Contacts of the strand formed by residues 213 - 218 (chain B) in PDB entry 2W8B
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 LYS 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B TRP* 3.6 8.0 - - - -
208B SER* 3.0 39.3 + - - +
210B ASP* 4.8 5.1 + - - -
211B GLY 3.5 0.4 - - - -
212B SER* 1.3 100.3 + - - +
214B LEU* 1.3 65.2 + - - +
228B ILE* 3.7 23.3 - - + -
229B GLN 3.3 7.2 - - - +
230B THR* 3.3 32.4 - - - +
231B LEU* 4.5 2.9 - - - +
251B PHE* 4.5 4.0 - - + -
1432B SO4 4.4 26.0 + - - +
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ALA* 3.9 14.8 - - + -
182B LEU* 4.0 21.8 - - + -
184B VAL* 3.9 25.4 - - + -
195B VAL* 4.2 3.4 - - + -
205B PRO* 4.6 1.8 - - + -
206B ALA 3.4 10.3 - - - +
207B TRP* 3.4 48.2 - - + -
213B LYS* 1.3 73.3 + - - +
215B ALA* 1.3 65.5 + - - +
216B TYR* 3.6 12.1 - - + -
228B ILE* 3.5 3.8 - - - -
229B GLN* 2.8 38.1 + - + +
231B LEU* 4.2 19.0 - - + +
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Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B SER 3.7 0.3 - - - +
205B PRO* 3.2 2.3 - - - +
206B ALA* 2.9 32.0 + - + +
214B LEU* 1.3 75.3 - - - +
216B TYR* 1.3 65.6 + - - +
226B LEU* 4.6 1.8 - - + -
227B VAL 3.1 12.6 - - - +
228B ILE* 4.0 10.1 - - + +
249B PRO* 3.7 26.7 - - + -
251B PHE* 3.7 20.7 - - + -
258B LEU* 4.2 3.6 - - + -
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Residues in contact with TYR 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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182B LEU* 3.4 27.8 - - + -
196B HIS* 3.4 37.3 + + + -
202B LEU* 4.2 11.7 - - + -
203B MET 3.6 12.1 - - - +
204B SER 4.0 4.3 - - - -
205B PRO* 4.1 9.9 - - + -
214B LEU* 3.6 11.0 - - + -
215B ALA* 1.3 74.7 - - - +
217B VAL* 1.3 75.1 + - - +
218B THR* 4.3 7.6 - - + -
226B LEU* 3.4 6.3 - - - +
227B VAL* 3.0 52.1 + - + +
229B GLN* 2.8 43.5 + - + +
236B VAL* 4.7 4.2 - - - +
249B PRO* 4.4 1.8 - - - -
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 3.1 9.8 - - - +
203B MET* 2.8 45.4 + - + +
216B TYR* 1.3 78.9 - - - +
218B THR* 1.3 64.7 + - - +
219B PHE* 4.0 25.4 - - + -
224B SER* 4.0 9.2 - - - -
225B ALA 3.4 7.2 - - - +
226B LEU* 4.3 5.4 - - + -
245B HIS* 4.4 4.0 - - + -
246B ASN 3.6 14.6 - - - +
247B GLY* 3.4 29.8 - - - -
248B ALA 4.0 2.7 - - - +
249B PRO* 4.3 2.5 - - + -
116C GLU* 3.9 11.9 - - - +
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Residues in contact with THR 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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196B HIS* 5.1 0.2 - - - +
198B SER* 3.8 0.3 + - - -
201B PRO 3.7 4.0 - - - -
202B LEU* 3.4 18.5 - - - +
216B TYR* 4.3 12.8 - - + -
217B VAL* 1.3 74.3 - - - +
219B PHE* 1.3 61.3 + - - +
220B GLU* 2.5 49.7 + - + +
221B SER 5.1 0.3 + - - -
223B ARG 3.4 2.4 - - - +
224B SER* 3.5 0.5 - - - -
225B ALA* 2.9 47.8 + - + +
227B VAL* 4.6 11.7 - - + -
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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