Contacts of the helix formed by residues 320 - 337 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLN* 5.8 2.0 - - - +
61C LEU* 4.1 22.4 - - + +
64C SER* 5.3 1.8 - - - +
313C TRP* 4.5 9.4 - - - +
316C LYS 4.4 2.2 - - - +
317C LYS* 3.1 62.8 - - + +
318C GLU 3.3 1.8 - - - -
319C ASN* 1.3 78.5 - - - +
321C ALA* 1.3 63.9 + - - +
323C GLY* 3.2 1.2 + - - -
324C GLN* 3.0 50.2 + - + +
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Residues in contact with ALA 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C GLU 4.8 5.3 + - - +
319C ASN 3.3 0.4 - - - -
320C ILE* 1.3 78.7 - - - +
322C ALA* 1.3 57.3 - - - +
324C GLN* 3.4 12.8 + - - +
325C ASN* 2.8 41.5 + - - +
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C ALA* 4.0 14.6 - - + +
318C GLU 5.3 0.4 + - - -
319C ASN* 3.1 24.0 + - + +
321C ALA* 1.3 76.4 - - - +
323C GLY* 1.3 66.7 + - - +
325C ASN* 3.1 16.6 + - - +
326C GLU* 3.2 17.0 + - - +
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Residues in contact with GLY 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 4.6 6.1 - - - -
309C VAL* 3.7 28.6 - - - +
312C ALA* 3.8 17.1 - - - +
313C TRP 4.5 1.6 - - - -
319C ASN 2.9 13.5 + - - -
320C ILE 3.7 2.9 - - - -
322C ALA* 1.3 74.7 - - - +
324C GLN* 1.3 62.2 + - - +
326C GLU* 3.0 15.8 + - - +
327C LEU 3.2 9.4 + - - -
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Residues in contact with GLN 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 2.9 35.0 + - + +
64C SER* 3.1 20.6 + - - +
65C THR* 3.3 36.1 - - + +
66C ASP 5.0 1.6 + - - +
320C ILE* 3.0 34.2 + - - +
321C ALA* 3.6 10.2 - - - +
323C GLY* 1.3 75.5 - - - +
325C ASN* 1.3 59.4 + - - +
327C LEU* 3.4 7.0 + - - +
328C LEU* 3.1 35.1 + - + +
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Residues in contact with ASN 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ALA* 2.8 30.3 + - - +
322C ALA* 3.1 11.8 + - - +
324C GLN* 1.3 78.0 - - - +
326C GLU* 1.3 62.6 + - - +
328C LEU* 3.4 16.3 + - - +
329C LYS* 3.0 34.8 + - + +
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C SER* 3.7 34.8 + - - +
309C VAL* 4.1 16.2 - - + +
312C ALA* 3.8 11.0 - - + +
322C ALA* 3.2 15.9 + - - +
323C GLY 3.0 8.4 + - - +
325C ASN* 1.3 76.6 - - - +
327C LEU* 1.3 60.1 + - - +
329C LYS* 3.5 29.0 + - - +
330C ARG* 3.0 31.7 + - - +
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Residues in contact with LEU 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 4.6 21.1 - - + -
61C LEU* 5.7 0.2 - - + -
62C LEU* 3.7 32.1 - - + +
65C THR* 3.6 23.6 - - + +
69C LEU* 3.8 25.1 - - + -
73C ILE* 5.8 1.1 - - + -
305C LEU* 4.1 27.1 - - + +
306C GLN* 5.8 0.4 - - + -
309C VAL* 3.6 18.1 - - + +
323C GLY 3.2 4.3 + - - +
324C GLN* 3.5 9.6 - - - +
326C GLU* 1.3 76.3 - - - +
328C LEU* 1.3 58.9 + - - +
330C ARG* 3.4 1.4 + - - +
331C ALA* 2.9 33.8 + - + +
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Residues in contact with LEU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C THR* 3.5 26.5 - - + -
66C ASP* 4.2 17.7 - - + +
68C LYS* 4.5 11.4 - - + -
69C LEU* 3.9 31.6 - - + +
72C ASN* 5.2 0.7 + - - -
324C GLN* 3.1 24.7 + - + +
325C ASN* 3.7 18.2 - - - +
326C GLU 3.3 0.2 - - - -
327C LEU* 1.3 77.6 - - - +
329C LYS* 1.3 62.7 + - - +
331C ALA* 3.4 3.9 + - - +
332C LYS* 3.0 24.9 + - - +
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Residues in contact with LYS 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C ASN* 3.0 22.9 + - + +
326C GLU* 3.7 29.8 + - - +
327C LEU 3.3 0.2 - - - -
328C LEU* 1.3 77.6 - - - +
330C ARG* 1.3 57.5 + - + +
