Contacts of the helix formed by residues 256 - 263 (chain B) in PDB entry 1ZSV
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 PRO 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A ARG* 6.1 0.7 - - - +
251A LEU* 3.8 13.9 - - + -
224B ASN* 4.2 26.2 - - + +
227B ILE* 4.3 7.6 - - + -
254B GLY 3.6 2.0 - - - +
255B PRO* 1.3 84.9 - - + +
257B PRO* 1.4 71.1 - - + +
258B GLU* 3.2 2.5 - - + -
259B ILE* 3.1 41.7 + - + +
260B VAL* 3.3 11.0 + - - +
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Residues in contact with PRO 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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238A ILE* 5.8 4.0 - - + -
241A ALA* 3.5 32.5 - - + -
244A THR* 3.9 17.7 - - + +
247A ARG* 5.5 0.7 - - - +
251A LEU* 4.1 16.6 - - + -
255B PRO 3.3 11.1 - - - +
256B PRO* 1.4 81.8 - - + +
258B GLU* 1.3 69.1 + - + +
260B VAL* 3.7 8.4 - - + +
261B ILE* 2.9 40.7 + - + +
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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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52A VAL* 3.8 35.1 - - + +
55A LYS* 3.2 32.9 + - - -
56A ARG* 5.4 2.8 + - - +
244A THR* 3.7 18.2 + - - +
245A TYR* 3.8 17.5 - - + -
247A ARG* 3.8 17.5 + - - -
256B PRO* 3.2 1.7 + - + -
257B PRO* 1.3 82.0 - - + +
259B ILE* 1.3 59.8 + - + +
261B ILE* 4.1 6.4 - - - +
262B TYR* 3.1 28.9 + - - +
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Residues in contact with ILE 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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227B ILE* 3.7 28.0 - - + +
228B GLY* 4.1 16.8 - - - +
256B PRO* 3.1 35.2 + - + +
258B GLU* 1.3 78.4 - - + +
260B VAL* 1.3 64.6 + - - +
262B TYR* 3.7 3.8 - - - +
263B GLN* 3.0 34.9 + - + +
265B LEU* 5.6 0.2 - - + -
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Residues in contact with VAL 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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238A ILE* 4.7 15.9 - - + -
269A ALA* 3.5 17.0 - - + +
227B ILE* 3.7 21.5 - - + -
255B PRO* 4.3 15.3 - - + +
256B PRO 3.3 13.9 + - - +
257B PRO* 3.4 11.2 + - + +
259B ILE* 1.3 76.9 - - - +
261B ILE* 1.3 56.5 + - - +
263B GLN 3.8 0.3 - - - -
264B GLU 3.1 22.5 + - - -
265B LEU* 3.2 18.4 + - + +
267B MET* 3.6 30.3 - - + -
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Residues in contact with ILE 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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238A ILE* 3.7 31.2 - - + +
239A CYS 3.9 8.3 - - - +
240A GLY* 3.6 34.8 - - - -
241A ALA* 4.2 2.5 - - + +
245A TYR* 4.6 5.2 - - + +
269A ALA* 3.7 6.3 - - + -
270A PHE 3.7 17.8 - - - +
271A VAL* 3.4 20.0 - - + +
257B PRO* 2.9 30.2 + - + +
258B GLU* 4.1 6.7 - - - +
260B VAL* 1.3 74.3 - - - +
262B TYR* 1.3 64.9 + - - +
264B GLU* 3.2 12.6 + - - +
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Residues in contact with TYR 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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56A ARG* 3.6 46.7 + - - +
271A VAL* 4.6 10.5 - - + +
232B LYS* 4.5 11.0 - - + +
258B GLU 3.1 21.0 + - - +
259B ILE* 3.4 6.9 + - - +
261B ILE* 1.3 79.5 - - - +
263B GLN* 1.3 74.4 + - + +
264B GLU* 3.3 6.1 + - - +
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Residues in contact with GLN 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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227B ILE 5.0 2.2 - - - +
228B GLY 6.4 0.4 - - - -
230B MET 2.8 27.3 + - - +
231B LYS* 3.5 1.0 - - - +
232B LYS* 3.4 28.1 - - - +
233B PHE 2.7 32.4 + - - -
259B ILE* 3.0 33.1 + - + +
262B TYR* 1.3 95.8 - - + +
264B GLU* 1.3 60.6 + - - +
265B LEU* 3.3 22.1 + - + +
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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