Contacts of the helix formed by residues 255 - 265 (chain D) in PDB entry 5Y1Z
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D MET* 5.7 2.5 - - - -
251D GLU 3.3 5.1 + - - +
252D ILE 3.7 2.9 - - - -
253D GLU 3.4 0.4 - - - -
254D VAL* 1.3 85.2 - - + +
256D PRO* 1.3 68.8 - - - +
257D GLU* 3.7 9.4 - - - -
258D CYS* 3.3 19.4 - - + +
259D TYR* 3.0 27.2 + - - +
274D CYS* 3.8 4.7 - - - -
278D HIS* 3.6 13.7 - - + +
296D LEU* 4.8 1.6 - - + -
503D ZN 2.2 37.7 - - - -
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Residues in contact with PRO 256 (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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145D ALA* 3.7 33.0 - - + +
148D MET* 4.0 21.8 - - + -
149D LEU* 3.8 31.4 - - + -
157D LEU* 3.9 15.0 - - + +
252D ILE 3.4 16.4 - - - +
255D CYS* 1.3 84.4 - - - +
257D GLU* 1.3 64.4 + - + +
259D TYR* 3.8 4.0 - - + +
260D LEU* 2.9 30.7 + - - +
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Residues in contact with GLU 257 (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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148D MET* 4.6 20.1 - - - +
149D LEU* 6.5 0.2 - - + -
255D CYS* 3.4 5.2 - - - -
256D PRO* 1.3 71.6 - - + +
258D CYS* 1.3 66.4 + - - +
260D LEU* 3.3 7.0 + - - +
261D ALA* 2.9 26.3 + - - +
274D CYS* 3.0 26.0 - - - +
275D SER* 2.7 50.3 + - - -
276D ASN 4.2 1.6 + - - -
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Residues in contact with CYS 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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255D CYS* 3.3 18.1 - - + +
257D GLU* 1.3 78.8 - - - +
259D TYR* 1.3 57.0 + - - +
261D ALA* 3.4 4.6 + - - +
262D ALA* 2.9 30.2 + - - +
269D TRP* 5.1 1.4 - - - -
274D CYS* 4.0 5.6 - - - -
278D HIS* 3.8 7.6 - - - -
294D LYS* 4.7 13.9 - - - -
296D LEU* 4.1 13.9 - - + -
306D ARG* 4.6 21.3 + - - +
503D ZN 2.4 31.1 - - - -
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Residues in contact with TYR 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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157D LEU* 3.9 28.0 - - + -
160D PHE* 3.9 3.5 - - + -
161D ALA* 3.5 27.0 + - - +
164D LYS* 4.2 3.8 + - - -
248D GLU* 2.9 35.3 + - - +
251D GLU* 3.5 35.2 - - + +
252D ILE* 3.6 27.8 - - + -
255D CYS 3.0 16.4 + - - +
256D PRO* 3.8 3.8 - - + +
258D CYS* 1.3 73.3 - - - +
260D LEU* 1.3 68.7 + - - +
262D ALA* 3.2 7.0 + - + +
263D CYS* 2.9 48.8 + - - -
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Residues in contact with LEU 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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156D TYR* 4.1 11.2 - - + -
157D LEU* 3.8 20.9 - - + -
160D PHE* 3.9 21.1 - - + -
256D PRO 2.9 18.5 + - - +
257D GLU* 3.8 5.8 - - - +
259D TYR* 1.3 77.3 - - - +
261D ALA* 1.3 64.9 + - - +
263D CYS* 2.9 6.5 + - - +
264D GLN* 2.9 55.1 + - + +
266D ARG* 5.6 3.8 - - - +
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Residues in contact with ALA 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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257D GLU 2.9 17.8 + - - +
258D CYS* 3.7 5.2 - - - +
260D LEU* 1.3 75.0 - - - +
262D ALA* 1.3 63.1 + - - +
263D CYS 3.1 0.2 + - - -
264D GLN* 3.2 2.9 + - - +
265D LYS* 2.9 22.9 + - - -
266D ARG* 4.1 12.7 + - - +
269D TRP* 3.9 19.5 - - + +
272D GLU* 3.3 29.2 - - + +
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Residues in contact with ALA 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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164D LYS* 5.6 3.7 + - - +
258D CYS 2.9 16.8 + - - +
259D TYR* 3.2 8.0 + - + +
261D ALA* 1.3 75.0 - - - +
263D CYS* 1.3 61.1 + - - +
265D LYS* 3.5 21.0 - - - +
269D TRP* 3.4 36.5 - - + -
306D ARG* 4.6 9.6 - - - +
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Residues in contact with CYS 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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160D PHE* 3.6 44.4 - - + -
164D LYS* 3.8 20.9 - - - +
259D TYR* 2.9 52.6 + - - +
260D LEU* 2.9 8.0 + - - +
262D ALA* 1.3 78.0 - - - +
264D GLN* 1.3 65.6 + - - +
265D LYS* 3.5 3.8 + - - +
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Residues in contact with GLN 264 (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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156D TYR* 3.5 36.5 + - - -
160D PHE* 3.8 10.5 - - - -
260D LEU* 2.9 38.9 + - + +
261D ALA 3.9 2.5 - - - +
263D CYS* 1.3 75.7 - - - +
265D LYS* 1.3 68.6 + - - +
266D ARG* 3.3 34.7 + - + +
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Residues in contact with LYS 265 (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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107B GLU* 4.8 6.3 - - + +
261D ALA 2.9 12.3 + - - -
262D ALA 3.5 17.5 - - - +
263D CYS 3.3 5.5 - - - +
264D GLN* 1.3 80.5 - - - +
266D ARG* 1.3 68.1 + - - +
267D ASP* 3.8 1.0 + - - -
269D TRP* 3.6 30.9 - - + +
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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