Contacts of the strand formed by residues 211 - 218 (chain B) in PDB entry 3NYO
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 MET 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 5.7 4.3 - - + +
15B ALA* 3.7 34.1 - - + +
16B ARG* 4.5 6.1 - - - -
189B TYR* 4.0 12.3 - - + -
202B ALA* 5.8 1.1 - - + -
203B CYS 3.2 24.7 - - - +
204B GLN* 3.6 33.2 - - + +
209B GLY 4.4 1.6 - - - +
210B LYS* 1.3 87.3 - - - +
212B TYR* 1.3 74.4 + - - +
265B LEU* 3.7 30.6 + - + +
267B ASN* 6.3 0.7 - - - +
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Residues in contact with TYR 212 (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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202B ALA* 3.6 1.7 - - - +
203B CYS* 2.7 44.2 + - - +
205B VAL* 3.6 25.8 - - + -
210B LYS* 3.5 36.8 + - + +
211B MET* 1.3 85.3 - - - +
213B ALA* 1.3 56.3 + - - +
248B SER* 5.8 2.2 - - - -
250B ALA* 3.6 23.2 - - + +
251B TYR* 4.4 2.0 - + - -
262B VAL* 3.2 28.9 - - + -
263B LEU 3.6 20.4 - - - -
264B THR* 4.3 6.7 - - - -
265B LEU* 3.8 11.3 - - - +
510B PRO* 4.4 5.3 + - + +
514B GLU* 2.7 39.5 + - - +
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Residues in contact with ALA 213 (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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192B LEU* 5.1 1.3 - - + -
200B VAL* 4.6 7.9 - - + -
201B CYS 3.8 5.4 - - - +
202B ALA* 5.0 0.2 - - - -
212B TYR* 1.3 73.0 - - - +
214B CYS* 1.3 61.0 + - - +
215B LYS 3.9 0.6 + - - +
261B LEU 3.6 0.9 - - - +
262B VAL* 3.3 3.7 - - - -
263B LEU* 2.7 44.9 + - + +
264B THR 4.2 0.2 - - - +
265B LEU* 3.5 22.2 - - + +
577B AMP 3.6 33.2 - - + +
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Residues in contact with CYS 214 (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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188B GLN* 4.9 4.3 - - - +
199B GLU 3.9 0.7 - - - +
200B VAL* 3.6 1.7 - - - -
201B CYS* 2.7 42.2 + - - +
203B CYS* 3.8 20.9 - - + -
212B TYR 4.0 0.6 + - - -
213B ALA* 1.3 74.0 - - - +
215B LYS* 1.3 60.1 + - - +
216B LYS* 3.4 21.9 + - - +
253B TYR* 3.7 26.2 - - - -
260B CYS* 3.8 22.2 - - - -
261B LEU 3.4 5.4 - - - -
262B VAL* 4.5 2.9 - - + +
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Residues in contact with LYS 215 (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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195B GLY* 5.2 0.4 - - - -
196B GLY* 4.9 7.8 - - - +
197B PHE* 6.1 0.9 - - - -
199B GLU 4.0 2.5 - - - -
200B VAL* 3.9 20.3 - - + +
213B ALA 3.9 2.0 + - - -
214B CYS* 1.3 68.7 - - - +
216B LYS* 1.3 62.4 + - - +
217B LEU* 4.0 26.9 + - + +
234B GLU* 2.9 31.3 + - - +
260B CYS* 3.3 3.5 - - - -
261B LEU* 2.7 49.8 + - + +
263B LEU* 3.9 22.9 - - + +
329B ASP* 2.3 34.1 + - - +
577B AMP 3.0 26.5 + - - +
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Residues in contact with LYS 216 (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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183B LYS* 5.9 4.6 - - - +
188B GLN* 3.0 33.7 + - - +
198B GLY* 3.4 21.6 - - - +
199B GLU* 2.9 38.1 + - + +
201B CYS* 4.7 11.1 - - - -
214B CYS* 3.4 17.5 + - - +
215B LYS* 1.3 75.0 - - - +
217B LEU* 1.3 69.4 + - - +
218B GLU* 4.1 3.8 - - + +
253B TYR* 5.7 0.4 - - - -
255B THR* 4.7 18.7 - - - +
258B ALA* 4.6 11.2 - - + -
259B LEU 3.8 2.9 - - - -
260B CYS* 4.4 9.2 - - - -
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Residues in contact with LEU 217 (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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197B PHE* 3.4 35.7 - - + +
215B LYS* 4.0 33.2 - - + +
216B LYS* 1.3 83.3 - - - +
218B GLU* 1.3 64.8 + - - +
219B LYS 3.4 0.3 + - - -
222B ILE* 3.8 16.5 - - + +
231B ALA* 4.2 29.6 - - + -
234B GLU* 5.7 4.3 - - + +
258B ALA* 3.3 2.4 - - - +
259B LEU* 2.8 43.0 + - + +
261B LEU* 4.9 18.2 - - + -
502B PHE* 5.3 7.0 - - + -
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Residues in contact with GLU 218 (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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197B PHE* 2.8 21.0 + - - +
198B GLY* 4.3 9.2 - - - -
199B GLU* 5.5 7.1 - - - +
216B LYS* 5.2 3.1 - - + +
217B LEU* 1.3 70.3 - - - +
219B LYS* 1.3 66.2 + - - +
220B LYS* 3.2 2.0 - - + +
221B ARG* 2.8 48.1 + - + +
222B ILE* 3.0 23.6 + - - +
257B ASP* 3.8 9.3 - - + +
258B ALA* 4.0 6.5 - - + -
482B GLN* 5.8 1.4 + - - -
485B THR* 4.4 12.2 - - - +
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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