Contacts of the helix formed by residues 258 - 268 (chain A) in PDB entry 1YI8
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 ASN 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A THR* 2.9 36.2 + - - +
243A ASP* 3.9 3.7 + - + +
254A ARG 4.0 7.9 - - - +
255A VAL 3.3 7.6 + - - +
256A GLU 3.2 4.6 + - - -
257A GLY* 1.3 72.1 - - - +
259A PRO* 1.3 59.6 - - - +
260A VAL* 3.0 38.7 - - - +
261A PHE* 2.6 56.3 + - + +
262A THR* 3.3 3.9 + - - +
281A TYR* 2.8 31.1 + - - -
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Residues in contact with PRO 259 (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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208A PRO* 4.4 4.3 - - + -
209A GLY 3.8 15.3 - - - +
210A LEU 3.6 7.0 - - - +
212A GLY* 4.9 2.5 - - - +
240A MET* 3.2 25.1 - - + -
241A TYR* 2.6 43.3 - - + +
257A GLY 2.7 14.3 - - - +
258A ASN* 1.3 77.6 - - - +
260A VAL* 1.3 52.6 + - + +
262A THR* 3.1 16.0 - - + +
263A PHE* 2.6 48.0 + - + +
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Residues in contact with VAL 260 (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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240A MET* 3.9 12.5 - - + +
242A THR* 3.5 22.9 - - + -
258A ASN* 2.9 18.6 + - - +
259A PRO* 1.3 78.3 - - + +
261A PHE* 1.3 58.1 + - + +
263A PHE* 3.6 0.7 - - - +
264A LEU* 2.8 29.5 + - + +
291A VAL* 4.1 12.8 - - + -
292A LYS* 3.8 30.1 - - + +
295A LEU* 3.3 40.4 - - + +
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Residues in contact with PHE 261 (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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255A VAL* 3.2 51.4 - - + +
258A ASN* 2.6 41.3 + - + +
260A VAL* 1.3 69.8 - - + +
262A THR* 1.3 55.5 + - - +
263A PHE 2.7 6.3 + - - -
264A LEU* 2.6 32.0 + - + +
265A ASP* 2.8 16.9 + - - +
274A VAL* 5.1 1.1 - - + +
277A LEU* 4.4 4.3 - - + -
278A LYS* 3.3 29.2 - - + -
281A TYR* 3.2 59.2 - + + -
291A VAL* 4.1 17.7 - - + -
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Residues in contact with THR 262 (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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206A ARG 5.3 1.4 + - - -
207A LEU* 4.4 3.5 - - - +
208A PRO* 3.3 33.2 - - + +
255A VAL* 5.1 1.2 + - - +
257A GLY* 4.5 4.9 - - - +
258A ASN 3.3 3.5 + - - +
259A PRO* 3.1 35.2 - - + +
261A PHE* 1.3 75.8 - - - +
263A PHE* 1.3 58.3 + - - +
265A ASP* 2.5 21.9 + - - +
266A ALA* 3.6 12.6 - - - +
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Residues in contact with PHE 263 (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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37A LEU* 4.3 19.7 - - + -
207A LEU* 4.5 13.9 - - + -
208A PRO* 3.2 40.2 - - + -
210A LEU* 3.7 35.9 - - + -
216A MET* 5.2 4.0 - - + -
224A ILE* 4.9 5.2 - - + -
240A MET* 4.1 10.3 - - + -
259A PRO* 2.6 32.7 + - + +
260A VAL* 3.6 5.6 - - - +
261A PHE 2.7 0.6 + - - -
262A THR* 1.3 72.9 - - - +
264A LEU* 1.3 64.7 + - - +
266A ALA* 3.0 12.2 + - - -
267A PHE* 3.3 28.0 + + - +
295A LEU* 3.9 27.6 - - + -
299A LEU* 4.2 12.6 - - + -
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Residues in contact with LEU 264 (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 VAL 2.8 18.9 + - - +
261A PHE* 2.6 18.1 + - + +
263A PHE* 1.3 71.5 - - - +
265A ASP* 1.3 51.4 + - - +
267A PHE* 4.9 0.9 - - - +
268A ASP* 2.6 43.5 + - + +
274A VAL* 4.4 20.6 - - + +
277A LEU* 4.6 16.8 - - + -
291A VAL* 4.4 21.5 - - + -
294A HIS* 3.6 32.8 - - + +
295A LEU* 4.1 23.3 - - + +
298A VAL* 4.1 18.4 - - + -
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Residues in contact with ASP 265 (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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261A PHE 2.8 14.4 + - - +
262A THR* 2.5 45.3 - - - +
264A LEU* 1.3 72.4 - - - +
266A ALA* 1.3 57.4 + - - +
268A ASP* 3.9 8.7 - - - +
271A PRO* 6.0 3.6 - - + +
274A VAL* 3.6 25.7 - - + +
278A LYS* 4.7 14.4 + - - +
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Residues in contact with ALA 266 (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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41A ALA* 5.0 11.1 - - - +
45A GLN* 4.3 19.1 + - - +
207A LEU* 4.6 9.9 - - + -
262A THR 3.6 16.2 - - - +
263A PHE 3.0 4.9 + - - +
265A ASP* 1.3 80.4 + - - +
267A PHE* 1.3 76.4 + - + +
268A ASP 4.5 2.4 - - - +
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Residues in contact with PHE 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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37A LEU* 3.7 36.6 - - + -
40A LEU* 3.8 25.6 - - + -
41A ALA* 3.6 34.8 - - + -
45A GLN* 5.2 3.6 - - - -
207A LEU* 4.3 13.2 - - + -
263A PHE* 3.3 25.4 + + - +
266A ALA* 1.3 83.0 - - + +
268A ASP* 1.3 68.1 + - - +
269A PRO* 3.7 1.9 - - - +
295A LEU* 5.9 0.4 - - + -
298A VAL* 4.1 9.7 - - + +
299A LEU* 3.9 26.0 - - + -
302A VAL* 4.4 28.5 - - + +
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Residues in contact with ASP 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 2.6 30.4 + - + +
265A ASP* 3.9 4.7 - - - +
266A ALA 4.5 2.6 - - - +
267A PHE* 1.3 84.4 + - - +
269A PRO* 1.3 70.7 - - + +
270A ASP* 2.9 23.3 - - - +
273A ARG* 3.2 26.8 + - - +
274A VAL* 2.8 24.5 - - - +
294A HIS* 4.9 0.9 - - + -
298A VAL* 3.5 25.6 - - + +
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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