Contacts of the helix formed by residues 266 - 278 (chain A) in PDB entry 2FYU
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 ASP 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A PRO* 4.3 0.9 - - - +
264A HIS* 3.0 23.0 + - - -
265A PRO* 1.3 76.3 - - + +
267A ASN* 1.3 56.5 + - - +
268A VAL 3.2 1.0 + - - -
269A ALA* 3.4 6.1 + - + +
270A LEU* 3.1 35.1 + - - +
410A VAL* 3.6 30.0 - - + +
413A LYS* 4.3 9.5 + - - +
414A TYR* 2.8 38.3 + - - -
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Residues in contact with ASN 267 (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 PRO* 4.4 14.5 + - - +
261A GLY 2.7 31.3 + - - -
262A TRP 3.7 10.5 + - - +
264A HIS* 3.2 19.3 + - - +
265A PRO 4.8 0.2 - - - +
266A ASP* 1.3 74.5 + - - +
268A VAL* 1.3 57.7 + - + +
270A LEU* 3.6 6.6 + - - +
271A GLN* 3.1 35.3 + - - +
311A ASN* 2.7 31.0 + - - +
313A CYS* 3.6 13.5 - - - -
57I GLY 4.7 12.8 - - - +
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PRO* 3.5 15.1 + - + +
266A ASP 3.2 1.4 - - - -
267A ASN* 1.3 75.7 - - + +
269A ALA* 1.3 56.3 + - - +
271A GLN* 3.2 6.6 + - - +
272A VAL* 3.0 29.4 + - + +
361A LEU* 3.8 4.0 - - + +
395A TRP* 3.9 32.3 - - + -
398A ARG* 3.5 42.0 - - + +
399A ILE* 3.8 22.2 - - + -
402A VAL* 4.2 4.5 - - + -
57I GLY* 4.0 13.7 - - - -
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASP* 3.4 6.6 + - + +
268A VAL* 1.3 75.9 - - - +
270A LEU* 1.3 60.3 + - - +
272A VAL* 3.6 3.6 - - - +
273A ALA* 3.1 25.6 + - - +
402A VAL* 3.9 19.7 - - + +
406A VAL* 3.9 29.2 - - + +
407A VAL* 4.0 6.6 - - + +
410A VAL* 3.8 24.0 - - + -
411A CYS* 5.2 0.5 - - - -
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Residues in contact with LEU 270 (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 PRO* 4.0 20.4 - - + -
266A ASP 3.1 23.3 + - - +
267A ASN* 3.7 7.6 - - - +
268A VAL 3.3 0.2 - - - -
269A ALA* 1.3 73.2 - - - +
271A GLN* 1.3 58.4 + - - +
273A ALA* 3.4 6.3 + - + +
274A ASN* 2.9 33.7 + - - +
311A ASN* 4.4 7.4 - - - +
320A LEU* 3.8 40.3 - - + +
410A VAL* 3.8 19.1 - - + +
411A CYS* 4.6 5.2 - - - -
414A TYR* 3.8 31.4 - - + -
415A PHE* 4.5 10.7 - - + -
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Residues in contact with GLN 271 (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 ASN 3.1 21.8 + - - +
268A VAL* 3.2 6.7 + - - +
270A LEU* 1.3 73.9 - - - +
272A VAL* 1.4 55.3 + - - +
274A ASN* 3.3 14.9 + - - +
275A ALA* 2.9 34.8 + - - +
310A PHE* 5.2 0.4 - - - +
311A ASN* 3.9 30.9 + - - +
361A LEU* 3.8 21.9 - - + +
55I LEU* 3.3 42.4 - - - +
56I ARG 3.1 22.2 - - - +
57I GLY 4.7 5.1 - - - -
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 3.0 19.2 + - + +
269A ALA 3.6 7.9 - - - +
271A GLN* 1.4 74.2 - - - +
273A ALA* 1.3 60.7 + - - +
275A ALA* 3.4 5.2 + - - +
276A ILE* 3.2 29.1 + - + +
354A VAL* 3.6 31.4 - - + +
357A GLY* 3.6 8.3 - - - -
358A LYS* 3.9 17.9 - - + +
361A LEU* 3.8 15.4 - - + +
399A ILE* 4.8 3.1 - - + -
402A VAL* 4.0 22.2 - - + -
407A VAL* 3.9 18.2 - - + -
