Contacts of the strand formed by residues 194 - 206 (chain B) in PDB entry 4HXG
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 PRO 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B ASP* 3.7 13.0 - - - +
137B VAL* 4.1 6.5 - - + -
188B PRO* 4.4 10.3 - - + -
189B HIS 3.6 7.9 - - - +
190B ARG* 3.3 39.5 - - + +
193B ILE* 1.3 101.3 - - + +
195B ARG* 1.3 62.5 + - - +
196B TYR* 3.5 47.3 + - + +
506B TRP* 5.6 1.7 - - - -
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PRO* 4.3 2.7 - - - +
189B HIS* 2.8 26.7 + - + +
191B ASP* 2.7 42.3 + - - +
193B ILE* 3.5 18.6 - - - +
194B PRO* 1.3 72.1 - - - +
196B TYR* 1.3 62.4 + - - +
198B LYS* 4.1 29.6 - - + +
199B TYR* 3.0 59.1 + - + +
200B TRP* 5.8 0.2 + - - -
216B LYS* 4.7 2.0 - - - +
506B TRP* 6.3 1.1 - - - -
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Residues in contact with TYR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP* 5.1 1.4 + - - -
137B VAL* 3.0 29.7 + - + -
138B PRO* 4.0 14.8 - - + -
141B PHE* 6.4 1.3 - + - -
147B PHE* 6.0 0.4 - + - -
172B ARG* 3.9 24.7 + - + +
173B PHE* 3.8 39.9 - + + -
188B PRO* 4.0 15.9 - - + -
193B ILE* 6.4 0.4 - - + -
194B PRO* 3.5 41.4 + - + +
195B ARG* 1.3 70.6 - - - +
197B PHE* 1.3 83.2 + - + +
198B LYS* 2.9 13.5 + - - +
200B TRP* 6.0 0.4 - - - +
240B VAL* 4.9 0.2 - - - +
506B TRP* 4.0 36.9 - + - +
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Residues in contact with PHE 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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141B PHE* 4.5 15.0 - + - -
173B PHE* 4.4 23.8 - + - -
195B ARG 3.8 1.0 + - - -
196B TYR* 1.3 80.8 - - + +
198B LYS* 1.3 57.6 + - - +
200B TRP* 3.5 39.3 - + - -
220B TYR* 6.1 2.9 - + - -
237B LYS* 4.8 10.2 + - - +
240B VAL* 4.0 17.7 - - + +
503B ILE* 5.3 0.7 - - + -
506B TRP* 3.3 40.8 - + + -
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Residues in contact with LYS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ARG* 4.1 25.5 - - + +
196B TYR 2.9 9.1 - - - +
197B PHE* 1.3 79.7 - - - +
199B TYR* 1.3 91.7 + - + +
200B TRP* 4.2 1.6 - - - -
218B SER* 3.0 34.3 + - - -
237B LYS* 3.5 32.6 + - + +
238B LYS* 3.5 18.5 + - - +
240B VAL* 3.6 28.0 - - + +
506B TRP* 6.5 0.7 - - + -
510B GLU* 4.5 3.4 - - - -
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Residues in contact with TYR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PRO* 3.8 1.4 - - - +
189B HIS* 3.1 27.6 + - + -
195B ARG* 3.0 43.4 + - + +
198B LYS* 1.3 118.0 + - + +
200B TRP* 1.3 71.1 + - - +
216B LYS* 3.5 53.8 - - + -
217B VAL 3.3 2.5 - - - -
218B SER* 3.8 15.9 - - - -
236B GLU* 3.2 30.1 + - + -
237B LYS 3.9 11.6 + - - -
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Residues in contact with TRP 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE 5.2 3.4 + - - -
175B SER* 5.8 0.8 + - - -
186B SER* 4.3 5.1 - - - -
187B VAL 3.2 30.5 - - - +
188B PRO* 3.9 10.0 - - + +
189B HIS* 3.9 2.0 - - - +
195B ARG 5.7 0.2 - - - -
197B PHE* 3.5 48.4 - + - +
198B LYS 4.0 4.0 - - - -
199B TYR* 1.3 78.5 + - - +
201B ASP* 1.3 68.7 + - - +
202B ILE* 4.5 4.0 - - + -
216B LYS 3.0 6.6 + - - -
217B VAL* 2.7 50.5 + - + +
218B SER* 3.4 22.2 - - - -
