Contacts of the helix formed by residues 221 - 233 (chain A) in PDB entry 1YA8
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 SER 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A PHE* 5.6 0.4 - - - -
141A GLY* 4.3 4.7 - - - -
142A GLY 4.4 0.2 + - - -
143A GLY* 4.7 0.9 + - - -
220A GLU* 1.3 84.7 - - - +
222A ALA* 1.3 64.7 + - - +
223A GLY 2.9 0.7 - - - -
224A GLY* 2.8 4.4 + - - +
225A GLU* 2.7 33.9 + - - +
246A GLU 3.0 12.5 + - - -
247A SER 3.2 15.8 + - - -
248A GLY* 3.9 6.2 - - - -
255A LEU* 5.1 0.9 - - - -
426A PHE* 5.6 1.4 - - - -
468A HIS* 3.4 16.1 + - - -
4001A SMB 2.7 24.4 + - - -
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Residues in contact with ALA 222 (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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140A HIS 4.7 0.4 - - - -
141A GLY* 3.9 2.0 - - - -
142A GLY 3.6 7.0 - - - +
143A GLY* 3.2 34.1 - - - +
144A LEU* 3.5 19.9 - - + +
170A TYR* 4.7 2.0 - - - +
220A GLU 3.2 0.2 + - - -
221A SER* 1.3 81.9 + - - +
223A GLY* 1.3 56.1 + - - +
225A GLU* 3.1 6.1 - - - +
226A SER* 2.8 30.7 + - - -
255A LEU* 3.7 19.5 - - + +
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Residues in contact with GLY 223 (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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139A ILE* 3.2 33.2 - - - +
140A HIS 3.7 6.7 - - - -
141A GLY* 3.6 2.8 - - - -
170A TYR* 4.7 0.2 - - - -
219A GLY* 3.7 6.8 - - - -
220A GLU 2.9 8.6 + - - -
222A ALA* 1.3 78.2 - - - +
224A GLY* 1.3 59.6 + - - +
226A SER* 3.2 4.0 + - - -
227A VAL* 3.0 31.0 + - - +
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Residues in contact with GLY 224 (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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219A GLY* 3.3 18.6 - - - -
220A GLU 3.4 8.7 - - - -
221A SER 2.8 8.2 + - - -
223A GLY* 1.3 75.4 - - - +
225A GLU* 1.3 57.7 + - - +
227A VAL* 3.3 1.8 + - - -
228A SER* 3.0 23.9 + - - -
245A SER* 3.2 18.1 + - - -
246A GLU 4.4 1.1 - - - -
248A GLY 3.2 16.4 - - - +
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Residues in contact with GLU 225 (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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144A LEU* 3.6 13.7 - - - +
191A HIS* 4.1 2.4 - - - -
221A SER 2.7 11.1 + - - +
222A ALA 3.1 12.2 - - - +
224A GLY* 1.3 77.3 - - - +
226A SER* 1.3 59.8 + - - +
228A SER* 3.3 3.8 + - - -
229A VAL* 3.0 44.5 + - - +
248A GLY* 3.6 3.5 + - - -
249A VAL 3.5 27.8 - - - +
250A ALA* 4.9 1.0 - - - -
252A THR* 5.0 4.0 - - + +
255A LEU* 3.5 39.1 - - + +
256A VAL* 3.7 11.9 - - + +
321A THR* 3.0 27.2 + - - -
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Residues in contact with SER 226 (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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139A ILE* 4.0 7.6 - - - -
144A LEU* 4.1 7.1 - - - +
170A TYR* 4.7 0.5 + - - -
191A HIS* 3.7 19.9 - - - -
194A GLN* 3.0 37.6 + - - +
222A ALA 2.8 15.8 + - - -
223A GLY* 3.4 11.0 - - - -
224A GLY 3.2 0.2 - - - -
225A GLU* 1.3 75.1 + - - +
227A VAL* 1.3 65.7 + - - +
229A VAL* 3.2 2.9 + - - +
230A LEU* 2.9 29.8 + - - +
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Residues in contact with VAL 227 (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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139A ILE* 4.4 9.6 - - + -
217A ILE* 3.8 19.5 - - + +
218A PHE* 3.8 11.2 - - - +
219A GLY* 3.7 22.4 - - - +
