Contacts of the helix formed by residues 320 - 339 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B ALA 3.3 20.2 - - - +
314B TRP* 3.3 25.6 - - - +
315B ARG* 4.4 4.5 - - - +
317B GLN* 3.2 18.9 + - - +
319B ASP* 1.3 90.2 + - - +
321B ALA* 1.3 64.2 + - - +
322B GLY 3.4 0.7 - - - -
323B ALA* 3.1 12.7 + - + +
324B ALA* 2.8 23.2 + - - +
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.6 12.9 - - + +
314B TRP* 4.2 13.0 - - + +
317B GLN 3.4 4.6 + - - +
318B ARG* 3.2 22.0 - - + +
319B ASP 2.9 2.4 + - - +
320B ASN* 1.3 77.5 - - - +
322B GLY* 1.3 57.4 + - - +
324B ALA* 3.1 3.4 + - - +
325B THR* 2.9 33.3 + - - -
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Residues in contact with GLY 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ASP 3.8 5.2 + - - -
320B ASN 3.4 0.4 - - - -
321B ALA* 1.3 78.8 - - - +
323B ALA* 1.3 57.2 + - - +
325B THR* 3.3 9.4 + - - -
326B GLU* 3.0 34.0 + - - +
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Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ALA* 4.4 10.5 - - + -
319B ASP 4.8 1.0 + - - +
320B ASN* 3.1 17.2 + - + +
322B GLY* 1.3 72.1 - - - +
324B ALA* 1.3 65.9 + - - +
326B GLU* 3.0 10.7 + - - +
327B GLU* 2.9 27.1 + - - +
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.3 18.4 - - + -
310B ALA* 3.2 31.7 - - - +
313B ALA* 3.8 7.5 - - - +
314B TRP* 3.5 15.9 - - + +
320B ASN 2.8 12.4 + - - +
321B ALA 3.3 9.4 - - - +
323B ALA* 1.3 76.8 - - - +
325B THR* 1.3 63.4 + - - +
327B GLU* 3.0 14.4 + - - +
328B PHE* 3.1 9.5 + - - +
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Residues in contact with THR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 2.8 31.9 + - - +
63B LEU 4.9 0.2 - - - +
65B SER* 3.8 9.4 + - - +
66B ALA* 3.6 30.7 - - + +
67B ASP 5.1 0.2 - - - +
321B ALA 2.9 16.2 + - - -
322B GLY* 3.5 12.1 - - - -
324B ALA* 1.3 76.2 - - - +
326B GLU* 1.3 59.3 + - - +
328B PHE* 3.4 5.8 + - + +
329B ILE* 3.0 39.9 + - + +
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ARG* 2.5 42.4 + - - -
322B GLY 3.0 19.8 + - - +
323B ALA* 3.0 11.6 + - - +
325B THR* 1.3 76.8 - - - +
327B GLU* 1.3 70.9 + - - +
328B PHE 3.1 0.2 + - - -
329B ILE* 3.2 7.3 + - - +
330B LYS* 2.8 29.9 + - - +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B SER* 3.1 38.3 - - - +
310B ALA* 3.5 15.3 - - - +
313B ALA* 4.7 6.2 - - + +
323B ALA* 2.9 16.0 + - - +
324B ALA* 3.0 10.0 + - - +
326B GLU* 1.3 78.9 - - - +
328B PHE* 1.3 62.8 + - - +
330B LYS* 3.4 28.8 + - + +
331B ARG* 3.2 28.0 + - - +
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Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.7 39.9 - - + -
62B VAL 5.0 0.9 - - - -
63B LEU* 3.4 48.0 - - + -
66B ALA* 3.9 17.5 - - + -
70B VAL* 4.0 18.4 - - + -
74B ILE* 4.7 3.8 - - + -
306B LEU* 3.6 29.8 - - + -
310B ALA* 3.8 12.3 - - + +
324B ALA 3.1 10.8 + - - +
325B THR* 3.5 8.7 - - - +
326B GLU 3.1 0.2 - - - -
327B GLU* 1.3 72.7 - - - +
329B ILE* 1.3 72.0 + - - +
330B LYS 2.9 2.0 + - - -
331B ARG* 2.9 4.0 + - - +
332B ALA* 2.8 35.2 + - + -
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Residues in contact with ILE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ALA* 3.7 32.1 - - + -
67B ASP* 3.8 18.4 - - - +
69B ARG* 3.6 62.4 - - + +
70B VAL* 4.8 4.9 - - + +
325B THR* 3.0 23.3 + - + +
326B GLU* 3.7 6.3 - - - +
328B PHE* 1.3 76.0 - - + +
330B LYS* 1.3 62.8 + - - +
332B ALA* 3.6 7.6 - - + +
333B GLU* 2.9 30.1 + - + +
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Residues in contact with LYS 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ARG* 5.6 0.6 - - - +
326B GLU* 2.8 17.7 + - - +
327B GLU* 3.4 33.7 + - - +
