Contacts of the helix formed by residues 255 - 266 (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 CYS 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B THR* 2.8 19.0 + - - -
254B SER* 1.3 85.3 + - - +
256B LEU* 1.3 56.1 + - - +
257B LYS* 3.4 31.9 - - - -
258B GLU* 2.8 39.4 + - + +
259B THR* 3.0 1.6 + - - -
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Residues in contact with LEU 256 (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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253B THR 5.1 0.4 + - - -
254B SER 4.3 0.6 - - - -
255B CYS* 1.3 71.0 - - - +
257B LYS* 1.3 59.0 + - + +
259B THR* 3.4 16.5 - - + -
260B TYR* 3.1 69.0 + - + +
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Residues in contact with LYS 257 (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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255B CYS* 2.9 17.2 + - - -
256B LEU* 1.3 77.9 - - + +
258B GLU* 1.3 64.1 + - - +
260B TYR* 3.0 24.2 + - + +
261B LEU* 3.1 12.1 + - - +
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Residues in contact with GLU 258 (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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253B THR* 3.2 28.2 - - + +
254B SER* 4.6 8.5 + - - -
255B CYS* 2.8 24.9 + - + +
257B LYS* 1.3 72.5 - - - +
259B THR* 1.3 61.1 + - - +
261B LEU* 3.3 15.4 + - + +
262B ARG* 3.2 42.6 + - + +
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Residues in contact with THR 259 (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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251B PHE* 3.3 24.6 + - + +
252B GLU* 4.1 2.3 - - - +
253B THR* 2.6 34.6 + - - -
255B CYS 3.0 7.0 + - - -
256B LEU* 3.4 21.1 - - + +
258B GLU* 1.3 73.7 - - - +
260B TYR* 1.3 67.4 + - + +
262B ARG* 3.2 5.6 + - - +
263B ILE* 3.1 39.2 + - + +
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Residues in contact with TYR 260 (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* 3.5 25.1 - - + +
215B PRO 5.3 0.3 + - - -
218B ILE* 3.6 25.8 - - + -
223B LEU* 3.6 29.8 - - + +
256B LEU* 3.1 53.3 + - + +
257B LYS* 3.0 18.0 + - + +
259B THR* 1.3 80.6 - - + +
261B LEU* 1.3 62.5 + - - +
263B ILE* 3.4 7.1 + - + +
264B LYS* 3.1 33.9 + - - +
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Residues in contact with LEU 261 (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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257B LYS 3.1 10.5 + - - +
258B GLU* 3.4 18.4 - - + +
260B TYR* 1.3 76.1 - - - +
262B ARG* 1.3 57.9 + - + +
264B LYS* 3.3 14.7 + - + +
265B LYS* 2.9 60.7 + - + +
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Residues in contact with ARG 262 (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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250B PRO 5.1 4.8 + - - -
251B PHE* 3.8 17.5 + - + +
252B GLU 3.9 9.7 + - - -
253B THR* 3.4 29.3 - - - +
258B GLU* 3.2 33.3 + - + +
259B THR* 3.2 8.0 + - - +
261B LEU* 1.3 73.8 - - + +
263B ILE* 1.3 60.7 + - - +
265B LYS* 3.2 2.9 + - - +
266B ASN* 2.8 25.1 + - - -
267B GLU* 2.9 47.7 + - - +
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Residues in contact with ILE 263 (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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216B ASN 6.1 0.2 - - - +
217B TYR* 6.2 0.2 - - - -
218B ILE* 3.3 48.2 - - + +
220B PRO* 3.8 21.2 - - + +
223B LEU* 3.9 8.1 - - + -
235B TRP* 3.8 19.5 - - + +
251B PHE* 3.7 31.2 - - + -
259B THR* 3.1 32.5 + - + +
260B TYR* 3.6 9.9 - - + +
261B LEU 3.3 0.2 - - - -
262B ARG* 1.3 74.1 - - - +
264B LYS* 1.3 63.9 + - - +
266B ASN* 3.2 13.5 + - - +
288B THR* 4.7 0.7 + - - -
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Residues in contact with LYS 264 (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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220B PRO* 4.8 9.4 - - - +
223B LEU* 3.9 43.8 + - + -
224B SER* 5.7 1.7 - - - +
260B TYR* 3.1 22.4 + - - +
261B LEU* 3.3 17.5 + - + +
263B ILE* 1.3 78.3 - - - +
265B LYS* 1.3 61.5 + - + +
266B ASN 3.3 0.9 + - - -
288B THR* 4.3 15.2 + - - +
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Residues in contact with LYS 265 (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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261B LEU* 2.9 48.1 + - + +
262B ARG* 4.1 1.3 - - - +
264B LYS* 1.3 76.9 - - + +
266B ASN* 1.3 70.2 + - - +
267B GLU* 3.1 42.1 + - + +
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Residues in contact with ASN 266 (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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235B TRP* 3.7 20.6 - - - -
251B PHE* 4.4 2.4 - - - -
262B ARG 2.8 6.3 + - - -
263B ILE 3.2 7.9 + - - -
264B LYS 3.3 0.8 - - - -
265B LYS* 1.3 79.5 - - - +
267B GLU* 1.3 58.1 + - - +
268B TYR* 3.5 23.1 + - - +
286B LEU 3.1 34.2 + - - +
287B GLN* 3.9 5.2 - - - +
288B THR* 3.4 23.4 + - - +
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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