Contacts of the helix formed by residues 279 - 292 (chain A) in PDB entry 4FLL
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 ARG 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A ARG* 3.1 48.0 - - + +
278A TYR* 1.3 77.1 - - - +
280A GLU* 1.3 67.9 + - - +
281A LEU 3.3 0.4 + - - -
282A GLY 3.8 1.7 + - - -
283A ASN* 4.0 15.3 + - - +
320A LYS* 5.9 0.2 - - - -
321A ASN* 3.2 56.6 + - - +
322A LYS* 4.8 7.6 - - - +
323A ALA* 3.6 23.5 + - - +
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Residues in contact with GLU 280 (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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271A ALA* 5.8 0.4 - - + -
276A VAL* 4.2 16.2 - - + -
277A ARG* 3.1 19.7 + - + +
279A ARG* 1.3 84.6 + - + +
281A LEU* 1.4 66.7 + - - +
283A ASN* 2.9 42.9 + - - +
284A ILE* 3.4 26.8 + - + +
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Residues in contact with LEU 281 (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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268A ALA* 3.4 37.5 - - + +
271A ALA* 4.2 13.0 - - + -
272A VAL* 4.2 3.6 - - + +
276A VAL* 5.0 3.1 - - + -
277A ARG 4.8 0.2 - - - +
278A TYR* 3.3 11.2 + - + +
280A GLU* 1.4 76.6 - - - +
282A GLY* 1.3 57.0 + - - +
284A ILE* 3.1 10.3 + - + +
285A ILE* 3.0 34.9 + - + +
315A VAL* 3.8 25.8 - - + -
316A PRO 4.8 0.7 - - - +
327A MET* 3.7 31.0 - - + -
333A PHE* 4.0 4.9 - - + -
335A ILE* 3.7 24.5 - - + -
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Residues in contact with GLY 282 (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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278A TYR 4.6 0.2 + - - -
279A ARG 3.8 3.8 + - - -
280A GLU 3.3 0.8 - - - -
281A LEU* 1.3 74.2 - - - +
283A ASN* 1.3 64.5 + - - +
285A ILE* 4.4 0.2 - - - -
286A GLN* 3.0 19.4 + - - +
316A PRO 3.7 9.4 + - - -
317A HIS* 3.4 19.6 - - - +
318A TYR 3.3 33.1 - - - -
319A ALA 3.5 1.2 + - - -
321A ASN* 4.0 1.8 - - - -
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Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 4.0 17.1 + - - +
280A GLU* 2.9 37.5 + - - +
282A GLY* 1.3 79.0 - - - +
284A ILE* 1.3 61.9 + - - +
286A GLN* 4.2 0.5 - - - +
287A LYS* 2.9 26.9 + - - +
319A ALA* 3.2 12.3 - - + +
320A LYS* 2.9 34.5 + - - +
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Residues in contact with ILE 284 (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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267A GLN* 3.8 41.7 - - + +
268A ALA* 3.9 3.4 - - - +
271A ALA* 3.2 35.4 - - + -
280A GLU* 3.8 31.6 - - + +
281A LEU* 3.1 15.0 + - + +
283A ASN* 1.3 76.5 - - - +
285A ILE* 1.3 66.3 + - - +
287A LYS* 3.4 6.6 + - - +
288A HIS* 3.2 22.2 + - - +
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Residues in contact with ILE 285 (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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264A CYS* 3.6 35.3 - - + +
268A ALA* 3.9 16.8 - - + -
281A LEU* 3.0 21.9 + - + +
284A ILE* 1.3 77.4 - - - +
286A GLN* 1.3 57.6 + - - +
288A HIS 3.2 2.1 + - - -
289A ALA* 2.9 25.3 + - - +
296A VAL* 4.3 2.7 - - + -
317A HIS* 3.4 47.6 - - + +
335A ILE* 4.1 9.4 - - + -
337A PRO* 4.0 22.7 - - + -
339A ILE* 4.1 16.8 - - + -
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Residues in contact with GLN 286 (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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282A GLY 3.0 17.0 + - - +
285A ILE* 1.3 74.4 - - - +
287A LYS* 1.4 67.2 + - - +
289A ALA* 3.2 0.7 + - + -
290A GLN* 2.9 49.8 + - + +
296A VAL* 3.8 24.0 - - + +
298A ARG* 4.5 8.0 + - - +
318A TYR* 3.5 12.2 - - - +
319A ALA* 2.8 42.4 + - + +
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Residues in contact with LYS 287 (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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283A ASN 2.9 20.0 + - - +
284A ILE* 3.7 6.7 - - - +
285A ILE 3.2 0.2 - - - -
286A GLN* 1.4 77.1 - - - +
288A HIS* 1.3 60.9 + - - +
290A GLN* 3.9 4.7 - - - +
291A ALA* 3.1 23.9 + - + +
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Residues in contact with HIS 288 (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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260A THR* 3.7 25.5 - - + +
263A GLU* 2.7 38.1 + - + +
264A CYS* 3.8 10.5 - - - -
267A GLN* 3.4 35.7 + - - +
284A ILE 3.2 6.3 + - - +
285A ILE 3.2 7.2 + - - +
286A GLN 3.2 0.4 - - - -
287A LYS* 1.3 77.1 - - - +
289A ALA* 1.3 67.6 + - - +
290A GLN 3.4 0.2 + - - -
291A ALA* 3.4 10.2 + - + +
292A ASN* 3.0 40.8 + - - -
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Residues in contact with ALA 289 (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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260A THR* 4.3 7.2 - - - -
264A CYS* 3.8 7.7 - - - -
285A ILE 2.9 16.9 + - - +
286A GLN 3.8 2.7 - - - +
288A HIS* 1.3 76.0 - - - +
290A GLN* 1.3 58.8 + - - +
292A ASN* 3.0 14.0 + - - +
293A GLY 3.2 0.2 + - - -
294A PHE* 2.9 37.1 + - - +
296A VAL* 3.8 22.4 - - + -
339A ILE* 4.0 18.4 - - + -
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Residues in contact with GLN 290 (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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286A GLN* 2.9 44.6 + - + +
287A LYS* 3.9 4.7 - - - +
289A ALA* 1.3 78.4 - - - +
291A ALA* 1.3 60.9 + - - +
293A GLY* 3.1 13.5 + - - +
294A PHE 3.7 11.6 + - - +
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Residues in contact with ALA 291 (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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287A LYS* 3.1 18.6 + - + +
288A HIS* 3.7 11.9 - - + +
289A ALA 3.3 0.2 - - - -
290A GLN* 1.3 76.0 - - - +
292A ASN* 1.3 63.3 + - - +
293A GLY 3.4 1.1 + - - -
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Residues in contact with ASN 292 (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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256A LYS* 2.8 40.8 + - - +
260A THR* 3.7 25.5 + - + +
263A GLU* 4.9 0.6 + - - -
288A HIS* 3.0 45.3 + - - -
289A ALA 3.0 8.5 + - - +
291A ALA* 1.3 82.4 - - - +
293A GLY* 1.3 62.7 - - - +
294A PHE* 3.3 13.7 + - + -
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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
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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