328B PHE 2.9 0.2 + - - -
329B ILE* 1.3 76.9 - - - +
331B ARG* 1.3 67.6 + - + +
333B GLU* 3.0 11.9 + - - +
334B VAL* 2.8 29.3 + - + +
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Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLU* 2.8 68.9 + - - +
278B GLU* 2.5 30.1 + - - -
281B SER* 3.0 17.6 + - - -
305B ALA 3.6 3.9 + - - +
306B LEU* 3.7 20.2 - - + +
309B SER* 4.0 3.4 - - - +
327B GLU 3.2 16.6 - - - +
328B PHE 2.9 4.8 + - - +
330B LYS* 1.3 79.5 - - + +
332B ALA* 1.3 63.4 + - - +
334B VAL* 3.1 31.6 - - - +
335B ASN* 2.9 38.1 + - - +
343B TYR* 4.4 1.0 + - - -
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 4.4 2.7 - - + -
73B CYS* 3.1 25.2 - - - +
74B ILE* 4.0 15.3 - - + -
300B PHE* 4.4 2.6 - - - -
306B LEU* 3.6 11.1 - - - +
328B PHE* 2.8 40.0 + - + +
329B ILE* 3.6 9.9 - - - +
331B ARG* 1.3 72.9 - - - +
333B GLU* 1.3 57.9 + - - +
335B ASN* 4.0 2.4 - - - +
336B GLY* 3.0 20.4 + - - -
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Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ARG* 3.2 28.0 + - - +
72B LYS* 2.7 42.1 + - - +
73B CYS* 3.7 12.6 - - - +
329B ILE* 2.9 29.9 + - + +
330B LYS* 3.5 7.3 - - - +
332B ALA* 1.3 75.8 - - - +
334B VAL* 1.3 67.0 + - - +
336B GLY* 3.0 11.1 + - - -
337B LEU* 3.0 18.0 + - + +
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B SER* 3.7 14.1 - - - +
330B LYS* 2.8 24.8 + - + +
331B ARG* 3.1 43.5 - - - +
333B GLU* 1.3 72.6 - - - +
335B ASN* 1.3 55.5 + - - +
337B LEU* 2.9 11.6 + - - +
338B ALA* 2.8 24.4 + - - +
343B TYR* 3.3 43.5 - - + +
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Residues in contact with ASN 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B SER* 2.7 32.7 + - - -
284B LEU* 4.0 2.2 - - + +
300B PHE* 3.5 28.5 - - + -
302B TYR* 3.5 24.9 + - - -
305B ALA 4.0 1.2 + - - -
306B LEU* 3.7 16.0 - - - +
331B ARG* 2.9 42.3 + - - +
334B VAL* 1.3 72.8 - - - +
336B GLY* 1.3 60.6 + - - +
338B ALA* 3.7 6.7 - - - +
339B ALA* 2.8 30.0 + - - +
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Residues in contact with GLY 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLY* 3.2 30.7 - - - -
73B CYS* 3.7 7.4 - - - -
300B PHE* 3.9 6.5 - - - -
332B ALA 3.0 13.4 + - - -
333B GLU 3.0 9.7 + - - -
335B ASN* 1.3 77.4 - - - +
337B LEU* 1.3 59.3 + - - +
339B ALA* 3.6 2.1 - - - +
340B GLN* 3.1 22.4 + - - +
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B GLU* 3.0 14.4 + - + +
334B VAL* 2.9 12.2 + - - +
336B GLY* 1.3 75.7 - - - +
338B ALA* 1.3 52.9 + - - +
339B ALA 2.9 4.7 - - - -
340B GLN* 2.7 31.2 + - - +
342B LYS* 3.1 52.2 + - + +
343B TYR* 3.8 21.8 - - + -
344B GLU 5.5 0.7 - - - +
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B SER* 3.3 30.1 - - - +
284B LEU* 3.6 10.6 - - + +
285B ASN* 3.2 30.0 - - + +
288B ASN* 2.9 16.3 + - - -
334B VAL 2.8 13.3 + - - +
335B ASN* 3.2 12.5 + - - +
337B LEU* 1.3 75.4 - - - +
339B ALA* 1.3 56.2 + - - +
340B GLN 2.9 3.2 + - - -
341B GLY 3.1 5.9 + - - -
343B TYR* 3.7 5.1 - - + +
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Residues in contact with ALA 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY* 4.3 11.1 + - - -
284B LEU* 4.2 4.0 - - - -
288B ASN* 3.2 22.1 + - - +
298B LEU 4.2 3.7 + - - +
299B THR* 3.8 33.5 - - + +
300B PHE* 4.4 5.2 - - + -
335B ASN 2.8 18.0 + - - +
336B GLY* 3.6 12.8 - - - +
337B LEU 2.9 0.8 - - - -
338B ALA* 1.3 75.2 - - - +
340B GLN* 1.3 60.9 + - - +
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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) + - + + + + + -
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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