Contacts of the helix formed by residues 219 - 224 (chain B) in PDB entry 2V5Q
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 ALA 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B TYR 3.3 5.3 + - - -
218B ILE* 1.3 76.3 - - - +
220B PRO* 1.3 73.9 - - + +
221B GLU* 3.4 26.0 - - - +
222B VAL* 3.0 18.9 + - + +
223B LEU* 3.3 7.6 + - - +
232B VAL* 4.0 20.2 - - + +
235B TRP* 3.6 23.3 - - + -
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Residues in contact with PRO 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ILE 3.6 0.4 - - - -
219B ALA* 1.3 85.1 - - + +
221B GLU* 1.3 63.3 + - - +
223B LEU* 3.1 22.7 + - + +
224B SER* 3.2 12.3 + - - -
235B TRP* 3.6 39.5 - - + -
263B ILE* 3.8 25.4 - - + +
264B LYS* 4.8 6.9 - - - +
288B THR* 3.9 28.5 - - + +
293B ARG* 3.6 11.2 - - - +
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ALA* 3.4 12.9 - - - +
220B PRO* 1.3 73.1 - - - +
222B VAL* 1.3 64.3 + - - +
224B SER* 3.0 24.6 + - - +
226B LYS* 3.4 22.2 - - + +
227B GLY 4.0 11.8 - - - +
228B HIS* 3.9 21.9 - - + +
231B GLU* 4.2 1.9 - - - +
232B VAL* 3.6 15.7 + - + +
288B THR 4.2 1.5 + - - +
290B PRO* 3.7 25.8 - - + +
293B ARG* 2.8 45.3 + - - -
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Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B LYS* 4.6 5.7 + - - +
211B LEU* 3.3 28.0 - - + -
215B PRO* 4.8 2.5 - - + -
218B ILE* 3.3 28.5 - - + -
219B ALA* 3.0 17.6 + - + +
221B GLU* 1.3 76.7 - - - +
223B LEU* 1.3 63.9 + - - +
224B SER 3.4 6.8 + - - +
226B LYS 5.3 0.7 - - - -
228B HIS* 4.0 19.7 - - + +
232B VAL* 3.7 30.1 - - + -
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B THR* 6.3 0.2 - - + -
218B ILE* 4.0 27.4 - - + -
219B ALA 3.3 1.9 + - - +
220B PRO 3.1 10.1 + - - +
222B VAL* 1.3 78.9 - - - +
224B SER* 1.3 57.3 + - - +
225B LYS* 5.8 0.2 - - - +
260B TYR* 3.6 59.0 - - + +
263B ILE* 3.9 24.7 - - + -
264B LYS* 3.9 33.6 + - + -
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Residues in contact with SER 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LYS* 3.1 18.7 + - - -
220B PRO 3.2 10.8 + - - -
221B GLU* 3.0 19.2 + - - +
222B VAL 3.2 3.9 - - - +
223B LEU* 1.3 81.4 - - - +
225B LYS* 1.3 63.5 + - - +
226B LYS* 3.0 25.4 + - - +
264B LYS* 5.7 1.8 - - - +
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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