223A GLY 3.0 17.6 + - - +
224A GLY 3.3 7.6 + - - +
226A SER* 1.3 74.6 - - - +
228A SER* 1.3 64.0 + - - +
230A LEU* 3.2 4.6 + - - +
231A VAL* 2.9 29.3 + - + +
243A ALA* 3.7 27.1 - - + -
244A ILE 3.6 14.1 - - - +
245A SER* 3.7 9.9 - - - +
346A TYR* 4.4 0.9 - - + -
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Residues in contact with SER 228 (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 GLY 3.0 12.3 + - - -
225A GLU 3.4 7.2 - - - -
227A VAL* 1.3 76.9 - - - +
229A VAL* 1.3 62.7 + - - +
231A VAL* 3.1 17.0 + - - +
232A LEU* 3.3 15.8 + - - +
249A VAL* 3.8 6.3 - - - +
250A ALA* 2.8 41.4 + - - +
336A GLN* 5.4 1.6 + - - -
346A TYR* 3.6 23.9 + - - -
433A VAL* 5.0 3.8 - - - +
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Residues in contact with VAL 229 (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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191A HIS* 4.3 8.7 - - + +
225A GLU* 3.0 39.3 + - - +
226A SER* 3.6 6.7 - - - +
228A SER* 1.3 75.8 - - - +
230A LEU* 1.3 59.4 + - + +
232A LEU* 2.9 24.7 + - - +
233A SER* 3.1 10.9 + - - -
250A ALA* 5.0 8.1 - - + -
256A VAL* 5.5 1.6 - - + -
321A THR* 4.2 13.0 - - + +
327A LEU* 3.9 26.5 - - + -
328A LEU* 3.9 27.0 - - + +
332A PRO* 6.0 1.1 - - + -
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Residues in contact with LEU 230 (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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139A ILE* 4.2 19.7 - - + -
191A HIS* 4.5 10.5 - - + +
194A GLN* 4.6 12.3 - - + +
195A VAL* 3.5 33.0 - - + +
198A LEU* 3.9 23.6 - - + -
217A ILE* 3.9 21.1 - - + -
226A SER 2.9 19.3 + - - +
227A VAL* 3.6 4.5 - - - +
229A VAL* 1.3 77.7 - - + +
231A VAL* 1.3 62.4 + - - +
232A LEU 3.2 0.7 + - - -
233A SER* 3.2 13.4 + - - +
236A ALA* 3.5 24.8 - - + +
240A PHE* 3.9 5.0 - - + -
327A LEU* 4.8 8.7 - - + -
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Residues in contact with VAL 231 (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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217A ILE* 4.9 0.2 - - + -
227A VAL* 2.9 21.9 + - + +
228A SER* 3.1 10.9 + - - +
230A LEU* 1.3 76.9 - - - +
232A LEU* 1.3 63.1 + - + +
233A SER 5.1 0.6 - - - +
240A PHE* 3.9 17.8 - - + -
243A ALA* 4.1 24.2 - - + -
341A PHE* 4.1 27.7 - - + -
342A HIS 5.6 1.3 - - - +
343A THR* 6.3 0.7 - - - -
344A VAL* 4.8 12.3 - - + +
346A TYR* 4.5 21.5 - - + -
437A HIS* 5.0 7.9 - - + +
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Residues in contact with LEU 232 (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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228A SER* 3.7 10.3 - - - +
229A VAL* 2.9 9.4 + - - +
231A VAL* 1.3 86.6 - - + +
233A SER* 1.3 57.7 + - - +
234A PRO* 3.8 6.1 - - - +
250A ALA* 4.1 13.2 - - + -
327A LEU 4.5 0.2 - - - +
328A LEU* 4.2 8.3 - - + +
332A PRO* 3.7 41.5 - - + +
335A LEU* 3.8 40.6 - - + +
336A GLN* 4.2 25.6 - - + +
341A PHE* 4.9 15.0 - - + -
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Residues in contact with SER 233 (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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229A VAL 3.1 11.7 + - - -
230A LEU* 3.2 15.0 + - - +
231A VAL 3.5 0.9 - - - +
232A LEU* 1.3 78.5 - - - +
234A PRO* 1.3 66.1 - - - +
235A LEU* 3.0 11.0 + - - +
236A ALA* 3.1 13.3 + - - -
237A LYS* 3.5 7.6 + - - +
327A LEU* 2.5 53.1 + - - +
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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