Contacts of the helix formed by residues 320 - 337 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLN* 5.8 2.5 - - - +
61A LEU* 4.1 27.1 - - + +
64A SER* 5.3 1.8 - - - +
313A TRP* 4.3 4.3 - - - +
316A LYS 4.3 2.0 - - - +
317A LYS* 3.0 59.5 - - + +
318A GLU 3.0 3.1 + - - +
319A ASN* 1.3 77.2 - - - +
321A ALA* 1.3 64.4 + - - +
323A GLY* 3.3 2.6 + - - -
324A GLN* 3.1 50.2 + - + +
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Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLU 4.1 5.8 + - - +
319A ASN 3.3 0.4 - - - -
320A ILE* 1.3 77.6 - - + +
322A ALA* 1.3 59.2 + - - +
324A GLN* 3.5 11.0 + - - +
325A ASN* 2.3 48.2 + - - +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ALA* 3.9 16.9 - - + +
318A GLU 5.3 0.2 + - - -
319A ASN* 3.3 20.3 + - + +
321A ALA* 1.3 79.2 - - - +
323A GLY* 1.3 60.8 - - - +
325A ASN* 3.4 7.6 + - - +
326A GLU* 3.3 26.7 + - - +
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Residues in contact with GLY 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 4.7 2.9 - - - -
309A VAL* 3.6 37.6 - - - +
312A ALA* 3.9 6.2 - - - +
313A TRP* 4.4 3.1 - - - -
319A ASN 3.1 12.8 + - - -
320A ILE 3.3 3.3 + - - -
321A ALA 3.3 0.2 - - - -
322A ALA* 1.3 75.3 - - - +
324A GLN* 1.3 64.2 + - - +
326A GLU* 3.0 16.1 + - - +
327A LEU 3.1 8.8 + - - -
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Residues in contact with GLN 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 2.6 41.0 + - + +
64A SER* 2.9 22.4 + - - +
65A THR* 3.5 31.0 - - + +
66A ASP 5.0 1.6 + - - -
320A ILE* 3.1 31.2 + - - +
321A ALA* 3.8 9.7 - - - +
322A ALA 3.4 0.2 - - - -
323A GLY* 1.3 75.5 - - - +
325A ASN* 1.3 59.7 + - - +
327A LEU* 3.3 8.1 + - - +
328A LEU* 3.0 34.2 + - + +
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Residues in contact with ASN 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A ALA* 2.3 44.3 + - - +
322A ALA* 3.6 8.0 - - - +
323A GLY 3.1 0.2 - - - -
324A GLN* 1.3 78.4 - - - +
326A GLU* 1.3 60.7 + - - +
328A LEU* 3.3 17.1 + - - +
329A LYS* 3.0 37.2 + - + +
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Residues in contact with GLU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A SER* 3.5 46.2 + - - +
309A VAL* 4.0 3.7 - - - +
312A ALA* 3.9 9.4 - - + +
322A ALA 3.3 16.1 + - - +
323A GLY 3.0 9.2 + - - +
325A ASN* 1.3 78.0 - - - +
327A LEU* 1.3 61.2 + - - +
329A LYS* 2.9 38.5 + - - +
330A ARG* 3.1 28.9 + - - +
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.4 19.1 - - + -
62A LEU* 4.0 29.4 - - + +
65A THR* 3.7 22.0 - - - +
69A LEU* 4.0 24.5 - - + -
73A ILE* 6.0 0.4 - - + -
305A LEU* 3.4 35.4 - - + +
309A VAL* 3.7 16.1 - - + +
323A GLY 3.1 6.8 + - - +
324A GLN* 3.4 9.0 - - - +
326A GLU* 1.3 76.6 - - - +
328A LEU* 1.3 60.2 + - - +
330A ARG* 3.4 1.6 + - - +
331A ALA* 2.9 32.9 + - + +
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A THR* 3.6 27.8 - - + -
66A ASP* 4.2 17.9 - - + +
68A LYS* 3.9 30.5 + - + +
69A LEU* 3.8 28.7 - - + +
324A GLN* 3.0 21.9 + - + +
325A ASN* 3.3 22.0 + - - +
327A LEU* 1.3 77.1 - - - +
329A LYS* 1.3 61.3 + - + +
331A ALA* 3.9 3.8 - - - +
332A LYS* 3.1 26.7 + - - +
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ASN* 3.0 19.8 + - + +
326A GLU* 2.9 43.4 + - - +
327A LEU 3.2 0.2 - - - -
328A LEU* 1.3 78.1 - - - +
330A ARG* 1.3 60.3 + - + +
332A LYS* 3.5 4.6 + - - +
333A ALA* 3.1 25.1 + - - +
