Contacts of the strand formed by residues 190 - 198 (chain B) in PDB entry 3HOT
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 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ARG* 5.6 5.5 - - - +
159B TRP* 3.3 48.1 - - + +
160B ILE 3.6 12.6 - - - +
161B PHE* 4.0 32.7 - - + +
162B PHE* 3.9 2.9 - - - -
186B ARG 4.6 1.0 + - - -
187B PHE* 4.0 29.1 - - - +
188B GLY 3.8 7.1 + - - +
189B LYS* 1.3 77.0 - - - +
191B THR* 1.3 62.5 + - - +
210B PRO* 3.4 21.5 - - - +
211B GLY* 3.9 6.3 + - - +
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Residues in contact with THR 191 (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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159B TRP* 3.4 4.1 - - - -
160B ILE* 2.8 45.8 + - - +
162B PHE* 3.5 21.4 - - + -
190B LYS* 1.3 73.7 - - - +
192B MET* 1.3 61.6 + - - +
193B LEU 4.0 0.4 - - - -
207B LEU* 3.7 15.9 - - + +
208B LEU 3.5 18.4 - - - +
210B PRO* 3.8 11.4 - - + -
303B TYR* 3.5 27.6 - - + -
306B VAL* 3.9 8.6 - - + +
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Residues in contact with MET 192 (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 GLU* 3.6 42.0 - - + +
158B LYS* 3.9 8.3 - - - +
159B TRP* 3.4 49.4 - - + +
191B THR* 1.3 74.0 - - - +
193B LEU* 1.3 62.1 + - - +
194B CYS* 3.5 10.1 + - - -
207B LEU* 4.0 2.0 - - - -
208B LEU* 3.4 51.7 + - + +
212B GLU 4.7 5.2 - - - +
214B VAL* 5.1 10.1 - - + -
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Residues in contact with LEU 193 (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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156B ASP 4.0 1.7 - - - +
157B GLU* 3.1 3.1 - - - -
158B LYS* 2.8 44.3 + - + +
160B ILE* 3.7 29.2 - - + -
191B THR 3.9 1.8 + - - -
192B MET* 1.3 71.0 - - - +
194B CYS* 1.3 64.4 + - - +
195B VAL* 4.1 9.8 + - + +
205B TYR* 3.6 27.6 - - + -
206B GLU 3.4 17.3 - - - +
207B LEU* 3.9 13.4 - - + +
288B PHE* 5.1 1.9 - - + -
291B MET* 4.1 16.4 - - + -
310B LEU* 3.7 22.2 - - + -
314B PHE* 4.5 10.3 - - + -
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Residues in contact with CYS 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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156B ASP 4.4 0.4 - - - -
157B GLU* 3.8 32.1 - - + +
192B MET* 3.5 8.2 + - - -
193B LEU* 1.3 71.5 - - - +
195B VAL* 1.3 60.3 + - - +
196B TRP* 3.7 15.4 - - + -
205B TYR* 3.1 4.2 - - - +
206B GLU 2.8 40.1 + - - +
208B LEU* 3.9 16.2 - - - -
214B VAL* 4.9 5.2 - - - -
222B GLN* 3.6 33.2 - - - +
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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
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155B GLY* 3.1 22.5 - - - -
156B ASP 3.3 19.1 + - - +
193B LEU* 4.5 9.6 - - + -
194B CYS* 1.3 75.8 - - - +
196B TRP* 1.3 78.3 + - - +
197B TRP* 4.7 2.4 - - + +
202B VAL* 4.1 7.0 - - + -
204B TYR 3.6 11.0 - - - +
205B TYR* 3.7 12.8 - - + -
283B SER* 6.1 0.2 - - - -
287B LEU* 4.1 16.6 - - + -
288B PHE* 3.9 22.4 - - + -
314B PHE* 3.9 24.7 - - + -
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Residues in contact with TRP 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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153B VAL* 5.0 3.1 - - + -
154B THR 3.4 6.3 - - - +
155B GLY* 3.5 25.5 - - - -
156B ASP* 5.7 2.2 - - - -
157B GLU* 5.9 3.6 - - - -
194B CYS* 3.7 36.1 - - + -
195B VAL* 1.3 78.3 - - - +
197B TRP* 1.3 65.3 + - - +
202B VAL* 3.6 4.2 - - - +
203B ILE* 2.9 21.2 + - + -
204B TYR* 2.8 42.8 + + - +
205B TYR* 4.7 1.6 - - - -
206B GLU* 4.8 2.2 - - - -
219B TYR* 4.0 26.0 + + - -
222B GLN* 3.8 28.3 - - + -
223B LEU* 5.5 3.6 - - + -
226B LEU* 3.8 30.5 - - + -
246B PHE* 3.5 36.6 - + - -
248B HIS* 5.7 0.2 - - - +
254B HIS* 6.3 0.2 - + - -
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Residues in contact with TRP 197 (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 VAL* 3.1 8.1 - - - +
154B THR* 3.0 57.0 + - + +
155B GLY* 4.6 1.8 - - - -
195B VAL* 4.7 2.0 - - + -
196B TRP* 1.3 81.6 - - - +
198B ASP* 1.3 72.8 + - - +
201B GLY 3.5 16.4 - - - +
202B VAL* 3.7 9.9 - - + +
203B ILE* 3.8 3.4 - - - +
282B PRO* 3.6 20.4 - - + -
283B SER* 3.5 39.1 + - - +
286B HIS* 4.0 19.1 - + - -
287B LEU* 4.1 27.3 - - + +
322B TYR* 3.6 40.8 - + + -
326B ILE* 3.7 23.1 - - + -
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Residues in contact with ASP 198 (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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150B HIS 5.2 3.0 - - - +
152B ILE 3.6 15.9 - - - +
153B VAL* 4.1 10.3 - - + +
197B TRP* 1.3 82.9 - - - +
199B GLN* 1.3 58.4 + - + +
200B SER* 2.6 22.3 + - - -
201B GLY* 2.7 15.4 + - - +
203B ILE* 3.9 7.6 - - - +
230B LEU* 5.5 0.2 - - - +
234B ARG* 3.0 46.6 + - - +
237B TYR* 4.0 15.7 + - - +
322B TYR* 4.1 0.2 - - - +
326B ILE* 3.6 13.0 - - - -
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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