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Residues in contact with ALA 273 (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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269A ALA 3.1 12.4 + - - +
270A LEU* 3.4 10.8 - - - +
271A GLN 3.3 0.2 - - - -
272A VAL* 1.3 75.7 - - - +
274A ASN* 1.3 64.5 + - - +
276A ILE* 3.3 24.6 + - - +
277A ILE* 3.3 11.9 + - - +
345A LEU* 3.6 15.7 - - + +
407A VAL* 4.2 5.4 - - + -
411A CYS* 3.5 32.1 - - - -
415A PHE* 5.8 2.2 - - + -
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Residues in contact with ASN 274 (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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270A LEU 2.9 19.6 + - - +
271A GLN* 3.3 16.4 + - - +
273A ALA* 1.3 76.6 - - - +
275A ALA* 1.3 52.2 + - - +
277A ILE* 3.5 3.6 + - - +
278A GLY* 2.7 28.2 + - - -
309A THR* 2.9 42.0 + - - +
310A PHE 3.1 28.6 + - - +
311A ASN* 4.0 5.0 - - - +
320A LEU* 3.6 17.0 - - - +
321A GLY 4.3 5.7 + - - -
342A TRP* 5.0 4.2 - - - +
415A PHE* 4.6 13.7 - - - -
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Residues in contact with ALA 275 (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 GLN 2.9 19.2 + - - +
272A VAL 3.5 6.1 - - - +
274A ASN* 1.3 74.4 - - - +
276A ILE* 1.3 63.3 + - - +
278A GLY* 3.2 15.2 + - - +
279A HIS* 6.4 0.7 - - - -
292A SER* 5.5 0.5 - - - -
356A ARG* 5.0 0.5 + - - -
357A GLY* 3.7 21.3 - - - +
360A LEU* 3.5 32.6 - - + +
361A LEU* 5.0 4.9 - - + +
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Residues in contact with ILE 276 (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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272A VAL* 3.2 20.9 + - + +
273A ALA* 3.3 16.6 + - - +
275A ALA* 1.3 72.9 - - - +
277A ILE* 1.3 65.5 + - + +
292A SER* 3.3 13.0 + - - -
293A PRO* 4.6 2.8 - - + +
344A ARG* 4.1 5.8 - - - +
345A LEU* 3.9 21.1 - - + -
353A GLU* 3.3 52.0 - - + +
354A VAL* 3.9 24.5 - - + -
356A ARG* 3.2 33.9 + - - +
357A GLY* 4.0 5.4 - - - +
407A VAL* 4.7 2.5 - - + -
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Residues in contact with ILE 277 (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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273A ALA 3.3 9.2 + - - +
274A ASN* 3.9 6.1 - - - +
276A ILE* 1.3 77.2 - - + +
278A GLY* 1.3 60.7 + - - +
292A SER* 2.5 24.3 + - - -
294A LEU* 3.7 29.4 - - + +
307A PHE* 3.5 10.5 - - + -
309A THR* 3.6 22.4 - - + -
322A ALA* 5.9 0.2 - - + -
338A LEU* 4.4 7.0 - - + -
341A GLN* 3.8 29.8 - - + +
342A TRP* 3.6 31.6 - - + +
345A LEU* 3.8 26.2 - - + -
415A PHE* 6.2 0.2 - - + -
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Residues in contact with GLY 278 (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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274A ASN 2.7 16.9 + - - -
275A ALA* 3.2 18.0 + - - -
277A ILE* 1.3 76.0 - - - +
279A HIS* 1.3 66.7 - - - -
292A SER* 5.0 3.1 - - - -
307A PHE* 3.6 4.9 - - - -
309A THR* 2.9 34.9 + - - +
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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
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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