Contacts of the helix formed by residues 320 - 337 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D GLN* 6.1 1.1 - - - +
61D LEU* 4.1 26.0 - - + +
64D SER* 5.3 1.6 - - - +
313D TRP* 4.8 1.6 - - + +
316D LYS 4.3 0.9 - - - +
317D LYS* 3.2 51.4 - - + +
318D GLU 3.4 2.2 - - - -
319D ASN* 1.3 76.5 - - - +
321D ALA* 1.3 59.2 + - - +
323D GLY* 3.4 0.7 + - - -
324D GLN* 2.9 61.2 + - + +
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Residues in contact with ALA 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D GLU 4.8 4.8 + - - +
319D ASN* 3.3 0.4 - - - +
320D ILE* 1.3 79.5 - - - +
322D ALA* 1.3 56.8 + - - +
324D GLN* 3.4 5.7 + - - +
325D ASN* 2.8 47.2 + - - +
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Residues in contact with ALA 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D ALA* 4.0 19.5 - - + +
319D ASN* 3.3 15.7 + - + +
321D ALA* 1.3 79.3 - - - +
323D GLY* 1.3 61.4 + - - +
325D ASN* 3.3 7.4 + - - +
326D GLU* 3.1 27.7 + - - +
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Residues in contact with GLY 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LEU* 4.3 5.8 - - - -
309D VAL* 3.6 35.5 - - - +
312D ALA* 4.1 5.3 - - - +
313D TRP* 4.4 4.3 - - - -
319D ASN 2.9 15.5 + - - -
320D ILE 3.7 1.1 - - - -
322D ALA* 1.3 76.0 - - - +
324D GLN* 1.3 61.5 + - - +
326D GLU* 3.2 14.2 + - - +
327D LEU 3.3 8.8 + - - -
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Residues in contact with GLN 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LEU* 2.8 34.8 + - + +
64D SER* 3.0 29.0 + - - +
65D THR* 3.5 31.0 - - + +
66D ASP* 4.6 3.1 + - - +
320D ILE* 2.9 40.1 + - - +
321D ALA* 4.1 5.3 - - - +
323D GLY* 1.3 71.2 - - - +
325D ASN* 1.3 56.8 + - - +
327D LEU* 3.2 7.3 + - - +
328D LEU* 3.0 35.8 + - + +
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Residues in contact with ASN 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D ALA* 2.8 36.2 + - - +
322D ALA* 3.5 8.0 - - - +
323D GLY 3.2 0.2 - - - -
324D GLN* 1.3 74.0 - - - +
326D GLU* 1.3 60.8 + - + +
328D LEU* 3.4 16.6 + - - +
329D LYS* 3.0 40.8 + - + +
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Residues in contact with GLU 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D SER* 3.7 33.0 + - - +
309D VAL* 4.0 17.9 - - + +
312D ALA* 3.7 11.5 - - + +
322D ALA 3.1 17.5 + - - +
323D GLY 3.2 8.3 + - - +
325D ASN* 1.3 76.8 - - - +
327D LEU* 1.3 61.7 + - - +
329D LYS* 3.5 33.7 + - - +
330D ARG* 3.1 32.4 + - - +
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Residues in contact with LEU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 4.6 25.6 - - + -
61D LEU* 6.2 0.2 - - + -
62D LEU* 4.0 25.6 - - + +
65D THR* 3.8 20.9 - - + +
69D LEU* 3.8 31.2 - - + -
73D ILE* 6.0 0.9 - - + -
305D LEU* 3.9 27.6 - - + +
306D GLN* 5.4 0.9 - - + -
309D VAL* 3.6 17.4 - - + +
323D GLY 3.3 5.7 + - - +
324D GLN* 3.2 10.8 + - - +
326D GLU* 1.3 74.3 - - - +
328D LEU* 1.3 62.1 + - - +
330D ARG* 3.3 1.4 + - - +
331D ALA* 2.9 33.1 + - + +
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Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D THR* 3.6 26.7 - - + -
66D ASP* 4.3 18.8 - - + +
68D LYS* 3.8 30.5 + - + +
69D LEU* 3.8 28.9 - - + +
324D GLN* 3.0 25.2 + - + +
325D ASN* 3.4 17.4 + - - +
327D LEU* 1.3 74.2 - - - +
329D LYS* 1.3 63.8 + - + +
331D ALA* 3.8 3.8 - - - +
332D LYS* 3.1 25.5 + - - +
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Residues in contact with LYS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D ASN* 3.0 26.2 + - + +
326D GLU* 3.5 34.7 + - - +
327D LEU 3.2 0.2 - - - -
328D LEU* 1.3 77.6 - - - +
330D ARG* 1.3 60.0 + - + +
