Contacts of the helix formed by residues 221 - 232 (chain A) in PDB entry 2VHW
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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219A TYR* 3.3 6.7 + - - -
220A SER* 1.3 77.2 - - - +
222A ALA* 1.3 57.8 + - - +
223A TYR* 3.6 2.1 + - - -
224A GLU* 3.1 22.5 + - - +
225A LEU* 2.8 32.7 + - - +
21D ALA* 3.4 27.6 - - - +
25D GLU* 6.0 2.7 - - - -
318D MET* 4.8 16.8 - - - -
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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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221A SER* 1.3 72.6 - - - +
223A TYR* 1.3 57.3 + - - +
225A LEU* 3.7 7.6 - - - +
226A GLU* 2.9 47.0 + - - +
24D ALA* 6.1 3.8 - - + -
25D GLU* 5.0 12.4 + - - +
28D ARG* 5.8 6.7 - - - -
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Residues in contact with TYR 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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221A SER* 3.1 1.0 + - - -
222A ALA* 1.3 81.5 - - - +
224A GLU* 1.3 71.1 + - - +
226A GLU* 3.6 13.1 + - - +
227A GLY* 3.5 14.9 + - - -
20D PRO* 3.5 35.7 - - + +
21D ALA* 3.6 37.9 + - + +
24D ALA* 4.6 14.0 - - + +
49D ASP* 5.0 9.9 + - - +
52D ALA* 6.5 0.7 - - + -
53D ALA* 4.7 9.0 - - + -
311D TYR* 6.0 4.0 - + - -
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Residues in contact with GLU 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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197A LEU* 3.9 4.7 - - + -
218A ARG* 3.6 38.5 + - + +
219A TYR 3.5 23.3 - - - +
221A SER* 3.1 19.7 + - - +
223A TYR* 1.3 83.2 - - - +
225A LEU* 1.3 64.7 + - - +
227A GLY* 3.4 1.8 + - - -
228A ALA* 3.1 23.7 + - + +
231A ARG* 4.5 11.6 + - - -
167B GLU* 5.0 3.8 - - - +
21D ALA* 5.5 2.6 - - + +
311D TYR* 5.4 9.2 - - - -
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Residues in contact with LEU 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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174A ILE* 4.2 19.5 - - + -
197A LEU* 4.2 14.1 - - + +
220A SER* 3.9 20.2 - - - +
221A SER 2.8 17.9 + - - +
222A ALA* 3.7 7.6 - - - +
224A GLU* 1.3 75.1 - - - +
226A GLU* 1.3 66.5 + - + +
227A GLY 3.3 0.2 + - - -
228A ALA* 3.3 2.6 + - - -
229A VAL* 2.9 37.1 + - + +
249A LEU* 3.4 47.3 - - + +
250A VAL* 4.0 18.2 - - + -
254A LEU* 4.3 5.4 - - + -
1373A NAI 5.5 0.2 - - - +
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Residues in contact with GLU 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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222A ALA* 2.9 31.2 + - - +
223A TYR* 3.8 14.0 - - - +
225A LEU* 1.3 77.8 - - + +
227A GLY* 1.3 61.1 + - - +
229A VAL 3.6 0.2 + - - -
230A LYS* 3.2 41.6 + - - +
254A LEU* 3.6 33.0 - - + +
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Residues in contact with GLY 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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223A TYR 3.5 7.5 + - - -
224A GLU 3.4 5.4 + - - -
225A LEU 3.3 0.6 - - - -
226A GLU* 1.3 75.3 - - - +
228A ALA* 1.3 65.0 + - - +
230A LYS* 3.5 9.7 + - - +
231A ARG* 3.4 41.5 + - - +
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Residues in contact with ALA 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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170A ASP* 4.6 0.5 - - - +
172A VAL* 3.5 26.3 - - + +
195A THR* 5.2 7.6 - - + -
197A LEU* 4.2 20.2 - - + -
218A ARG* 5.9 1.6 - - + -
224A GLU* 3.1 18.4 + - - +
225A LEU 3.9 2.7 - - - +
227A GLY* 1.3 74.4 - - - +
229A VAL* 1.3 63.6 + - - +
231A ARG* 3.2 30.9 + - - +
232A ALA 3.3 9.4 + - - -
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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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172A VAL* 4.7 6.7 - - + -
174A ILE* 4.6 3.6 - - + -
225A LEU* 2.9 39.1 + - + +
226A GLU 4.0 2.7 - - - +
228A ALA* 1.3 77.3 - - - +
230A LYS* 1.3 60.9 + - - +
232A ALA* 3.2 16.0 + - - +
235A VAL* 4.3 16.8 - - + -
250A VAL* 4.3 16.2 - - + -
254A LEU* 3.8 22.4 - - + -
258A MET* 3.5 43.1 - - + +
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Residues in contact with LYS 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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226A GLU* 3.2 29.0 + - - +
227A GLY* 3.8 8.7 - - - +
228A ALA 3.3 0.4 - - - -
229A VAL* 1.3 76.3 - - - +
231A ARG* 1.3 61.5 + - + +
232A ALA 3.7 0.3 + - - +
254A LEU* 3.8 25.8 - - + +
257A HIS* 3.8 43.2 + - + +
258A MET* 4.6 6.6 - - - -
259A LYS* 3.9 23.2 + - - +
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Residues in contact with ARG 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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170A ASP* 3.6 24.4 + - - +
195A THR* 6.3 0.8 - - - +
218A ARG* 5.5 4.8 - - - +
224A GLU* 4.5 13.1 + - - -
227A GLY* 3.4 29.2 + - - +
228A ALA* 3.2 30.9 + - - +
230A LYS* 1.3 79.0 - - + +
232A ALA* 1.3 59.0 + - - +
259A LYS* 2.9 25.5 + - - +
167B GLU* 4.9 10.6 + - - -
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Residues in contact with ALA 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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170A ASP* 3.5 11.9 - - - +
172A VAL* 3.6 28.0 - - + -
228A ALA 3.3 1.9 + - - +
229A VAL 3.2 17.8 + - - +
230A LYS 4.7 0.3 - - - +
231A ARG* 1.3 78.5 - - - +
233A ASP* 1.3 60.9 + - - +
234A LEU 3.7 3.8 - - - +
235A VAL* 3.7 20.6 - - + -
258A MET* 4.3 1.9 - - - +
259A LYS* 3.5 13.6 + - - +
262A ALA* 3.9 13.0 - - - +
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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