Contacts of the helix formed by residues 262 - 270 (chain B) in PDB entry 1WNY
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 GLU 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B THR* 2.8 42.3 + - + +
249B ALA* 4.1 17.5 - - + -
251B PHE* 3.6 9.2 - - + -
260B LEU 3.3 4.9 + - - -
261B GLU* 1.3 78.0 - - - +
263B GLY* 1.3 74.0 + - - +
265B GLY 3.3 0.2 + - - -
266B ARG* 2.8 70.3 + - - +
278B THR* 5.9 1.6 - - + -
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Residues in contact with GLY 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B GLU* 3.0 10.0 + - - -
262B GLU* 1.3 86.3 - - - +
264B LEU* 1.3 64.0 + - - +
266B ARG* 3.3 24.5 + - - +
267B LYS* 3.1 22.0 + - - +
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LEU* 3.9 8.5 - - + -
261B GLU* 2.9 20.8 + - + +
263B GLY* 1.3 76.8 - - - +
265B GLY* 1.3 58.6 + - - +
267B LYS* 3.4 17.1 + - + +
268B LEU* 2.9 31.4 + - - +
311B GLN* 3.7 23.1 - - - +
312B GLU* 3.8 22.0 - - - +
313B ASP 3.8 9.9 - - - +
314B GLY 3.6 21.5 - - - +
315B THR* 3.5 26.7 - - - +
316B GLY* 3.6 7.9 - - - +
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Residues in contact with GLY 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B PHE* 3.6 24.2 - - - -
260B LEU* 3.5 23.5 - - - +
261B GLU 2.9 10.7 + - - -
264B LEU* 1.3 79.1 - - - +
266B ARG* 1.3 56.4 + - - +
268B LEU* 4.5 0.9 - - - -
269B LEU* 2.8 36.3 + - - +
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Residues in contact with ARG 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B PHE* 4.0 14.8 - - + -
262B GLU* 2.8 51.9 + - + +
263B GLY* 3.3 13.2 + - - +
265B GLY* 1.3 75.9 - - - +
267B LYS* 1.3 57.8 + - - +
270B GLY* 2.8 36.5 + - - +
271B GLU* 2.6 65.5 + - - +
275B VAL* 5.6 2.5 - - + -
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLY 3.1 12.6 + - - +
264B LEU* 3.7 20.6 - - + +
266B ARG* 1.3 80.3 - - - +
268B LEU* 1.3 62.6 + - - +
270B GLY* 4.2 2.6 + - - -
312B GLU 5.6 4.4 + - - -
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B TYR* 3.7 38.8 - - + +
225B LEU* 3.7 31.0 - - + -
260B LEU* 4.0 13.2 - - + -
264B LEU 2.9 17.9 + - - +
265B GLY 4.0 2.0 - - - +
267B LYS* 1.3 82.3 - - - +
269B LEU* 1.3 69.3 + - + +
314B GLY 5.9 0.2 - - - +
377B PHE* 4.0 11.6 - - + -
378B LYS* 4.0 26.7 + - - +
380B GLU* 5.9 0.7 - - - +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B PHE* 3.6 41.3 - - + -
253B VAL* 3.9 20.9 - - + -
258B LEU* 4.4 6.1 - - + -
260B LEU* 4.1 13.0 - - + -
265B GLY 2.8 20.3 + - - +
268B LEU* 1.3 85.8 - - + +
270B GLY* 1.3 53.9 + - - +
273B THR* 2.7 31.5 + - + +
377B PHE* 3.5 34.5 - - + -
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Residues in contact with GLY 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B PHE* 5.3 1.0 - - - -
266B ARG* 2.8 22.6 + - - +
267B LYS 4.2 3.0 + - - -
268B LEU 3.6 1.4 - - - -
269B LEU* 1.3 78.3 - - - +
271B GLU* 1.3 65.2 + - - -
272B GLY 3.1 4.0 - - - -
273B THR* 3.1 19.4 + - - +
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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