Contacts of the helix formed by residues 320 - 337 (chain B) in PDB entry 1FBA
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 ILE 320 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLN* 5.8 5.8 - - - +
61B LEU* 4.1 22.0 - - + +
64B SER* 5.2 1.1 - - - +
313B TRP* 4.1 11.9 - - + +
316B LYS 4.0 2.9 - - - +
317B LYS* 3.2 45.3 + - + +
318B GLU 3.4 0.8 - - - -
319B ASN* 1.3 77.7 - - - +
321B ALA* 1.3 58.7 + - - +
323B GLY* 3.2 2.8 + - - -
324B GLN* 3.0 58.5 + - - +
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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
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318B GLU 5.0 3.5 + - - +
319B ASN 3.3 0.6 - - - -
320B ILE* 1.3 79.4 - - - +
322B ALA* 1.3 57.4 + - - +
324B GLN* 3.4 13.1 + - - +
325B ASN* 2.9 37.3 + - - +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA* 4.0 13.9 - - + +
318B GLU 5.5 0.8 + - - +
319B ASN* 3.3 22.1 + - + +
320B ILE 3.2 0.6 - - - -
321B ALA* 1.3 76.8 - - - +
323B GLY* 1.3 62.6 + - - +
325B ASN* 3.3 9.3 + - - +
326B GLU* 3.2 27.0 + - - +
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Residues in contact with GLY 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.4 5.6 - - - -
309B VAL* 3.4 41.5 - - - +
312B ALA* 3.9 6.4 - - - +
313B TRP 4.5 1.6 - - - -
319B ASN 3.0 13.0 + - - -
320B ILE 3.2 3.1 + - - -
322B ALA* 1.3 77.4 - - - +
324B GLN* 1.3 60.5 + - - +
326B GLU* 3.1 3.3 + - - +
327B LEU 3.1 17.5 + - - -
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Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 2.8 30.8 + - + +
64B SER* 3.1 22.0 + - - +
65B THR* 3.5 36.9 - - + +
66B ASP 5.1 1.3 + - - +
320B ILE* 3.0 39.3 + - - +
321B ALA* 3.8 10.9 - - - +
322B ALA 3.3 0.2 - - - -
323B GLY* 1.3 76.0 - - - +
325B ASN* 1.3 56.8 + - - +
327B LEU* 3.4 6.6 + - - +
328B LEU* 2.9 37.2 + - + +
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Residues in contact with ASN 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ALA* 2.9 20.7 + - - +
322B ALA* 3.3 13.7 - - - +
324B GLN* 1.3 75.7 - - - +
326B GLU* 1.3 68.0 - - - +
328B LEU* 3.4 15.4 + - - +
329B LYS* 3.0 39.7 + - + +
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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
----------------------------------------------------------
308B SER* 3.6 32.9 + - - +
309B VAL* 3.9 17.0 - - + +
312B ALA* 3.9 8.8 - - + +
322B ALA 3.2 13.2 + - - +
323B GLY 3.1 8.6 + - - +
325B ASN* 1.3 81.1 - - - +
327B LEU* 1.3 62.4 + - - +
329B LYS* 3.4 31.1 + - - +
330B ARG* 3.1 29.7 + - - +
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Residues in contact with LEU 327 (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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30B LEU* 4.6 21.8 - - + -
61B LEU* 5.7 0.4 - - + -
62B LEU* 3.9 30.7 - - + +
65B THR* 3.7 23.6 - - - +
69B LEU* 4.1 24.0 - - + -
73B ILE* 6.0 0.9 - - + -
305B LEU* 3.9 30.5 - - + +
306B GLN* 5.5 0.4 - - + -
309B VAL* 3.4 17.1 - - + +
323B GLY 3.1 7.6 + - - +
324B GLN* 3.5 8.1 - - - +
325B ASN 3.3 0.2 - - - -
326B GLU* 1.3 76.3 - - - +
328B LEU* 1.3 57.1 + - - +
330B ARG* 3.3 2.0 + - - +
331B ALA* 2.9 32.1 + - - +
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Residues in contact with LEU 328 (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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65B THR* 3.6 27.6 - - + -
66B ASP* 4.3 15.5 - - + +
68B LYS* 4.3 28.0 - - + +
69B LEU* 3.8 30.5 - - + +
72B ASN* 5.2 0.5 + - - -
324B GLN* 2.9 25.7 + - + +
325B ASN* 3.8 15.9 - - - +
326B GLU 3.4 0.2 - - - -
327B LEU* 1.3 76.0 - - - +
329B LYS* 1.3 62.7 + - + +
331B ALA* 3.5 4.9 + - + +
332B LYS* 3.1 25.1 + - - +
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Residues in contact with LYS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ASN* 3.0 29.9 + - + +
326B GLU* 3.4 33.7 + - - +
