Contacts of the helix formed by residues 256 - 263 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247C ARG* 6.1 0.7 - - - +
251C LEU* 3.8 13.2 - - + -
224D ASN* 4.1 26.9 - - + +
227D ILE* 4.4 6.7 - - + -
228D GLY 5.5 0.2 - - - +
254D GLY 3.6 2.4 - - - +
255D PRO* 1.3 84.2 - - + +
257D PRO* 1.3 71.7 - - + +
258D GLU* 3.3 2.2 - - + -
259D ILE* 3.1 40.2 + - + +
260D VAL* 3.3 10.1 + - - +
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Residues in contact with PRO 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C ILE* 5.8 4.7 - - + -
241C ALA* 3.6 31.0 - - + -
244C THR* 4.1 14.1 - - + +
247C ARG* 5.4 1.1 - - - +
251C LEU* 4.0 22.2 - - + -
255D PRO 3.2 10.5 - - - +
256D PRO* 1.3 81.5 - - + +
258D GLU* 1.3 74.0 + - + +
259D ILE 3.2 0.2 - - - -
260D VAL* 3.7 8.7 - - + +
261D ILE* 3.0 34.4 + - + +
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Residues in contact with GLU 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL* 3.6 35.8 - - + +
55C LYS* 3.2 32.5 + - - -
56C ARG* 5.8 2.4 + - - +
244C THR* 3.9 3.9 + - - +
245C TYR* 3.8 25.6 - - + -
247C ARG* 3.8 21.7 + - - -
256D PRO* 3.3 1.5 + - + -
257D PRO* 1.3 82.0 - - + +
259D ILE* 1.3 59.5 + - + +
261D ILE* 4.0 6.3 - - - +
262D TYR* 3.1 31.2 + - - +
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Residues in contact with ILE 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ILE* 3.7 27.1 - - + +
228D GLY* 4.0 18.6 - - - +
256D PRO* 3.1 33.0 + - + +
258D GLU* 1.3 77.0 - - + +
260D VAL* 1.3 59.7 + - - +
262D TYR* 4.5 3.4 - - - -
263D GLN* 2.9 42.6 + - + +
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Residues in contact with VAL 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ILE* 4.8 12.6 - - + -
269C ALA* 3.4 17.0 - - + +
227D ILE* 3.7 21.3 - - + -
255D PRO* 4.3 14.6 - - + -
256D PRO 3.3 15.0 + - - +
257D PRO* 3.7 9.6 - - + +
259D ILE* 1.3 75.3 - - - +
261D ILE* 1.3 57.6 + - + +
264D GLU 3.1 20.3 + - - -
265D LEU* 3.2 18.3 + - + +
267D MET* 3.3 31.6 - - + -
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Residues in contact with ILE 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ILE* 4.0 26.7 - - + +
239C CYS 3.9 10.8 - - - +
240C GLY* 3.8 33.7 - - - -
241C ALA* 4.3 3.1 - - + +
245C TYR* 4.6 5.4 - - + +
269C ALA* 3.8 5.6 - - - -
270C PHE 3.8 18.1 - - - +
271C VAL* 3.3 12.0 - - + +
257D PRO* 3.0 28.4 + - + +
258D GLU* 4.0 6.1 - - - +
260D VAL* 1.3 75.6 - - - +
262D TYR* 1.3 66.5 + - - +
264D GLU* 3.2 21.8 + - - +
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Residues in contact with TYR 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ARG* 3.7 46.4 + - - +
271C VAL* 4.5 9.4 - - + +
232D LYS* 3.6 21.5 - - + -
258D GLU 3.1 19.9 + - - +
259D ILE* 3.8 4.9 - - - +
261D ILE* 1.3 81.2 - - - +
263D GLN* 1.3 75.8 + - + +
264D GLU* 3.2 2.8 + - - +
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Residues in contact with GLN 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ILE 5.1 2.0 - - - +
228D GLY 6.4 0.4 - - - -
230D MET 2.8 28.1 + - - +
231D LYS* 3.4 0.6 - - - +
232D LYS* 3.3 30.4 - - - +
233D PHE 2.7 31.9 + - - -
259D ILE* 2.9 32.6 + - + +
262D TYR* 1.3 96.6 - - + +
264D GLU* 1.3 59.1 + - - +
265D LEU* 3.3 21.5 + - + +
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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