Contacts of the helix formed by residues 195 - 210 (chain B) in PDB entry 2XXA
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 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ASP* 3.3 25.0 + - - +
275A VAL 4.3 2.7 + - - -
276A GLY* 3.6 26.5 - - - -
277A GLU* 4.1 9.9 - - - +
192B LEU* 2.7 27.1 + - + +
194B ASN* 1.4 77.6 - - - +
196B SER* 1.3 58.1 + - - +
197B HIS* 3.3 21.2 + - + +
198B LEU* 3.1 34.5 + - + +
199B MET* 3.1 27.9 + - - +
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Residues in contact with SER 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLN 5.1 0.7 - - - -
194B ASN 2.9 13.0 + - - -
195B LYS* 1.3 68.0 - - - +
197B HIS* 1.3 60.8 + - - +
199B MET* 3.1 11.1 + - - +
200B GLU* 2.8 45.3 + - - +
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Residues in contact with HIS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LYS* 4.1 28.0 + - + +
196B SER* 1.3 83.6 + - - +
198B LEU* 1.4 91.4 + - + +
200B GLU* 3.6 6.1 + - - +
201B GLU* 3.1 25.7 + - - +
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU* 4.5 10.8 - - - +
137B PHE* 6.0 4.0 - - + -
189B ALA* 5.1 4.7 - - + -
190B GLY 4.4 9.6 - - - +
191B ARG* 2.9 69.2 + - + +
195B LYS* 3.1 35.2 + - + +
197B HIS* 1.4 105.3 - - + +
199B MET* 1.3 60.7 + - - +
201B GLU* 3.4 10.3 - - + +
202B LEU 3.3 10.4 + - - -
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Residues in contact with MET 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ARG* 3.8 27.4 - - + -
192B LEU 4.1 2.2 - - - +
193B GLN* 3.4 39.9 - - - +
195B LYS 3.1 11.8 + - - +
196B SER* 3.1 12.1 + - - +
198B LEU* 1.3 74.1 - - - +
200B GLU* 1.4 57.4 + - - +
201B GLU 3.1 4.3 - - - -
202B LEU* 3.2 25.2 + - + +
203B LYS* 3.2 22.7 + - - +
238B LEU* 4.5 17.0 - - + +
239B PHE* 3.7 33.4 - - + -
242B ALA* 4.7 11.1 - - + +
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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
----------------------------------------------------------
196B SER* 2.8 21.9 + - - +
197B HIS* 3.9 7.1 - - - +
199B MET* 1.4 74.7 - - - +
201B GLU* 1.4 57.3 + - - +
202B LEU 3.3 0.2 - - - -
203B LYS* 3.6 32.9 + - + +
204B LYS* 3.0 26.2 + - - +
207B ARG* 4.6 8.7 + - - +
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Residues in contact with GLU 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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164B ASP* 4.5 5.7 - - - +
165B SER* 3.7 26.3 + - - -
166B ALA* 4.6 0.9 + - - +
189B ALA* 5.5 0.3 - - - +
191B ARG* 2.9 33.0 + - - -
197B HIS 3.1 17.8 + - - +
198B LEU* 3.4 15.0 - - + +
199B MET 3.1 0.2 - - - -
200B GLU* 1.4 75.4 - - - +
202B LEU* 1.3 58.7 + - - +
203B LYS 3.3 0.4 - - - -
204B LYS* 3.4 14.4 - - + +
205B ILE* 3.2 33.3 + - - +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 4.9 3.1 - - + -
104B VAL* 3.6 26.5 - - + -
188B THR* 4.1 6.7 - - + -
191B ARG* 3.5 26.7 - - - +
198B LEU 3.3 9.2 + - - +
199B MET* 3.2 19.4 + - + +
201B GLU* 1.3 78.0 - - - +
203B LYS* 1.4 61.6 + - - +
205B ILE* 3.4 31.6 + - + +
206B VAL* 3.6 13.5 - - - +
239B PHE* 3.7 33.4 - - + -
242B ALA* 5.7 1.1 - - + -
243B VAL* 3.8 21.5 - - + -
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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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199B MET* 3.2 16.6 + - - +
200B GLU* 3.7 33.8 + - + +
201B GLU 3.3 0.2 - - - -
202B LEU* 1.4 76.5 - - - +
