Contacts of the helix formed by residues 254 - 261 (chain A) in PDB entry 2Y60
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 GLY 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ASP* 3.4 14.4 - - - -
218A SER* 3.2 22.7 + - - -
219A LEU 2.9 10.9 + - - -
253A CYS* 1.3 76.4 - - - +
255A SER* 1.3 61.4 + - - -
256A TYR 3.1 3.6 - - - -
257A MET* 3.0 19.6 + - - +
258A ALA 3.2 8.3 + - - -
267A ALA* 3.5 8.7 - - - +
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Residues in contact with SER 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A GLU* 3.7 24.0 - - - +
216A ASP 2.9 16.0 + - - -
217A VAL* 4.6 2.8 - - - +
254A GLY* 1.3 69.7 - - - -
256A TYR* 1.3 64.6 + - - +
258A ALA* 3.7 6.8 - - - +
259A HIS* 3.0 23.0 + - - +
267A ALA* 3.6 8.6 - - - +
316A TYR* 2.6 31.4 + - - -
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Residues in contact with TYR 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A SER 3.2 12.1 + - - +
219A LEU* 4.1 8.3 - - + -
254A GLY 3.1 1.2 + - - -
255A SER* 1.3 77.8 - - - +
257A MET* 1.4 58.1 + - - +
259A HIS* 3.2 6.8 + + - +
260A LEU* 2.9 67.4 + - + +
288A LEU* 4.2 10.8 - - + -
292A SER 3.9 6.9 + - - -
294A ILE* 3.6 20.8 + - + -
311A LEU* 2.7 38.6 + - + -
313A TYR* 3.5 33.2 - + + -
316A TYR* 3.1 48.9 + + + -
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Residues in contact with MET 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 5.0 0.9 - - + -
160A TYR* 3.9 19.5 - - + -
164A LEU* 4.2 4.3 - - - -
171A PHE* 3.6 38.1 - - + -
218A SER 4.1 0.8 + - - -
219A LEU* 3.3 43.7 - - + +
220A ILE* 3.9 21.1 - - + -
253A CYS* 3.6 20.2 - - + -
254A GLY 3.0 8.0 + - - +
256A TYR* 1.4 76.1 - - - +
258A ALA* 1.4 65.3 + - - +
260A LEU* 3.3 2.7 + - - +
261A THR* 3.0 41.6 + - - +
265A TYR* 4.1 11.9 - - + -
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Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A GLU* 5.7 0.9 - - - +
254A GLY 3.2 3.4 + - - -
255A SER* 3.8 14.4 - - - +
256A TYR 3.3 0.4 - - - -
257A MET* 1.4 79.3 - - - +
259A HIS* 1.3 63.2 + - - +
261A THR* 3.9 0.4 - - - -
262A ASN* 3.1 3.1 + - - -
263A ASN* 2.7 48.2 + - - +
265A TYR 3.3 18.9 + - - +
267A ALA* 3.6 16.6 - - + +
308A ARG* 4.2 3.4 - - - +
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Residues in contact with HIS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A SER 3.0 14.7 + - - +
256A TYR* 3.2 14.3 + + + +
258A ALA* 1.3 79.3 - - - +
260A LEU* 1.3 71.6 + - + +
261A THR 3.2 0.7 + - - -
262A ASN 3.2 6.9 + - - -
296A PRO* 3.8 15.5 - - + +
308A ARG* 3.1 64.2 + - + +
309A GLU 2.9 30.3 + - - -
311A LEU* 3.9 31.0 - - + +
316A TYR* 6.2 0.9 - - + -
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PHE* 3.7 29.2 - - + -
219A LEU* 4.1 6.5 - - + -
256A TYR* 2.9 51.7 + - + +
257A MET* 3.3 4.0 + - - +
259A HIS* 1.3 84.3 - - + +
261A THR* 1.3 61.5 + - + +
262A ASN 3.4 0.2 - - - -
294A ILE* 3.2 49.4 - - + +
296A PRO* 4.2 8.5 - - + -
297A PHE* 2.8 42.1 + - + +
311A LEU 6.3 0.2 - - - +
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Residues in contact with THR 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.8 36.6 - - + -
257A MET* 3.0 36.3 + - + +
260A LEU* 1.3 78.1 - - + +
262A ASN* 1.3 68.5 + - - +
263A ASN 3.7 1.6 + - - -
264A TYR* 3.0 21.8 + - - +
265A TYR* 3.0 31.3 + - + -
297A PHE* 3.3 15.8 - - + +
299A PRO* 3.7 12.0 - - - +
300A ARG* 4.2 0.7 + - - -
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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