Contacts of the strand formed by residues 193 - 205 (chain B) in PDB entry 3BX9
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 TYR 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B HIS* 3.0 26.3 + + - -
76B ILE* 3.9 17.3 - - + -
77B PRO 5.0 1.4 + - - -
79B PHE 5.2 0.7 + - - -
80B PHE* 3.8 18.0 - - - -
146B MET* 3.6 2.8 - - - +
147B LEU* 2.8 57.0 + - + +
148B TYR* 6.1 0.2 - - - -
154B LEU* 3.9 6.0 - - + +
190B PRO* 3.8 24.2 - - + -
191B GLY 3.4 13.7 - - - -
192B VAL* 1.3 76.8 - - - +
194B TYR* 1.3 86.6 + - - +
195B VAL* 4.0 12.0 - - + +
219B ALA* 3.7 30.5 - - + -
220B ARG 3.7 8.1 - - - +
221B TYR* 3.9 15.3 - + + -
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Residues in contact with TYR 194 (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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144B THR* 4.1 10.5 - - + -
145B GLU 3.3 6.5 - - - +
146B MET* 3.7 35.4 - - + -
147B LEU 4.9 0.2 - - - +
192B VAL* 3.7 21.7 - - + +
193B TYR* 1.3 87.6 - - - +
195B VAL* 1.3 63.5 + - - +
196B ASP 4.2 0.4 - - - -
219B ALA* 3.2 3.8 - - - +
220B ARG* 2.8 76.7 + - - +
222B CYS* 3.9 31.2 - - + +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 4.1 21.5 - - + -
143B SER 3.8 0.7 - - - +
144B THR* 3.1 3.6 - - - -
145B GLU* 2.8 38.5 + - - +
147B LEU* 3.5 24.5 - - + -
193B TYR* 4.0 5.4 - - + +
194B TYR* 1.3 75.6 - - - +
196B ASP* 1.3 71.1 + - - +
197B ARG* 3.7 25.7 + - - +
217B ALA* 4.1 19.3 - - + -
218B VAL 3.4 8.5 - - - +
219B ALA* 3.9 16.8 - - + -
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Residues in contact with ASP 196 (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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143B SER 3.5 5.4 - - - +
144B THR* 2.8 27.4 + - - +
195B VAL* 1.3 70.9 - - - +
197B ARG* 1.3 63.9 + - - +
216B VAL 4.6 0.2 - - - -
217B ALA* 3.4 1.0 - - - -
218B VAL* 3.0 39.0 + - + +
220B ARG* 2.8 42.2 + - - +
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Residues in contact with ARG 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B NRQ 3.5 36.6 - - - +
67B LYS* 3.6 9.7 - - - +
70B ILE* 6.1 0.6 - - - +
142B ALA* 3.2 7.7 - - - +
143B SER* 2.9 55.5 + - - +
144B THR 4.2 0.2 - - - -
145B GLU* 2.7 55.4 + - - +
160B MET* 5.9 1.1 - - - -
195B VAL* 3.7 18.4 + - - +
196B ASP* 1.3 75.8 - - - +
198B ARG* 1.3 63.6 + - - +
199B LEU* 5.3 7.2 - - + +
215B GLU* 3.1 28.9 + - - +
216B VAL 3.2 12.3 - - - +
217B ALA* 4.0 4.5 - - + -
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Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA* 4.2 26.6 - - + +
197B ARG* 1.3 77.5 - - - +
199B LEU* 1.3 60.8 + - - +
200B GLU* 3.7 30.8 + - + +
214B HIS* 5.6 0.2 + - - -
215B GLU* 3.3 8.1 - - - +
216B VAL* 3.0 47.8 + - + +
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Residues in contact with LEU 199 (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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59B ALA* 3.7 30.3 - - + +
60B THR* 3.9 23.3 - - + -
63B NRQ 3.7 29.6 - - + +
140B TRP* 4.0 38.0 + - + +
141B GLU 5.6 1.4 + - - +
142B ALA* 5.6 1.2 - - - +
160B MET* 4.9 7.2 - - + -
197B ARG* 5.3 5.8 - - + +
198B ARG* 1.3 74.0 - - - +
200B GLU* 1.3 63.2 + - - +
213B GLN* 3.6 31.9 - - + +
214B HIS 3.5 3.8 - - - +
215B GLU* 4.0 9.9 - - + +
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Residues in contact with GLU 200 (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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140B TRP 5.8 0.9 - - - +
198B ARG* 3.7 30.9 + - + +
199B LEU* 1.3 86.1 - - - +
201B ARG* 1.3 67.8 + - - +
202B ILE* 3.4 12.9 + - + +
213B GLN* 3.3 8.1 - - - +
214B HIS* 2.8 55.5 + - + +
216B VAL* 6.0 0.5 - - - +
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Residues in contact with ARG 201 (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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55B PHE* 3.9 18.9 - - - +
56B ASP* 3.9 26.5 + - - +
137B THR 5.9 0.6 + - - -
139B GLY* 5.9 4.9 - - - -
199B LEU 4.4 0.4 + - - -
200B GLU* 1.3 74.0 - - - +
202B ILE* 1.3 61.4 + - - +
203B LYS* 3.8 17.3 - - - +
204B GLU* 3.2 29.3 - - + +
208B GLU* 3.6 26.8 + - - +
211B VAL* 3.8 27.8 - - + +
212B GLU 3.7 3.4 - - - -
213B GLN* 4.6 3.6 - - - +
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Residues in contact with ILE 202 (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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40B THR* 5.1 1.6 - - + -
200B GLU* 4.2 13.0 - - + +
201B ARG* 1.3 76.5 - - - +
203B LYS* 1.3 63.8 + - + +
212B GLU* 2.8 51.8 + - + +
214B HIS* 3.5 36.3 - - + +
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Residues in contact with LYS 203 (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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201B ARG* 3.5 9.8 - - - -
202B ILE* 1.3 84.1 - - + +
204B GLU* 1.3 69.0 + - - +
205B ALA* 6.3 2.2 - - + -
211B VAL* 3.6 0.9 - - - -
212B GLU* 2.9 58.4 + - + +
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Residues in contact with GLU 204 (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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201B ARG* 3.2 33.0 - - - +
203B LYS* 1.3 83.4 - - - +
205B ALA* 1.3 65.6 + - - +
206B ASP 5.0 0.3 + - - -
207B LYS* 3.5 8.7 + - - -
208B GLU* 2.7 41.1 + - + +
210B TYR 3.2 13.5 - - - +
211B VAL* 4.2 7.2 - - + -
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Residues in contact with ALA 205 (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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203B LYS* 6.3 3.1 - - + -
204B GLU* 1.3 77.9 - - - +
206B ASP* 1.3 82.0 + - - +
207B LYS 3.4 2.2 - - - -
208B GLU 3.4 1.6 + - - -
209B THR 3.3 15.2 + - - -
210B TYR* 3.0 24.5 + - + +
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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