Contacts of the strand formed by residues 193 - 205 (chain H) in PDB entry 3BXB
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72H HIS* 3.2 32.5 + - - -
76H ILE* 3.9 9.6 - - + -
77H PRO 4.9 0.3 + - - -
79H PHE* 4.9 1.6 - - - +
80H PHE* 4.0 6.2 - - - -
146H MET* 3.4 4.5 - - - +
147H LEU* 2.6 72.1 + - + +
154H LEU* 3.8 11.6 - - + +
190H PRO* 3.6 30.5 - - + +
191H GLY 3.1 19.5 + - - -
192H VAL* 1.3 74.8 - - - +
194H TYR* 1.3 88.4 + - - +
195H VAL* 3.8 13.0 - - + -
219H ALA* 3.8 14.4 - - + -
220H ARG 3.7 9.4 - - - +
221H TYR* 3.8 15.0 - - + -
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Residues in contact with TYR 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G GLU* 4.0 1.6 + - - +
142G ALA* 2.5 48.6 + - + +
143G SER* 4.5 6.7 - - - -
144G THR* 4.6 10.3 - - - -
144H THR* 4.3 5.8 - - + -
145H GLU 3.1 7.6 - - - +
146H MET* 3.6 28.7 - - + -
192H VAL* 3.7 20.6 - - + +
193H TYR* 1.3 88.8 - - - +
195H VAL* 1.3 61.3 + - - +
196H ASP 4.3 0.7 - - - -
219H ALA* 3.2 3.8 - - - -
220H ARG* 2.8 71.9 + - - +
222H CYS* 4.0 27.6 - - + -
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Residues in contact with VAL 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H ILE* 4.2 21.3 - - + -
144H THR* 3.3 0.7 - - - -
145H GLU* 2.8 31.5 + - + +
147H LEU* 3.8 12.3 - - + -
193H TYR* 3.8 14.4 - - + +
194H TYR* 1.3 78.3 - - - +
196H ASP* 1.3 64.0 + - - +
197H ARG* 2.8 34.5 + - - +
217H ALA* 4.0 26.0 - - + -
218H VAL 3.5 10.1 - - - +
219H ALA* 3.8 18.2 - - + -
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Residues in contact with ASP 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220G ARG* 3.2 24.2 + - - +
222G CYS* 6.2 1.8 - - - -
224G LEU* 3.4 18.7 - - + +
143H SER 3.4 4.7 - - - +
144H THR* 2.7 27.3 + - - +
195H VAL* 1.3 71.9 - - - +
197H ARG* 1.3 63.8 + - - +
217H ALA* 3.3 1.0 - - - -
218H VAL* 3.1 34.7 + - + +
220H ARG* 2.6 36.4 + - - +
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Residues in contact with ARG 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G LEU* 3.7 6.1 - - - +
63H NRQ 3.0 50.0 + - + +
67H LYS* 5.1 3.0 - - - +
70H ILE* 6.2 1.1 - - - -
142H ALA* 3.2 5.7 - - - +
143H SER* 2.8 66.4 + - - +
145H GLU* 3.1 39.8 + - - +
158H SER* 3.5 14.5 + - - -
174H LEU* 5.3 0.6 - - - +
195H VAL* 2.8 41.5 + - - -
196H ASP* 1.3 75.0 - - - +
198H ARG* 1.3 60.0 + - - +
215H GLU* 3.6 19.3 - - + +
216H VAL 3.2 14.6 - - - +
217H ALA* 3.6 7.9 - - + -
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Residues in contact with ARG 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222G CYS* 2.9 51.2 + - - +
224G LEU* 2.4 33.3 + - + +
225G PRO 4.4 1.5 - - - -
226G SER* 4.1 15.2 + - - +
140H TRP 5.6 1.8 - - - +
141H GLU 5.5 0.2 - - - -
142H ALA* 4.1 19.0 - - + +
197H ARG* 1.3 75.3 - - - +
199H LEU* 1.3 62.3 + - - +
200H GLU* 3.3 37.2 - - + +
214H HIS 3.7 0.7 - - - +
215H GLU* 3.2 24.5 - - - +
216H VAL* 3.2 19.7 + - + +
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Residues in contact with LEU 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H ALA* 3.8 19.5 - - + +