348A ALA* 3.8 30.8 + - + +
349A GLY* 5.8 1.2 - - - -
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Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLU* 3.7 40.7 + - - +
277A GLU* 3.1 21.0 + - - +
280A THR* 3.0 32.2 + - - -
304A ALA 3.9 8.3 - - - +
305A LEU* 3.8 21.5 - - + +
308A SER* 5.5 3.6 - - - -
326A GLU* 3.1 16.5 + - - +
327A LEU 4.1 1.6 - - - +
329A LYS* 1.3 79.9 - - + +
331A ALA* 1.3 60.4 + - - +
333A ALA* 3.3 10.1 + - - +
334A ASN* 2.9 37.9 + - - +
342A TYR* 3.7 7.5 + - - -
348A ALA* 3.9 18.3 + - - +
349A GLY 3.7 19.4 + - - -
352A GLY* 4.4 13.9 - - - -
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 6.1 0.4 - - - +
69A LEU* 4.0 22.7 - - + -
72A ASN* 3.4 18.4 - - + +
73A ILE* 4.0 20.0 - - + -
299A PHE* 4.4 2.0 - - - -
305A LEU* 3.7 10.0 - - + +
327A LEU* 2.9 19.0 + - + +
328A LEU* 3.9 4.7 - - + +
330A ARG* 1.3 75.1 - - - +
332A LYS* 1.3 57.9 + - - +
334A ASN* 3.4 2.9 + - - +
335A GLY 2.8 24.3 + - - -
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Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS* 4.5 14.4 - - - +
71A GLU* 5.6 2.9 + - - +
72A ASN* 3.5 31.3 + - - +
328A LEU 3.1 18.2 + - - +
329A LYS* 3.7 5.4 - - - +
331A ALA* 1.3 79.0 - - - +
333A ALA* 1.3 58.0 + - - +
335A GLY* 3.2 2.5 + - - -
336A ASP* 3.0 62.1 + - - +
339A GLN* 5.5 2.8 - - - +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A THR* 3.5 10.3 - - + +
329A LYS 3.1 17.2 + - - +
330A ARG* 3.3 18.6 + - - +
332A LYS* 1.3 77.0 - - - +
334A ASN* 1.3 57.7 + - - +
336A ASP* 3.3 9.0 + - - +
337A ALA 2.9 21.7 + - - -
342A TYR* 3.5 31.8 - - + -
348A ALA* 3.7 13.2 - - + -
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Residues in contact with ASN 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLU 5.2 0.6 + - - -
280A THR* 2.9 37.4 + - - -
283A LEU* 4.2 3.7 - - + +
299A PHE* 3.5 29.6 - - + -
301A TYR* 3.5 26.6 - - - -
304A ALA 4.6 3.6 + - - -
305A LEU* 3.8 16.2 - - - +
330A ARG* 2.9 29.5 + - - +
331A ALA 4.0 0.4 - - - +
333A ALA* 1.3 75.8 - - - +
335A GLY* 1.3 58.2 + - - +
337A ALA* 3.2 4.3 + - - +
338A ALA* 2.8 31.9 + - - +
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Residues in contact with GLY 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY* 3.3 32.3 - - - -
72A ASN* 3.6 10.3 - - - -
299A PHE* 3.7 5.9 - - - -
331A ALA 2.8 11.8 + - - -
332A LYS* 3.2 4.5 + - - -
334A ASN* 1.3 77.9 - - - +
336A ASP* 1.3 63.7 + - - +
338A ALA* 3.5 6.3 + - - +
339A GLN* 3.4 19.4 + - - -
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Residues in contact with ASP 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A LYS* 3.0 47.9 + - - +
333A ALA* 3.5 10.7 - - - +
334A ASN 3.1 0.2 - - - -
335A GLY* 1.3 76.4 - - - +
337A ALA* 1.3 59.3 + - - +
339A GLN* 3.0 19.2 + - - +
341A LYS* 2.8 60.1 + - + +
342A TYR* 4.0 8.6 - - + +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 3.4 33.2 - - + +
283A LEU* 4.1 11.0 - - + -
284A SER* 3.5 24.3 - - - +
287A ASN* 3.3 10.7 + - - -
333A ALA 2.9 14.7 + - - +
334A ASN* 3.2 8.9 + - - +
336A ASP* 1.3 71.8 - - - +
338A ALA* 1.3 55.9 + - - +
339A GLN 2.9 5.4 - - - -
340A GLY* 2.8 21.8 + - - -
342A TYR* 4.0 1.9 - - + +
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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
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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