Contacts of the strand formed by residues 249 - 254 (chain B) in PDB entry 3NYN
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 LEU 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B LYS* 4.3 25.8 - - + +
238B LEU* 4.1 27.6 + - + +
239B GLU* 4.4 4.3 - - + +
247B VAL 4.2 0.4 + - - -
248B SER* 1.3 73.6 - - - +
250B ALA* 1.3 59.9 + - - +
251B TYR 3.5 12.6 - - - +
252B ALA* 4.5 4.5 - - + -
261B LEU* 3.5 27.8 - - + -
262B VAL 2.9 38.4 - - - +
263B LEU* 3.3 20.0 - - + -
507B VAL* 3.2 21.3 - - + +
510B PRO* 3.2 19.9 - - - +
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Residues in contact with ALA 250 (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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212B TYR* 3.6 31.0 - - + +
248B SER* 4.0 2.1 + - - +
249B LEU* 1.3 73.3 - - - +
251B TYR* 1.3 90.5 + - + +
262B VAL 2.9 7.1 + - - +
506B SER* 3.4 2.4 - - - -
507B VAL* 2.8 27.2 + - - +
510B PRO* 3.9 16.2 - - + -
511B TRP* 4.8 3.3 - - - +
514B GLU* 4.5 0.7 - - - +
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Residues in contact with TYR 251 (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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181B VAL* 3.7 32.5 - - + -
185B THR* 4.8 5.8 - - + +
186B PHE* 3.9 12.1 - + + -
205B VAL* 4.0 13.3 - - + +
212B TYR* 3.8 9.0 - + - -
249B LEU* 3.5 13.5 - - - +
250B ALA* 1.3 106.6 - - + +
252B ALA* 1.3 62.3 + - - +
253B TYR* 4.5 4.3 - - + -
261B LEU* 3.6 0.5 - - - -
262B VAL* 2.9 51.8 + - + -
505B GLY 3.6 6.1 - - - +
506B SER* 3.9 6.7 - - - -
507B VAL* 4.5 0.7 - - - -
511B TRP* 3.1 33.3 + + - -
514B GLU* 2.6 39.4 + - - -
515B MET* 4.8 0.3 - - - +
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Residues in contact with ALA 252 (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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235B LYS* 4.3 16.2 - - + -
249B LEU* 4.5 6.1 - - + -
251B TYR* 1.3 75.7 - - - +
253B TYR* 1.3 60.6 + - - +
260B CYS 3.4 9.2 - - - +
261B LEU* 4.7 1.1 - - + -
502B PHE* 4.0 25.8 - - + +
503B ALA* 3.6 2.6 - - - -
504B THR* 3.4 10.9 + - - +
505B GLY* 2.8 41.1 + - - +
507B VAL* 5.9 1.1 - - + -
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Residues in contact with TYR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B VAL* 3.7 31.0 - - + +
182B THR* 4.3 2.0 - - - -
183B LYS* 4.1 21.1 - - - -
186B PHE* 3.1 33.4 - + - -
188B GLN* 3.4 24.8 + - - -
214B CYS* 3.9 10.0 - - - -
216B LYS* 5.9 0.2 - - - -
251B TYR* 4.5 1.6 - - + -
252B ALA* 1.3 76.6 - - - +
254B GLU* 1.3 70.1 + - - +
255B THR* 3.9 12.0 - - + +
259B LEU* 3.8 1.8 - - - -
260B CYS* 2.9 53.4 + - + +
262B VAL* 3.5 22.4 - - + +
502B PHE* 4.3 2.8 - - - -
503B ALA* 3.9 11.6 - - - +
505B GLY* 5.5 0.7 - - - -
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Residues in contact with GLU 254 (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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181B VAL 5.4 0.5 - - - +
182B THR* 5.4 4.7 - - - -
183B LYS 5.4 0.5 + - - -
219B LYS* 3.2 22.6 + - - -
253B TYR* 1.3 83.2 - - - +
255B THR* 1.3 64.9 + - - +
258B ALA 3.5 3.4 - - - -
259B LEU* 3.5 21.1 - - + -
499B TYR* 3.7 21.4 - - - +
500B GLN* 5.7 0.5 + - - -
503B ALA* 3.9 14.4 - - + +
585B SO4 4.4 5.9 + - - -
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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