204B LYS* 1.4 55.0 + - - +
206B VAL* 3.2 8.8 + - - +
207B ARG* 3.1 41.9 + - + +
241B GLU 5.3 1.8 + - - -
242B ALA* 3.4 48.6 - - + +
243B VAL* 4.5 4.5 - - + +
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Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ASP* 2.8 37.8 + - - +
166B ALA* 3.8 14.8 - - + +
167B SER* 4.5 4.9 + - - -
200B GLU 3.0 18.9 + - - +
201B GLU* 3.4 17.3 - - + +
203B LYS* 1.4 73.9 - - - +
205B ILE* 1.4 61.7 + - - +
207B ARG* 3.5 31.5 + - - +
208B VAL* 3.3 39.7 + - + +
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Residues in contact with ILE 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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102B LEU* 3.9 23.3 - - + -
165B SER* 4.1 11.4 - - - +
166B ALA* 3.7 29.2 - - + +
169B ILE* 3.8 21.1 - - + -
188B THR* 3.9 13.9 - - + -
191B ARG* 4.2 9.2 - - - +
201B GLU* 3.2 22.5 + - - +
202B LEU* 3.4 30.5 - - + +
203B LYS 3.2 0.8 - - - -
204B LYS* 1.4 77.6 - - - +
206B VAL* 1.3 60.1 + - - +
208B VAL* 3.5 3.6 + - - +
209B MET* 3.3 30.3 + - + +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 3.8 17.5 - - + -
202B LEU 3.6 14.4 - - - +
203B LYS* 3.2 8.0 + - - +
205B ILE* 1.3 73.1 - - - +
207B ARG* 1.4 64.1 + - - +
209B MET* 3.2 17.3 + - - +
210B LYS* 3.2 29.9 + - + +
217B PRO* 3.7 25.1 - - + -
243B VAL* 3.7 31.6 - - + +
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Residues in contact with ARG 207 (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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200B GLU* 4.6 7.7 + - - +
203B LYS* 3.1 28.9 + - + +
204B LYS* 3.5 44.2 - - - +
205B ILE 3.3 0.4 - - - -
206B VAL* 1.4 77.1 - - - +
208B VAL* 1.3 62.7 + - + +
210B LYS* 3.6 17.2 + - - +
211B LYS* 4.1 10.4 + - - +
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Residues in contact with VAL 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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166B ALA* 4.3 19.1 - - + +
167B SER* 5.1 6.1 - - - +
170B PHE* 3.3 45.2 - - + -
204B LYS* 3.3 31.3 + - + +
205B ILE 3.5 3.1 + - - +
207B ARG* 1.3 75.4 - - + +
209B MET* 1.3 63.3 + - - +
210B LYS 3.4 0.2 - - - -
211B LYS* 3.4 35.2 - - + +
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Residues in contact with MET 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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100B VAL* 3.6 29.2 - - + -
102B LEU* 4.4 20.4 - - - -
166B ALA 5.8 1.1 - - - +
169B ILE* 4.4 10.8 - - + -
170B PHE* 5.3 3.8 - - - +
173B ILE* 3.7 28.5 - - + +
205B ILE* 3.3 16.2 + - - +
206B VAL* 3.2 15.0 + - - +
208B VAL* 1.3 76.3 - - - +
210B LYS* 1.3 59.9 + - - +
211B LYS 3.2 2.8 + - - -
212B LEU* 3.3 14.4 + - - +
213B ASP 3.4 12.4 + - - +
216B ALA* 3.8 16.3 - - + +
217B PRO* 3.5 38.4 - - + -
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Residues in contact with LYS 210 (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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206B VAL* 3.2 25.0 + - + +
207B ARG* 3.8 10.8 - - - +
208B VAL 3.4 0.4 - - - -
209B MET* 1.3 72.3 - - - +
211B LYS* 1.4 60.7 + - - +
212B LEU 3.2 2.2 + - - -
213B ASP 3.4 20.1 + - - -
214B VAL* 3.2 44.7 + - + +
215B GLU 4.2 4.2 + - - -
216B ALA 2.7 26.1 + - - +
217B PRO* 3.5 15.0 + - - +
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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