60H THR* 5.1 1.3 - - + -
63H NRQ 3.7 52.0 + - + +
140H TRP* 3.8 40.6 + - + +
141H GLU 5.3 1.0 + - - -
142H ALA* 5.2 1.4 - - - +
160H MET* 6.0 0.4 - - + -
197H ARG 4.5 0.2 + - - -
198H ARG* 1.3 76.1 - - - +
200H GLU* 1.3 64.7 + - - +
201H ARG 4.4 0.5 + - - -
213H GLN* 3.6 31.0 - - + +
214H HIS 3.4 7.6 - - - +
215H GLU* 3.4 26.0 - - + +
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Residues in contact with GLU 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G PRO 4.9 1.6 - - - +
226G SER* 3.1 25.8 + - - -
227G LYS* 3.3 23.7 + - - +
228G LEU* 3.7 27.4 + - + +
140H TRP 5.7 1.3 - - - +
198H ARG* 3.3 32.1 - - + +
199H LEU* 1.3 79.9 - - - +
201H ARG* 1.3 61.3 + - - +
202H ILE* 3.4 12.4 + - + +
213H GLN* 3.7 9.1 - - - +
214H HIS* 2.9 41.7 + - - +
216H VAL* 5.7 0.9 - - - +
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Residues in contact with ARG 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C LYS* 5.0 13.5 - - - +
165C VAL* 5.6 0.3 - - - +
228G LEU* 3.8 21.6 - - + +
55H PHE* 3.8 11.5 - - - +
56H ASP* 2.9 51.9 + - - +
59H ALA* 6.2 0.8 - - - +
137H THR 5.5 0.4 + - - -
138H LEU 6.0 1.8 - - - +
139H GLY* 5.8 7.0 - - - -
199H LEU 4.4 0.2 + - - -
200H GLU* 1.3 70.9 - - - +
202H ILE* 1.3 61.7 + - - +
203H LYS 4.4 9.6 - - - +
204H GLU* 4.2 20.2 - - + +
208H GLU* 2.8 35.7 + - - +
211H VAL* 3.6 31.0 - - - +
212H GLU 4.0 1.6 - - - -
213H GLN* 4.9 5.4 + - - +
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Residues in contact with ILE 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL* 3.9 22.0 - - - +
166C GLY* 4.7 7.5 - - - -
227G LYS* 3.8 37.7 - - + +
228G LEU* 4.5 6.4 - - + +
40H THR* 5.8 2.2 - - + -
200H GLU* 4.0 16.2 - - + +
201H ARG* 1.3 78.5 - - - +
203H LYS* 1.3 58.4 + - + +
212H GLU* 2.8 41.6 + - + +
213H GLN 4.6 0.4 - - - -
214H HIS* 3.8 24.0 - - + +
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Residues in contact with LYS 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL 4.9 2.0 - - - +
166C GLY* 3.3 30.5 - - - +
167C GLY* 5.0 4.5 - - - -
201H ARG* 4.4 4.7 - - - -
202H ILE* 1.3 80.1 - - + +
204H GLU* 1.3 72.0 + - - +
205H ALA* 5.2 10.7 - - - +
210H TYR* 4.9 16.6 - - + -
211H VAL* 3.4 6.2 - - - +
212H GLU* 2.8 52.8 + - + +
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Residues in contact with GLU 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ASN* 4.8 10.2 + - - +
134C GLN* 5.7 4.6 + - - +
201H ARG* 4.2 26.0 - - + +
203H LYS* 1.3 84.8 - - - +
205H ALA* 1.3 69.4 + - - +
207H LYS* 4.8 1.6 + - - -
208H GLU* 3.3 35.5 + - + +
210H TYR* 3.4 11.4 - - - +
211H VAL* 4.6 2.7 - - + -
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Residues in contact with ALA 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203H LYS* 5.2 10.8 - - - +
204H GLU* 1.3 82.1 + - - +
206H ASP* 1.3 77.2 + - + +
207H LYS 3.8 0.9 - - - -
208H GLU 3.6 2.2 + - - -
209H THR 3.1 14.9 + - - -
210H TYR* 3.2 29.9 + - + +
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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