Contacts of the helix formed by residues 255 - 265 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C MET* 5.8 1.6 - - - -
251C GLU 3.2 4.5 + - - +
252C ILE 3.4 3.1 - - - -
253C GLU 3.4 0.4 - - - -
254C VAL* 1.3 87.7 - - + +
256C PRO* 1.3 74.0 - - - +
257C GLU* 3.5 12.6 - - - -
258C CYS* 3.3 19.5 - - + +
259C TYR* 3.0 21.7 + - - +
274C CYS* 3.9 7.2 - - - -
278C HIS* 3.7 12.6 - - + -
296C LEU* 5.1 0.2 - - + -
306C ARG* 5.0 0.4 - - - +
502C ZN 2.3 36.1 - - - -
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Residues in contact with PRO 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ALA* 3.6 34.5 - - + +
148C MET* 3.9 21.5 - - + -
149C LEU* 3.9 27.4 - - + -
157C LEU* 4.0 16.9 - - + +
252C ILE 3.1 17.2 - - - +
254C VAL 4.6 0.4 - - - -
255C CYS* 1.3 84.9 - - + +
257C GLU* 1.3 60.0 + - + +
259C TYR* 3.2 4.7 + - + +
260C LEU* 2.9 29.8 + - - +
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Residues in contact with GLU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C MET* 4.0 24.2 - - - +
149C LEU* 6.4 0.4 - - + -
255C CYS* 3.2 10.0 - - - -
256C PRO* 1.3 73.9 - - + +
258C CYS* 1.3 67.3 + - - +
260C LEU* 3.4 7.5 + - - +
261C ALA* 2.9 25.6 + - - +
274C CYS* 3.7 16.9 - - + +
275C SER* 2.7 49.6 + - - -
276C ASN 4.2 2.4 + - - -
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Residues in contact with CYS 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C CYS* 3.3 15.7 - - + +
257C GLU* 1.3 79.7 - - - +
259C TYR* 1.3 62.9 + - - +
261C ALA* 3.2 5.6 + - - +
262C ALA* 2.9 25.6 + - - +
269C TRP* 4.9 2.5 - - - -
270C PHE* 6.5 0.2 - - - -
274C CYS* 3.9 6.0 - - - -
278C HIS* 3.8 5.4 - - - -
294C LYS* 5.0 12.3 - - - -
296C LEU* 4.2 5.8 - - - -
306C ARG* 3.8 30.7 - - - +
502C ZN 2.3 33.6 - - - -
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Residues in contact with TYR 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C LEU* 3.8 24.9 - - + -
160C PHE* 4.0 4.1 - - + +
161C ALA* 3.6 24.6 + - - +
164C LYS* 4.1 1.5 - - - +
248C GLU* 2.7 32.2 + - + +
251C GLU* 3.6 30.1 - - + +
252C ILE* 3.5 36.1 - - + -
255C CYS 3.0 14.7 + - - +
256C PRO* 3.4 11.7 - - + +
257C GLU 3.2 0.2 - - - -
258C CYS* 1.3 75.0 - - - +
260C LEU* 1.3 66.2 + - - +
262C ALA* 3.1 8.1 + - + +
263C CYS* 2.9 48.0 + - - -
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Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C TYR* 6.2 1.6 - - + -
157C LEU* 3.9 20.2 - - + -
160C PHE* 3.9 20.4 - - + -
256C PRO 2.9 16.0 + - - +
257C GLU* 3.9 6.5 - - - +
259C TYR* 1.3 75.6 - - - +
261C ALA* 1.3 64.0 + - - +
263C CYS* 3.1 4.9 + - - +
264C GLN* 3.0 59.5 + - - +
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C GLU 2.9 17.6 + - - +
258C CYS* 3.7 5.6 - - - +
260C LEU* 1.3 78.0 - - - +
262C ALA* 1.3 58.3 + - - +
264C GLN* 4.4 5.7 - - - +
265C LYS 3.0 21.7 + - - -
266C ARG 4.4 0.2 + - - -
269C TRP* 3.4 38.8 - - + +
272C GLU* 5.3 9.4 - - + -
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C CYS 2.9 17.5 + - - +
259C TYR* 3.6 7.2 - - + +
261C ALA* 1.3 75.6 - - - +
263C CYS* 1.3 66.5 + - - +
265C LYS* 3.9 10.8 + - - +
269C TRP* 3.6 31.5 - - + -
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Residues in contact with CYS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C PHE* 3.7 43.2 - - + -
164C LYS* 4.6 16.2 - - - +
259C TYR* 2.9 54.1 + - - -
260C LEU 3.6 7.2 - - - +
262C ALA* 1.3 81.3 - - - +
264C GLN* 1.3 63.2 + - - +
265C LYS* 4.4 2.6 - - - +
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Residues in contact with GLN 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C PHE* 4.3 14.1 - - + -
260C LEU* 3.0 49.2 + - + +
261C ALA* 4.4 4.6 - - - +
263C CYS* 1.3 79.4 - - - +
265C LYS* 1.3 68.2 + - - +
266C ARG* 3.4 49.0 + - + +
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Residues in contact with LYS 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ALA 3.0 16.1 + - - -
262C ALA 4.2 10.3 - - - +
263C CYS 3.4 2.4 - - - +
264C GLN* 1.3 79.9 - - - +
266C ARG* 1.3 67.0 + - - +
269C TRP* 3.6 20.6 - - + +
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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