Contacts of the strand formed by residues 216 - 221 (chain B) in PDB entry 6BM0
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 216 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B PHE* 2.9 3.6 - - - +
211B SER* 2.7 43.4 + - - +
213B THR 4.4 0.6 + - - -
214B ASP 3.7 1.6 - - - -
215B ASN* 1.3 86.0 - - + +
217B PHE* 1.3 57.5 + - - +
228B ILE* 3.7 16.4 - - + -
229B TRP 3.3 16.6 - - - +
230B ASP* 5.1 2.5 - - - +
231B PHE* 4.2 2.5 - - - +
237B GLU* 3.3 31.1 + - - +
252B TRP* 3.7 23.9 - - + -
275B PRO* 4.9 11.4 + - + +
276B LYS* 5.5 7.1 - - - +
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Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 3.7 27.4 - - + -
185B VAL* 4.2 7.0 - - + -
187B TYR* 3.2 27.8 - + - -
198B PHE* 3.5 31.4 - + - -
208B ALA* 5.6 1.3 - - + -
209B SER 4.1 2.9 - - - +
210B PHE* 3.4 21.5 - - + +
216B LYS* 1.3 73.4 - - - +
218B ALA* 1.3 58.5 + - - +
219B THR* 3.7 29.6 - - + -
228B ILE* 3.5 2.6 - - - +
229B TRP* 2.6 57.1 + + + +
230B ASP 3.5 15.0 - - - -
231B PHE* 4.1 13.5 - + - -
252B TRP* 4.2 3.1 - - - +
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Residues in contact with ALA 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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207B GLU 4.0 0.7 - - - +
208B ALA* 3.4 5.9 - - - +
209B SER 3.2 26.2 + - - -
217B PHE* 1.3 75.7 - - - +
219B THR* 1.3 62.7 + - - +
220B CYS 4.2 0.6 + - - -
226B VAL* 4.4 7.9 - - + -
227B ARG 3.4 9.2 - - - +
228B ILE* 4.2 15.9 - - + -
250B VAL* 4.0 19.0 - - + +
252B TRP* 3.4 20.6 - - + +
259B VAL* 4.8 2.9 - - + -
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Residues in contact with THR 219 (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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185B VAL* 4.2 17.9 - - + -
200B ALA* 3.8 1.9 - - + +
201B HIS* 2.6 52.4 + - - -
205B ILE* 3.9 11.2 - - + -
207B GLU 3.8 3.8 - - - -
208B ALA* 4.3 11.9 - - + -
217B PHE* 3.7 28.7 - - + -
218B ALA* 1.3 77.0 - - - +
220B CYS* 1.3 57.6 + - - +
226B VAL* 4.6 2.2 - - - -
227B ARG 3.1 19.5 + - - -
229B TRP* 3.4 16.0 + - + -
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Residues in contact with CYS 220 (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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205B ILE* 3.3 6.1 - - - +
206B ARG 2.8 22.2 + - - -
207B GLU* 3.1 31.6 + - - -
218B ALA 4.2 0.6 + - - -
219B THR* 1.3 73.7 - - - +
221B SER* 1.3 61.9 - - - +
225B THR 3.8 4.0 - - - -
226B VAL* 3.9 3.6 - - + +
247B VAL* 3.7 20.2 - - + -
248B LYS 3.9 3.4 - - - -
249B CYS 3.6 27.4 - - - -
250B VAL* 3.6 26.2 - - + +
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Residues in contact with SER 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B HIS* 2.9 31.7 + - - -
203B GLU 3.6 8.7 - - - -
204B ALA 3.1 17.7 - - - -
205B ILE* 3.7 0.4 - - - -
206B ARG 4.1 1.1 - - - +
220B CYS* 1.3 76.8 - - - +
222B ASP* 1.3 60.2 + - - +
223B ASP* 2.3 35.3 + - - -
224B GLY 3.5 1.7 + - - -
225B THR 3.7 3.4 + - - -
247B VAL* 2.9 31.7 + - - +
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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