332C LYS* 3.4 5.9 + - - +
333C ALA* 3.1 28.2 + - - +
348C ALA* 3.1 40.0 + - + +
349C GLY* 4.7 4.6 - - - -
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Residues in contact with ARG 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C GLU* 3.5 31.5 + - - +
277C GLU* 3.2 30.5 + - - +
280C THR* 2.7 42.9 + - - +
304C ALA 4.2 15.9 - - - +
305C LEU* 3.7 21.3 - - + +
308C SER* 5.8 2.9 - - - -
326C GLU 3.0 17.0 + - - +
327C LEU 3.9 1.6 - - - +
329C LYS* 1.3 75.0 - - + +
331C ALA* 1.3 59.9 + - - +
333C ALA* 3.6 1.8 + - - +
334C ASN* 3.0 45.2 + - - +
342C TYR* 4.0 2.4 + - - -
348C ALA* 3.2 34.8 + - - +
349C GLY 4.4 0.8 - - - +
351C ALA 4.7 5.3 - - - +
352C GLY* 4.8 6.1 - - - +
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 4.1 11.2 - - + -
72C ASN* 3.4 18.1 - - + +
73C ILE* 3.9 33.4 - - + -
299C PHE* 4.4 2.0 - - - -
305C LEU* 3.8 8.7 - - + +
327C LEU* 2.9 18.2 + - + +
328C LEU* 3.9 3.8 - - + +
330C ARG* 1.3 75.2 - - - +
332C LYS* 1.3 56.2 + - - +
334C ASN* 3.4 3.4 + - - +
335C GLY 2.8 28.8 + - - -
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Residues in contact with LYS 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LYS* 6.4 2.9 - - - +
71C GLU* 5.5 5.3 + - - +
72C ASN* 3.5 25.6 + - - +
328C LEU 3.0 18.4 + - - +
329C LYS* 3.5 7.6 - - - +
331C ALA* 1.3 77.1 - - - +
333C ALA* 1.3 57.4 - - - +
335C GLY* 3.2 1.6 + - - -
336C ASP* 2.9 57.6 + - - +
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Residues in contact with ALA 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C THR* 3.5 12.9 - - + +
329C LYS 3.1 13.5 + - - +
330C ARG* 3.9 8.7 - - - +
332C LYS* 1.3 80.4 - - - +
334C ASN* 1.3 59.0 - - - +
336C ASP* 3.4 7.6 + - - +
337C ALA* 3.0 26.5 + - - +
342C TYR* 3.4 33.7 - - + -
348C ALA* 3.7 13.7 - - + -
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Residues in contact with ASN 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C GLU 5.2 0.2 + - - -
279C ALA 4.4 0.2 - - - +
280C THR* 2.8 37.5 + - - -
283C LEU* 3.9 1.2 - - - +
299C PHE* 3.4 35.4 - - + -
301C TYR* 3.5 31.7 - - - -
304C ALA 4.6 2.4 + - - -
305C LEU* 4.0 9.5 - - - +
330C ARG* 3.0 34.7 + - - +
331C ALA* 4.0 0.7 - - - +
333C ALA* 1.3 73.2 - - - +
335C GLY* 1.3 60.6 + - - +
337C ALA* 3.3 5.7 + - - +
338C ALA* 2.9 24.1 + - - +
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Residues in contact with GLY 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C GLY* 3.2 26.9 - - - -
72C ASN* 3.9 5.8 - - - -
299C PHE* 3.8 5.5 - - - -
331C ALA 2.8 17.4 + - - -
332C LYS 3.2 2.6 + - - -
334C ASN* 1.3 75.3 - - - +
336C ASP* 1.3 62.9 + - - +
338C ALA* 3.2 16.3 - - - +
339C GLN* 3.4 18.2 + - - -
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Residues in contact with ASP 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASN* 5.7 0.3 - - - +
332C LYS* 2.9 46.8 + - - +
333C ALA* 3.5 12.5 - - - +
335C GLY* 1.3 74.9 - - - +
337C ALA* 1.3 55.9 + - - +
339C GLN* 2.9 33.3 + - - +
341C LYS* 2.9 46.2 + - + +
342C TYR* 4.1 7.5 - - + +
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Residues in contact with ALA 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C THR* 3.4 30.1 - - + +
283C LEU* 3.5 21.4 - - + +
284C SER* 3.5 14.8 - - - +
287C ASN* 3.2 11.4 + - - -
333C ALA 3.0 15.6 + - - +
334C ASN* 3.4 12.3 - - - +
336C ASP* 1.3 70.3 - - - +
338C ALA* 1.3 55.6 + - - +
339C GLN 2.9 4.9 - - - -
340C GLY* 2.8 19.6 + - - -
342C TYR* 4.0 2.0 - - + +
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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