Contacts of the helix formed by residues 214 - 225 (chain A) in PDB entry 2YVX
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ASP* 3.6 23.5 - - - +
133A GLU* 4.2 4.7 - - - +
213A THR* 1.3 78.9 - - - +
215A GLN* 1.3 78.9 + - - +
216A GLU* 3.2 10.8 + - + +
217A GLU* 2.8 22.3 + - + +
218A VAL 3.0 5.7 + - - -
255A GLU* 3.0 25.6 - - - +
454A MG 3.8 10.5 - - - -
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Residues in contact with GLN 215 (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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131A GLU* 2.6 26.4 + - - +
132A ASP* 2.7 46.8 + - - +
137A LEU* 4.0 18.7 - - + +
213A THR 4.0 2.2 - - - -
214A ASP* 1.3 70.6 + - - +
216A GLU* 1.3 54.3 + - - +
218A VAL* 2.9 9.3 + - - +
219A ALA* 2.6 34.8 + - - +
248A VAL* 5.1 0.3 - - - +
251A VAL* 3.0 40.4 - - + +
254A ALA* 5.4 3.3 - - - +
255A GLU* 4.0 13.9 + - - +
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Residues in contact with GLU 216 (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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214A ASP* 3.3 10.3 + - + +
215A GLN* 1.3 78.1 - - - +
217A GLU* 1.3 64.0 + - - +
219A ALA* 2.9 9.3 - - + +
220A ARG* 2.9 60.0 + - - +
251A VAL* 4.1 2.2 - - - +
252A LEU* 5.7 2.7 - - + -
255A GLU* 3.4 35.4 + - + +
259A ASP* 4.6 3.3 - - - +
343A ALA* 5.0 6.6 - - - +
418A ASP* 4.8 4.5 - - - +
451A MG 3.5 22.7 - - - -
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Residues in contact with GLU 217 (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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213A THR* 3.4 20.2 - - + -
214A ASP* 2.8 23.2 + - + +
216A GLU* 1.3 75.8 - - - +
218A VAL* 1.3 65.2 + - - +
219A ALA 3.1 0.2 + - - -
220A ARG* 3.2 37.8 + - - +
221A LEU* 3.4 19.4 + - + +
345A ARG* 5.8 0.3 + - - -
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Residues in contact with VAL 218 (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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134A ALA* 4.7 10.5 - - + -
137A LEU* 5.5 7.0 - - + -
209A VAL* 3.5 28.9 - - + -
213A THR* 3.1 29.8 - - + +
214A ASP 3.5 1.3 - - - +
215A GLN* 2.9 8.7 + - - +
217A GLU* 1.3 76.5 - - - +
219A ALA* 1.3 66.8 + - - +
221A LEU* 3.3 18.5 + - - +
222A MET* 3.7 6.0 + - + +
230A LEU* 3.8 25.5 - - + +
243A VAL* 5.1 18.4 - - + -
248A VAL* 5.4 5.2 - - + -
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Residues in contact with ALA 219 (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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215A GLN 2.6 15.7 + - - +
216A GLU* 2.9 15.3 - - - +
218A VAL* 1.3 72.9 - - - +
220A ARG* 1.3 67.2 + - + +
222A MET* 2.8 22.1 + - - +
223A ALA* 3.6 5.1 + - - +
248A VAL* 3.6 23.2 - - + +
251A VAL* 4.5 1.3 - - + -
252A LEU* 3.4 32.8 - - + -
249B LEU* 5.4 1.6 - - - +
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Residues in contact with ARG 220 (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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216A GLU* 2.9 50.5 + - + +
217A GLU* 3.2 43.0 + - - +
219A ALA* 1.3 71.5 - - + +
221A LEU* 1.3 65.9 + - + +
223A ALA* 2.8 21.0 + - - +
224A ASP* 3.1 17.8 + - - +
252A LEU* 5.3 0.4 - - - +
342A LEU 5.4 0.4 + - - -
343A ALA* 3.3 25.8 + - - +
345A ARG* 3.6 45.6 - - - +
413A ARG* 5.8 2.6 - - - +
253B GLU* 5.3 9.7 + - - +
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Residues in contact with LEU 221 (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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207A VAL* 6.0 4.5 - - + -
208A TYR 4.3 18.6 - - - +
209A VAL* 5.1 3.8 - - + -
213A THR* 6.4 0.7 - - + -
217A GLU* 3.4 17.9 + - + +
218A VAL* 3.3 11.6 + - - +
219A ALA 3.0 1.0 + - - -
220A ARG* 1.3 77.9 - - + +
222A MET* 1.3 57.5 + - - +
223A ALA 2.9 6.1 + - - -
224A ASP* 4.1 6.3 - - - +
225A TYR* 3.0 58.9 + - + +
227A PHE* 5.6 0.4 - - - -
230A LEU* 4.3 22.4 - - + -
345A ARG* 5.9 1.3 - - - +
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Residues in contact with MET 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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218A VAL* 3.7 5.3 + - + +
219A ALA* 2.8 15.7 + - - +
221A LEU* 1.3 73.0 - - - +
223A ALA* 1.3 57.3 + - - +
226A ASP* 4.0 2.4 - - - -
227A PHE* 3.5 44.0 + - + +
228A THR 3.7 17.0 - - - -
229A VAL 4.2 0.4 - - - -
230A LEU* 3.2 49.6 - - + +
243A VAL* 3.9 11.4 - - + +
244A THR 4.9 0.2 - - - +
245A VAL* 3.5 39.3 - - + +
248A VAL* 4.2 12.8 - - + -
246B ASP* 4.8 4.2 - - - +
249B LEU* 4.2 8.3 - - + +
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Residues in contact with ALA 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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219A ALA 3.6 2.9 + - - +
220A ARG* 2.8 18.5 + - - +
222A MET* 1.3 78.3 - - - +
224A ASP* 1.3 62.2 + - - +
226A ASP* 2.9 2.4 - - - +
252A LEU* 6.0 1.1 - - + -
345A ARG* 5.8 0.4 - - - +
453A MG 1.9 37.3 - - - -
246B ASP* 5.8 1.3 - - - -
249B LEU* 3.3 27.8 - - + -
250B ASP* 4.6 5.6 - - - +
253B GLU* 5.8 7.0 - - - +
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Residues in contact with ASP 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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220A ARG 3.1 15.7 + - - +
221A LEU* 4.0 9.0 + - - +
223A ALA* 1.3 76.3 - - - +
225A TYR* 1.3 64.0 + - + +
226A ASP* 2.7 27.7 + - - +
345A ARG* 2.7 47.8 + - - -
453A MG 3.8 1.0 - - - -
31B GLN* 3.2 36.7 + - + +
59B GLU* 5.1 0.5 - - - +
63B HIS* 4.2 3.4 - - - -
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Residues in contact with TYR 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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207A VAL* 4.3 28.3 - - + +
221A LEU* 3.0 45.6 + - + +
224A ASP* 1.3 84.6 - - + +
226A ASP* 1.3 58.6 + - - +
227A PHE* 2.6 48.9 - + + -
29B HIS* 3.4 49.1 - + + +
31B GLN* 4.0 15.1 - - + +
32B ASP* 4.2 13.2 + - - -
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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