327B LEU 3.2 0.2 - - - -
328B LEU* 1.3 76.3 - - + +
330B ARG* 1.3 60.5 + - + +
332B LYS* 3.4 6.1 + - - +
333B ALA* 3.1 26.9 + - - +
347B SER 5.8 0.2 - - - -
348B ALA* 2.9 40.4 + - + +
349B GLY* 4.9 2.0 - - - -
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Residues in contact with ARG 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU* 3.6 41.8 + - - +
277B GLU* 3.6 27.3 + - - +
280B THR* 2.8 36.8 + - - -
304B ALA 4.5 3.8 - - - +
305B LEU* 3.9 22.2 - - + +
308B SER* 5.4 4.5 - - - -
326B GLU* 3.1 20.7 + - - +
327B LEU 4.1 1.3 - - - +
329B LYS* 1.3 78.3 - - + +
331B ALA* 1.3 60.3 + - - +
333B ALA* 3.7 7.1 - - - +
334B ASN* 3.0 39.0 + - - +
342B TYR* 3.8 6.9 + - - -
348B ALA* 3.9 17.7 + - - +
349B GLY 3.7 12.5 + - - -
352B GLY* 4.2 14.5 - - - -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.9 24.0 - - + -
72B ASN* 3.4 23.9 - - + +
73B ILE* 4.0 13.9 - - + -
299B PHE* 4.4 2.2 - - - -
305B LEU* 3.8 10.4 - - + +
327B LEU* 2.9 17.6 + - + +
328B LEU* 3.9 4.3 - - + +
330B ARG* 1.3 73.2 - - - +
332B LYS* 1.3 61.3 + - - +
334B ASN* 3.4 4.0 + - - +
335B GLY 2.9 23.7 + - - -
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Residues in contact with LYS 332 (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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71B GLU* 5.6 4.3 - - - +
72B ASN* 3.1 38.1 + - - +
328B LEU 3.1 17.2 + - - +
329B LYS* 3.7 6.3 - - - +
331B ALA* 1.3 75.7 - - - +
333B ALA* 1.3 59.5 + - - +
335B GLY 3.2 2.6 + - - -
336B ASP* 2.8 66.5 + - - +
339B GLN* 4.5 6.1 - - - +
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Residues in contact with ALA 333 (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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280B THR* 3.4 10.7 - - + +
329B LYS 3.1 17.5 + - - +
330B ARG* 3.7 18.2 - - - +
331B ALA 3.3 0.2 - - - -
332B LYS* 1.3 77.7 - - - +
334B ASN* 1.3 57.4 - - - +
336B ASP* 3.3 7.9 + - - +
337B ALA 2.9 22.0 + - - -
342B TYR* 3.4 31.1 - - + -
348B ALA* 3.7 13.7 - - + -
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Residues in contact with ASN 334 (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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276B GLU 5.3 0.2 + - - -
279B ALA 4.5 0.2 - - - +
280B THR* 2.9 34.2 + - - -
283B LEU* 4.0 2.1 - - - +
299B PHE* 3.6 30.6 - - + -
301B TYR* 3.5 31.6 - - - -
304B ALA 4.4 6.5 + - - -
305B LEU* 3.9 14.5 - - - +
330B ARG* 3.0 25.5 + - - +
331B ALA* 3.9 1.6 - - - +
333B ALA* 1.3 73.0 - - - +
335B GLY* 1.3 59.0 + - - +
337B ALA* 3.2 6.7 + - - +
338B ALA* 2.9 28.9 + - - +
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Residues in contact with GLY 335 (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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26B GLY* 3.7 12.4 - - - -
72B ASN* 3.7 14.8 - - - -
299B PHE* 3.9 7.6 - - - -
331B ALA 2.9 15.9 + - - -
332B LYS* 3.2 5.8 + - - -
334B ASN* 1.3 73.3 - - - +
336B ASP* 1.3 62.4 + - - +
338B ALA* 3.4 14.6 + - - +
339B GLN* 3.0 22.8 + - - +
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Residues in contact with ASP 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LYS* 2.8 49.3 + - - +
333B ALA* 3.5 10.6 - - - +
335B GLY* 1.3 74.5 - - - +
337B ALA* 1.3 60.3 + - - +
339B GLN* 2.8 28.0 + - - +
341B LYS* 2.9 37.9 + - + +
342B TYR* 4.0 19.4 - - + +
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B THR* 3.3 35.4 - - + +
283B LEU* 3.5 12.9 - - + +
284B SER* 3.4 22.7 - - - +
287B ASN* 3.3 11.4 + - - -
333B ALA 2.9 15.3 + - - +
334B ASN* 3.2 9.1 + - - +
336B ASP* 1.3 76.8 - - - +
338B ALA* 1.3 55.5 + - - +
340B GLY* 2.9 18.5 + - - -
342B TYR* 3.9 1.3 - - - +
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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
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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