Contacts of the helix formed by residues 247 - 255 (chain A) in PDB entry 1Y9A
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 HIS 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A OHS 2.7 50.8 + - - +
246A VAL* 1.3 92.2 - - + +
248A THR* 1.3 63.3 + - - +
249A PHE 3.2 3.2 + - - -
250A ALA* 3.5 13.7 + - - +
251A GLN* 3.8 15.7 + - - +
273A ASN 5.6 0.4 + - - -
275A ASP* 3.3 30.3 - - - +
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Residues in contact with THR 248 (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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173A ILE* 3.6 37.7 - - + -
241A ILE* 3.9 22.0 - - + -
243A GLY 4.0 3.6 - - - +
244A GLY* 3.5 5.7 - - - -
245A OHS 2.9 35.6 + - - -
247A HIS* 1.3 78.0 - - - +
249A PHE* 1.3 63.6 + - - +
251A GLN* 3.1 21.0 + - - +
252A ALA* 3.0 20.3 + - - +
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Residues in contact with PHE 249 (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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241A ILE* 3.8 21.8 - - + -
245A OHS 4.2 4.5 - - - -
246A VAL 3.9 7.9 - - - +
247A HIS 3.2 0.8 - - - -
248A THR* 1.3 77.8 - - - +
250A ALA* 1.3 57.4 + - - +
252A ALA* 3.3 2.8 + - - +
253A VAL* 2.9 33.2 + - + +
262A ILE* 4.7 5.1 - - + +
264A ASN* 3.4 45.1 - - + -
268A LEU* 4.0 32.1 - - + -
274A ILE* 3.5 36.1 - - + -
275A ASP 4.5 0.7 - - - +
276A ILE* 3.8 11.2 - - + -
290A ILE* 4.1 27.6 - - + -
291A HIS 4.7 1.3 - - - -
292A GLY* 5.8 0.9 - - - -
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Residues in contact with ALA 250 (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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247A HIS 3.5 10.8 + - - +
248A THR 3.3 0.6 - - - -
249A PHE* 1.3 74.3 - - - +
251A GLN* 1.3 61.6 + - + +
253A VAL* 3.3 2.1 + - - +
254A LYS* 2.9 45.8 + - - +
275A ASP* 3.9 23.3 + - - +
277A PRO* 3.7 29.6 - - + -
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Residues in contact with GLN 251 (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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173A ILE* 4.8 3.4 - - + +
222A ASP* 6.1 1.0 - - - -
223A ILE* 3.8 33.7 + - + +
224A VAL* 3.6 25.8 - - + +
245A OHS 5.5 8.1 + - - +
247A HIS 3.8 10.9 - - - +
248A THR* 3.1 33.3 + - - +
250A ALA* 1.3 73.2 - - + +
252A ALA* 1.3 66.7 + - - +
254A LYS* 3.1 3.9 + - + -
255A MET* 3.0 27.3 + - + +
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Residues in contact with ALA 252 (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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173A ILE* 4.5 2.8 - - + +
239A VAL* 3.7 25.5 - - + +
241A ILE* 4.0 14.4 - - + -
248A THR 3.0 9.7 + - - +
249A PHE 3.5 8.3 - - - +
251A GLN* 1.3 80.9 - - - +
253A VAL* 1.3 61.8 + - - +
255A MET* 3.3 12.1 + - - +
256A ILE* 3.2 24.9 + - - +
262A ILE* 3.9 17.7 - - + -
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Residues in contact with VAL 253 (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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249A PHE* 2.9 22.5 + - + +
250A ALA 3.6 4.7 - - - +
252A ALA* 1.3 75.6 - - - +
254A LYS* 1.3 62.3 + - - +
255A MET 3.4 0.3 + - - -
256A ILE* 3.5 11.8 + - - +
262A ILE* 3.8 16.8 - - + -
276A ILE* 4.2 16.4 - - + -
277A PRO* 4.1 10.5 - - + -
280A GLU* 3.6 34.3 - - + +
281A TRP* 3.9 26.9 - - + +
288A LYS* 2.8 29.1 + - + -
290A ILE* 4.6 1.1 - - + -
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Residues in contact with LYS 254 (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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224A VAL* 3.9 25.1 - - + +
228A LEU* 4.2 11.3 - - - +
250A ALA* 2.9 29.9 + - - +
251A GLN* 3.7 6.5 - - - +
253A VAL* 1.3 78.1 - - - +
255A MET* 1.3 57.6 + - - +
256A ILE 4.8 1.5 - - - +
277A PRO* 4.1 15.4 - - + +
280A GLU* 2.7 53.8 + - + -
288A LYS* 5.0 1.2 + - - +
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Residues in contact with MET 255 (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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171A CYS* 3.6 36.1 - - - -
173A ILE* 3.9 15.9 - - + -
223A ILE* 3.9 28.3 - - + -
224A VAL* 4.3 17.3 - - + -
227A ILE* 4.2 28.1 - - + +
228A LEU* 4.5 5.4 - - - -
235A GLY* 3.3 10.7 - - - -
236A VAL* 3.0 23.5 + - + +
239A VAL* 4.0 12.8 - - + -
251A GLN 3.0 17.6 + - - +
252A ALA* 3.3 14.4 - - - +
254A LYS* 1.3 78.0 - - - +
256A ILE* 1.3 59.1 + - - +
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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