332D LYS* 3.6 5.2 + - - +
333D ALA* 3.1 26.6 + - - +
348D ALA* 3.8 33.0 + - + +
349D GLY* 5.5 1.8 - - - -
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Residues in contact with ARG 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D GLU* 3.8 45.1 + - - +
277D GLU* 2.9 30.3 + - - +
280D THR* 2.9 36.0 + - - +
304D ALA 4.5 2.7 - - - +
305D LEU* 3.9 23.8 - - + +
308D SER* 5.5 2.9 - - - -
326D GLU* 3.1 22.5 + - - +
327D LEU 4.1 0.7 - - - +
328D LEU 3.3 0.2 - - - -
329D LYS* 1.3 81.1 - - + +
331D ALA* 1.3 59.0 - - - +
333D ALA* 3.6 4.4 - - - +
334D ASN* 3.0 37.7 + - - +
342D TYR* 3.8 3.4 + - - -
348D ALA* 3.8 27.9 + - - +
349D GLY 4.0 6.7 + - - -
352D GLY* 4.4 7.9 - - - -
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Residues in contact with ALA 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 4.0 21.8 - - + -
72D ASN* 3.3 18.0 - - + +
73D ILE* 4.0 21.1 - - + -
299D PHE* 4.3 1.9 - - - -
305D LEU* 3.9 10.9 - - + +
327D LEU* 2.9 18.9 + - + +
328D LEU* 3.8 4.0 - - + +
330D ARG* 1.3 73.1 - - - +
332D LYS* 1.3 60.3 - - - +
334D ASN* 3.3 4.2 + - - +
335D GLY 2.9 23.7 + - - -
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Residues in contact with LYS 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LYS* 4.5 11.0 - - - +
71D GLU* 5.9 1.3 - - - +
72D ASN* 3.2 36.0 + - - +
328D LEU 3.1 18.0 + - - +
329D LYS* 3.7 6.7 - - - +
331D ALA* 1.3 74.3 - - - +
333D ALA* 1.3 59.9 + - - +
335D GLY 3.1 3.2 + - - -
336D ASP* 2.7 68.6 + - - +
339D GLN* 4.6 5.3 - - - +
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Residues in contact with ALA 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D THR* 3.3 14.2 - - + +
329D LYS 3.1 14.8 + - - +
330D ARG* 3.6 17.5 - - - +
331D ALA 3.4 0.2 - - - -
332D LYS* 1.3 78.9 - - - +
334D ASN* 1.3 57.7 + - - +
336D ASP* 3.7 4.1 + - - +
337D ALA 3.1 18.5 + - - -
342D TYR* 3.6 20.9 - - + -
348D ALA* 3.6 25.1 - - + -
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Residues in contact with ASN 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D GLU 5.4 0.2 + - - -
280D THR* 3.1 30.6 + - - -
283D LEU* 4.0 1.9 - - - +
299D PHE* 3.4 36.1 - - + -
301D TYR* 3.3 35.7 - - - -
304D ALA 4.5 6.7 + - - -
305D LEU* 3.8 12.9 - - - +
330D ARG* 3.0 26.1 + - - +
331D ALA 3.9 0.7 - - - +
332D LYS 3.1 0.2 - - - -
333D ALA* 1.3 76.5 - - - +
335D GLY* 1.3 58.4 + - - +
336D ASP 3.3 0.4 - - - -
337D ALA* 3.5 6.0 - - - +
338D ALA* 3.0 23.7 + - - +
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Residues in contact with GLY 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLY* 3.1 33.9 - - - -
72D ASN* 3.8 4.3 - - - -
299D PHE* 3.8 4.0 - - - -
331D ALA 2.9 14.4 + - - -
332D LYS* 3.1 5.6 + - - -
334D ASN* 1.3 73.4 - - - +
336D ASP* 1.3 62.8 + - - +
338D ALA* 3.5 7.7 + - - +
339D GLN* 3.1 23.4 + - - -
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Residues in contact with ASP 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D LYS* 2.7 53.7 + - - +
333D ALA* 3.8 8.3 - - - +
335D GLY* 1.3 75.1 - - - +
337D ALA* 1.3 56.0 - - - +
339D GLN* 3.0 22.9 + - - +
341D LYS* 2.8 55.4 + - + +
342D TYR* 3.9 8.7 - - + +
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Residues in contact with ALA 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D THR* 3.4 32.3 - - + +
283D LEU* 3.5 11.6 - - + +
284D SER* 3.4 25.8 - - - +
287D ASN* 3.3 10.4 + - - -
333D ALA 3.1 18.4 + - - +
334D ASN* 3.5 8.1 - - - +
335D GLY 3.4 0.4 - - - -
336D ASP* 1.3 73.1 - - - +
338D ALA* 1.3 56.7 + - - +
339D GLN 2.9 4.9 - - - -
340D GLY 2.9 15.2 + - - -
342D TYR* 3.9 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