219B PHE 3.6 20.2 - - - +
220B TYR* 3.3 49.0 - + + +
232B TYR 5.2 0.2 - - - -
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Residues in contact with ASP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B VAL 3.7 1.4 - - - +
186B SER* 3.7 1.6 - - - -
187B VAL* 2.8 36.8 + - + +
188B PRO 4.6 1.6 - - - +
189B HIS* 2.9 34.2 + - - -
190B ARG 4.9 0.7 + - - -
200B TRP* 1.3 74.3 - - - +
202B ILE* 1.3 60.7 + - - +
203B TYR* 3.9 29.3 + - + +
212B LYS* 4.3 11.4 - - - -
214B PHE 3.4 10.5 - - - +
215B GLU* 3.8 2.7 - - - +
216B LYS 2.9 23.7 + - - -
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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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184B VAL* 3.7 28.5 - - + -
185B VAL 3.4 6.1 - - - +
186B SER* 4.2 8.3 - - - +
200B TRP* 4.5 3.8 - - + -
201B ASP* 1.3 78.4 - - - +
203B TYR* 1.3 59.3 + - - +
212B LYS* 3.6 2.6 - - - -
213B LEU* 2.7 38.8 + - + -
214B PHE* 2.9 33.5 + - + +
217B VAL* 4.2 9.4 - - + -
219B PHE* 3.5 26.7 - - + +
220B TYR* 3.8 13.9 - - - -
221B ALA* 4.2 1.8 - - + +
231B LEU* 4.1 18.6 - - + -
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Residues in contact with TYR 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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170B LYS* 4.9 6.7 - - - -
183B ILE 3.5 0.5 - - - +
184B VAL* 3.4 6.2 - - - +
185B VAL* 2.7 51.9 + - + +
187B VAL* 4.1 21.5 - - + -
201B ASP* 3.9 24.9 + - + +
202B ILE* 1.3 76.1 - - - +
204B LEU* 1.3 60.6 + - - +
205B TRP* 4.0 1.1 - - + +
210B GLU* 3.7 44.4 - - + +
211B GLU 3.4 4.5 - - - +
212B LYS* 3.7 49.0 - - + -
213B LEU* 4.4 4.3 - - - -
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Residues in contact with LEU 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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179B HIS* 4.1 20.4 - - + -
182B SER* 3.5 33.0 - - - +
183B ILE 3.9 9.6 - - - +
184B VAL* 4.3 8.7 - - + -
203B TYR* 1.3 72.8 - - - +
205B TRP* 1.3 59.7 + - - +
206B LYS* 6.2 0.7 - - + -
210B GLU* 3.0 5.4 - - - -
211B GLU* 2.7 45.6 + - + +
213B LEU* 4.1 27.0 - - + +
229B ILE* 5.2 0.2 - - + -
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Residues in contact with TRP 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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156B VAL* 5.5 1.3 - - + -
166B GLU* 3.2 35.9 - - + -
167B GLN 5.2 0.7 - - - -
168B PHE* 3.3 59.6 - + + +
170B LYS* 4.9 3.3 - - - +
182B SER* 3.5 3.4 - - - -
183B ILE* 2.7 58.5 + - + +
185B VAL* 4.3 9.2 - - + -
203B TYR* 5.2 0.7 - - + +
204B LEU* 1.3 75.3 - - - +
206B LYS* 1.3 66.6 + - - +
207B ASP 3.5 14.8 - - - -
208B GLY* 3.2 31.3 + - - -
209B GLU 3.4 9.3 + - - -
210B GLU* 3.9 23.3 + - + -
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Residues in contact with LYS 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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181B ASP* 3.1 49.8 + - - +
182B SER* 4.0 14.3 + - - +
204B LEU* 4.2 0.6 + - + -
205B TRP* 1.3 78.7 - - - +
207B ASP* 1.3 96.0 + - + +
208B GLY 3.2 2.5 - - - -
209B GLU* 2.8 32.1 + - - +
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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