Contacts of the strand formed by residues 271 - 279 (chain B) in PDB entry 1YZ3
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 271 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A ILE* 4.2 6.1 - - - -
216B ALA 3.7 0.2 - - - -
217B LEU* 2.8 38.2 + - - +
256B TYR 2.9 14.6 - - - -
257B ILE* 4.2 0.9 - - - -
258B MET* 3.8 5.2 - - - -
269B VAL* 2.9 13.1 - - - +
270B LYS* 1.3 80.3 - - - +
272B VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 4.0 16.8 - - + -
56B TRP* 3.5 22.6 - - + -
57B LYS* 4.8 3.1 - - + -
182B PHE* 3.9 19.3 - - + -
214B ILE* 3.9 4.9 - - + -
215B GLY 3.2 16.6 - - - +
217B LEU* 4.0 4.2 - - - +
255B THR* 3.5 1.7 - - - +
256B TYR* 2.7 41.0 + - + -
258B MET* 4.2 6.1 - - + -
269B VAL* 4.7 0.2 - - + -
271B GLY* 1.3 79.5 - - - +
273B PHE* 1.3 68.1 + - - +
3002B SKA 3.7 26.9 - - + -
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Residues in contact with PHE 273 (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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56B TRP* 4.0 2.0 - - - -
185B GLU* 4.6 8.5 - - - -
194B PHE* 4.9 5.4 - + - -
213B LEU* 3.9 31.0 - - + -
214B ILE* 3.2 7.3 - - - +
215B GLY* 2.8 71.7 + - - -
216B ALA 3.9 7.6 - - - -
217B LEU* 3.5 32.5 - - + -
234B VAL* 4.5 4.7 - - + -
236B GLU* 5.5 2.9 - - + -
239B VAL* 3.7 41.7 - - + -
253B LEU* 4.5 8.7 - - + -
254B ARG 3.4 8.1 - - - +
255B THR* 4.7 2.5 - - - +
272B VAL* 1.3 80.0 - - - +
274B PHE* 1.3 62.7 + - - +
275B ALA* 4.3 5.4 - - + -
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Residues in contact with PHE 274 (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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56B TRP* 3.6 20.2 - - + -
60B CYS* 3.5 35.9 - - + -
61B LEU* 4.1 21.5 - - + -
64B THR* 3.3 29.8 - - - -
212B LEU* 4.2 18.4 - - + -
213B LEU 3.4 2.9 - - - -
214B ILE* 3.7 20.4 - - + +
252B ASP* 4.0 12.6 - - - -
253B LEU* 3.3 4.5 - - - +
254B ARG* 2.8 45.7 + - + +
273B PHE* 1.3 74.7 - - - +
275B ALA* 1.3 68.3 - - - +
276B TRP* 4.1 13.7 - - + -
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Residues in contact with ALA 275 (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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211B LEU* 3.4 3.5 - - - +
212B LEU* 3.5 2.6 - - - -
213B LEU* 2.7 46.2 + - + +
243B LEU* 3.7 26.5 - - + -
250B VAL* 5.5 0.7 - - + -
252B ASP 3.3 4.5 - - - +
253B LEU* 3.5 19.1 - - + -
273B PHE* 4.4 6.5 - - + -
274B PHE* 1.3 81.4 - - - +
276B TRP* 1.3 61.0 + - - +
277B ALA* 3.9 1.3 - - + -
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Residues in contact with TRP 276 (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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64B THR* 3.8 17.3 - - + -
67B THR* 3.9 26.9 - - + -
69B GLU* 4.1 12.1 - - + -
70B VAL* 3.7 23.3 - - + +
210B HIS* 3.0 23.5 + - + -
211B LEU 3.5 2.0 - - - -
212B LEU* 3.8 20.6 - - + -
250B VAL* 3.7 1.1 - - - -
251B ARG* 2.7 82.6 + - + +
252B ASP* 2.7 34.9 + - + +
274B PHE* 4.1 12.3 - - + -
275B ALA* 1.3 71.9 - - - +
277B ALA* 1.3 63.9 + - - +
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Residues in contact with ALA 277 (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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210B HIS* 3.5 2.1 - - - -
211B LEU* 2.7 42.7 + - + +
243B LEU* 4.1 25.8 - - + -
248B TYR* 3.7 30.2 - - + -
249B LYS 3.4 7.9 - - - +
250B VAL* 4.4 4.3 - - + -
275B ALA 3.9 0.6 - - - -
276B TRP* 1.3 79.8 - - - +
278B GLN* 1.3 60.6 + - - +
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Residues in contact with GLN 278 (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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208B GLY* 2.9 25.4 + - - +
209B GLY 3.4 10.5 - - - +
210B HIS* 3.4 25.9 + - + +
248B TYR* 3.3 2.9 - - - -
249B LYS* 2.9 44.0 + - + +
251B ARG* 2.8 35.2 + - + +
277B ALA* 1.3 74.3 - - - +
279B LYS* 1.3 71.7 + - - +
280B VAL* 3.3 2.0 + - + +
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Residues in contact with LYS 279 (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 THR* 2.9 38.0 + - + +
203B THR* 4.4 5.9 - - - +
205B LEU* 2.6 35.8 + - + +
206B ARG 3.5 15.6 - - - +
207B PRO* 4.1 13.2 - - + +
208B GLY* 2.9 27.7 + - - -
209B GLY 2.8 16.3 + - - +
246B SER 5.6 0.9 - - - +
247B GLY* 3.7 6.7 - - - +
248B TYR* 3.4 21.5 - - + -
278B GLN* 1.3 75.3 - - - +
280B VAL* 1.3 66.8 + - - +
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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