
335I ASN* 1.3 57.4 + - - +
337I LEU* 2.9 13.4 + - - +
338I ALA* 2.8 23.9 + - - +
343I TYR* 3.3 42.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 335 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I SER* 2.7 31.8 + - - -
284I LEU* 4.0 2.0 - - + +
300I PHE* 3.5 28.7 - - + -
302I TYR* 3.5 24.0 - - - -
305I ALA 4.0 0.8 + - - -
306I LEU* 3.7 16.2 - - - +
331I ARG* 2.9 41.4 + - - +
332I ALA 4.1 0.7 - - - +
334I VAL* 1.3 73.2 - - - +
336I GLY* 1.3 60.5 + - - +
338I ALA* 3.7 6.5 - - - +
339I ALA* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 336 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I GLY* 3.2 30.3 - - - -
73I CYS* 3.7 7.2 - - - -
300I PHE* 4.1 6.7 - - - -
332I ALA 3.0 13.0 + - - -
333I GLU 3.0 8.7 + - - -
335I ASN* 1.3 77.5 - - - +
337I LEU* 1.3 59.9 + - - +
339I ALA* 3.6 2.3 - - - +
340I GLN* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333I GLU* 3.0 14.4 + - + +
334I VAL* 2.9 11.1 + - - +
336I GLY* 1.3 76.9 - - - +
338I ALA* 1.3 52.6 + - - +
339I ALA 2.9 4.7 - - - -
340I GLN* 2.7 31.8 + - - +
342I LYS* 3.1 51.8 + - + +
343I TYR* 3.8 21.8 - - + -
344I GLU 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I SER* 3.3 29.4 - - - +
284I LEU* 3.6 9.3 - - + +
285I ASN* 3.2 30.1 - - + +
288I ASN* 2.9 16.6 + - - -
334I VAL 2.8 12.7 + - - +
335I ASN* 3.7 12.8 - - - +
337I LEU* 1.3 76.2 - - - +
339I ALA* 1.3 56.8 + - - +
340I GLN 2.9 3.0 + - - -
341I GLY 3.1 6.8 + - - -
343I TYR* 3.7 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I GLY* 4.3 11.3 + - - -
284I LEU* 4.1 3.8 - - - +
288I ASN* 3.2 23.9 + - - +
298I LEU 4.2 2.9 + - - +
299I THR* 3.8 32.2 - - + +
300I PHE* 4.4 5.2 - - + -
335I ASN 2.8 16.7 + - - +
336I GLY* 3.6 12.1 - - - +
337I LEU 2.9 0.4 - - - -
338I ALA* 1.3 75.8 - - - +
340I GLN* 1.3 61.2 + - - +
----------------------------------------------------------
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