Contacts of the strand formed by residues 205 - 212 (chain B) in PDB entry 1BLN
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 ILE 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 3.8 28.7 - - + -
157B TRP* 3.6 27.1 - - + -
162B ASN* 3.5 22.7 - - - +
166B LEU* 4.4 19.1 - - + -
191B VAL* 4.6 5.2 - - + -
193B VAL* 4.9 6.5 - - + -
198B THR* 4.2 20.6 - - + -
199B TRP* 4.0 15.0 - - + -
203B GLN* 3.7 14.8 - - + +
204B SER* 1.3 77.3 - - - +
206B THR* 1.3 58.9 + - - +
222B LYS* 3.6 1.9 - - - -
223B ILE* 2.8 33.4 + - + +
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Residues in contact with THR 206 (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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157B TRP* 3.4 11.8 - - - -
162B ASN* 2.7 43.2 + - - +
204B SER* 4.2 3.5 + - - -
205B ILE* 1.3 73.1 - - - +
208B CYS* 1.3 62.7 + - - +
209B ASN* 3.5 7.8 - - - +
220B ASP* 3.6 34.1 - - + +
221B LYS 3.6 12.6 - - - +
222B LYS* 3.3 24.3 - - + +
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Residues in contact with CYS 208 (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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121B VAL* 4.1 0.9 - - - -
142B CYS* 2.0 53.6 - - + -
154B LEU* 4.1 12.1 - - - -
156B THR 3.9 3.1 - - - -
157B TRP* 4.0 12.7 - - + -
206B THR* 1.3 70.7 - - - +
209B ASN* 1.3 60.2 + - - +
210B VAL* 3.6 19.6 - - - +
219B VAL 3.3 3.5 - - - +
220B ASP* 3.1 2.9 - - - -
221B LYS* 2.7 45.1 + - + +
223B ILE* 4.6 2.5 - - + -
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Residues in contact with ASN 209 (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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153B THR 3.6 0.7 - - - +
154B LEU* 3.1 6.1 - - - +
156B THR* 2.8 52.8 + - - +
162B ASN* 3.0 15.1 + - - +
163B SER* 2.8 41.3 + - - +
206B THR* 3.5 6.7 - - - +
208B CYS* 1.3 71.5 - - - +
210B VAL* 1.3 60.5 + - - +
218B LYS* 4.8 4.9 - - - +
219B VAL 3.7 4.0 - - - -
220B ASP* 3.1 32.7 + - - +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PRO* 4.6 9.9 - - + -
121B VAL* 3.8 29.4 - - + -
144B VAL* 3.8 26.2 - - + -
152B VAL* 4.0 15.0 - - + -
153B THR 3.2 7.6 - - - +
154B LEU* 4.1 6.1 - - + -
208B CYS* 3.6 25.8 - - - -
209B ASN* 1.3 79.2 - - - +
211B ALA* 1.3 66.3 + - - +
217B THR* 5.3 1.2 - - + +
218B LYS* 3.2 5.4 + - - +
219B VAL* 2.8 42.8 + - + +
220B ASP* 4.5 0.4 + - - -
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Residues in contact with ALA 211 (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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152B VAL* 3.5 3.3 - - - -
153B THR* 2.7 49.8 + - + +
210B VAL* 1.3 77.1 - - - +
212B HIS* 1.3 60.2 + - - +
213B PRO* 3.3 10.9 - - + +
217B THR 3.3 9.0 - - - +
218B LYS* 4.3 13.5 - - + -
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Residues in contact with HIS 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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116B THR* 4.2 1.3 - - + -
117B THR 3.3 26.0 + - - -
119B PRO* 3.7 25.8 - - + +
147B TYR* 3.8 12.1 - + + -
148B PHE 3.3 16.7 + - - -
149B PRO 2.9 24.2 + - - -
151B PRO 3.1 26.2 + - - -
152B VAL* 4.3 5.6 - - + -
210B VAL* 4.3 0.6 - - - +
211B ALA* 1.3 72.3 - - - +
213B PRO* 1.3 66.7 - - - +
214B ALA* 3.9 15.5 - - + +
215B SER* 2.8 26.6 + - - -
217B THR* 2.8 35.2 + - - +
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Residues in contact with PRO 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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151B PRO* 3.4 26.5 - - + +
152B VAL* 4.5 0.4 - - - -
153B THR* 5.1 6.5 - - - +
211B ALA* 3.3 15.9 - - + +
212B HIS* 1.3 81.8 - - - +
214B ALA* 1.3 63.1 + - - +
215B SER 2.8 2.4 + - - -
216B SER* 2.9 17.2 + - - +
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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