Contacts of the helix formed by residues 255 - 261 (chain A) in PDB entry 3CYV
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 TRP 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A GLY 4.3 5.5 + - - -
212A GLY* 4.4 5.1 + - - -
214A LEU 3.5 24.0 + - - -
215A THR* 4.3 1.1 - - - -
216A GLY* 3.1 34.3 - - - -
219A TYR* 3.5 51.0 - + + +
252A GLY* 3.3 20.2 + - - +
254A GLN* 1.3 109.7 - - + +
256A LEU* 1.3 63.1 + - - +
257A GLU* 2.9 5.8 + - - -
258A ALA* 3.0 18.7 + - + +
259A MET* 3.4 11.8 + - + +
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Residues in contact with LEU 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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252A GLY 3.6 5.5 + - - +
253A GLY* 2.9 24.1 + - - +
254A GLN 2.9 1.2 - - - -
255A TRP* 1.3 75.7 - - - +
257A GLU* 1.3 61.6 + - - +
259A MET* 3.8 15.2 - - - +
260A ALA 3.6 13.0 + - - -
267A LEU* 3.7 15.7 - - + +
268A GLY 4.8 6.1 - - - +
269A LEU* 3.7 26.2 - - + -
278A ALA* 4.3 10.8 - - + +
281A ARG* 3.2 26.7 - - - +
282A VAL* 3.4 46.9 - - + +
288A LEU* 5.1 2.5 - - + -
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Residues in contact with GLU 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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254A GLN 4.2 6.7 - - - +
255A TRP 2.9 5.6 + - - -
256A LEU* 1.3 69.8 - - - +
258A ALA* 1.3 65.3 + - - +
260A ALA* 3.5 14.9 + - - +
261A GLU* 3.8 10.6 + - - +
281A ARG* 3.3 60.8 + - - +
282A VAL* 4.3 3.3 - - - +
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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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220A GLN* 3.4 26.9 - - + +
224A LEU* 3.5 22.1 - - + +
255A TRP* 3.0 12.5 + - + +
257A GLU* 1.3 75.0 - - - +
259A MET* 1.3 61.8 + - - +
261A GLU* 2.8 33.7 + - - +
262A THR* 3.7 1.7 + - - -
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Residues in contact with MET 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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219A TYR* 3.3 31.9 - - + +
224A LEU* 3.7 6.0 - - + +
227A MET* 5.6 1.8 - - - -
247A LEU* 4.5 15.9 - - + -
248A PHE* 4.7 1.1 - - - +
249A THR* 3.4 27.8 - - - +
252A GLY 4.1 19.7 - - - +
255A TRP* 3.4 15.0 - - - +
256A LEU* 3.8 13.9 - - - +
258A ALA* 1.3 77.4 - - - +
260A ALA* 1.3 52.7 + - - +
262A THR* 2.6 44.6 + - - +
264A CYS* 3.7 4.3 - - - -
267A LEU* 3.5 37.0 - - + -
268A GLY 5.9 3.1 - - - +
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Residues in contact with ALA 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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256A LEU 3.6 9.4 + - - +
257A GLU 3.5 11.8 + - - +
258A ALA 3.2 0.8 - - - -
259A MET* 1.3 78.1 - - - +
261A GLU* 1.3 60.7 + - - +
262A THR 2.9 4.7 + - - -
263A GLY* 3.9 5.7 + - - -
264A CYS* 4.7 3.3 - - - +
267A LEU* 3.9 5.3 - - + +
282A VAL* 4.2 14.4 - - + -
285A LYS* 3.9 33.5 - - + +
286A VAL* 4.0 22.9 - - + +
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Residues in contact with GLU 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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228A HIS* 3.6 15.0 - - + -
257A GLU 4.0 10.5 - - - +
258A ALA* 2.8 17.6 + - - +
260A ALA* 1.3 79.2 - - - +
262A THR* 1.3 61.4 + - - +
263A GLY* 3.4 1.5 + - - -
285A LYS* 3.5 30.3 + - - +
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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