Contacts of the helix formed by residues 198 - 209 (chain B) in PDB entry 2HXO
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 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A THR* 6.0 0.2 - - - -
125A PRO* 4.2 11.0 - - + +
126A ARG* 3.4 47.5 + - + +
129A GLU* 3.4 28.9 - - + +
193B LEU* 3.9 47.5 - - + +
194B ASP* 2.8 21.1 + - + +
195B PRO 3.8 3.1 - - - -
197B ALA* 1.3 93.4 - - + +
199B PRO* 1.3 59.3 - - - +
200B PHE 3.3 2.5 - - - -
201B THR* 4.0 10.1 - - - -
202B ARG* 3.0 28.8 + - - +
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Residues in contact with PRO 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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129A GLU* 3.1 11.0 - - - +
133A ARG* 3.6 17.7 - - + +
136A GLN* 5.3 4.4 + - - +
195B PRO 3.6 14.5 - - - +
196B ASP 3.7 10.1 - - - +
197B ALA 3.3 8.5 - - - +
198B TYR* 1.3 88.5 - - - +
200B PHE* 1.3 63.3 + - + +
202B ARG* 4.1 2.6 - - + +
203B ALA* 3.2 23.4 + - - +
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Residues in contact with PHE 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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128A PHE* 3.4 33.9 - + + -
129A GLU* 3.1 15.9 + - - +
132A GLY* 3.3 25.8 - - - -
133A ARG* 4.3 7.6 - - + +
135A VAL* 5.1 0.4 - - + -
136A GLN* 3.7 26.6 + - - +
145A TRP* 3.6 34.1 - + + -
146A PHE* 4.9 0.7 - - - -
149A SER* 3.2 26.5 - - - -
199B PRO* 1.3 78.5 - - - +
201B THR* 1.3 68.4 + - - +
203B ALA* 3.0 7.8 + - - +
204B VAL* 2.9 51.5 + - + +
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Residues in contact with THR 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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125A PRO* 3.4 22.9 + - + -
128A PHE* 4.2 2.0 - - + +
129A GLU* 2.6 35.5 + - - +
190B TRP* 3.3 36.6 - - + -
193B LEU* 3.7 19.1 - - + -
198B TYR* 4.0 9.2 - - - -
200B PHE* 1.3 75.8 - - - +
202B ARG* 1.3 56.6 + - - +
204B VAL* 3.4 8.5 - - - +
205B ALA* 2.8 28.1 + - - +
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Residues in contact with ARG 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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190B TRP 3.3 16.6 - - - +
191B GLU* 2.6 47.6 + - - +
193B LEU* 3.2 27.9 + - + +
194B ASP 4.3 1.3 - - - +
195B PRO* 3.9 28.1 - - + +
198B TYR* 3.0 27.4 + - + +
199B PRO* 4.1 3.4 - - + +
201B THR* 1.3 73.4 - - - +
203B ALA* 1.3 66.2 + - - +
204B VAL 3.4 0.3 + - - -
205B ALA* 3.5 14.6 + - - +
206B ASP* 4.6 1.6 + - - +
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Residues in contact with ALA 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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136A GLN* 5.0 0.9 - - - +
142A GLU* 4.5 10.5 - - - +
145A TRP* 3.7 27.1 - - + -
199B PRO 3.2 18.1 + - - +
200B PHE* 3.0 6.4 + - - +
202B ARG* 1.3 82.1 - - - +
204B VAL* 1.3 59.0 + - - +
206B ASP* 4.7 7.3 + - - +
207B GLN* 5.2 2.6 - - - +
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Residues in contact with VAL 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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145A TRP* 3.9 15.3 - - + -
146A PHE* 4.3 20.0 - - + +
190B TRP* 4.5 11.2 - - + -
200B PHE* 2.9 52.4 + - + +
201B THR* 3.4 16.6 - - - +
203B ALA* 1.3 78.0 - - - +
205B ALA* 1.3 58.4 + - - +
206B ASP 3.0 3.8 - - - -
207B GLN* 2.6 55.1 + - - +
208B VAL* 3.5 3.7 + - - +
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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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187B SER* 2.6 27.4 + - - +
190B TRP* 3.8 22.4 - - + -
191B GLU* 3.5 28.9 - - + +
201B THR 2.8 18.7 + - - +
202B ARG 3.5 10.0 + - - +
204B VAL* 1.3 74.9 - - - +
206B ASP* 1.3 56.5 + - - +
208B VAL* 3.3 18.2 + - - +
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Residues in contact with ASP 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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187B SER* 4.0 3.6 - - - -
191B GLU* 4.2 11.5 + - - +
202B ARG 4.6 1.4 + - - +
203B ALA 4.9 6.3 - - - +
204B VAL 2.8 5.5 + - - -
205B ALA* 1.3 77.6 - - - +
207B GLN* 1.3 61.5 - - + +
208B VAL 3.1 1.6 + - - -
209B ARG* 3.2 36.9 + - - +
210B GLY 4.6 0.3 + - - -
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Residues in contact with GLN 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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142A GLU* 4.0 15.5 + - - +
143A ALA* 3.7 25.1 + - - +
145A TRP* 5.7 0.2 - - - -
146A PHE* 3.3 40.8 + - + +
203B ALA 5.2 2.5 - - - +
204B VAL* 2.6 31.5 + - - +
206B ASP* 1.3 71.3 - - + +
208B VAL* 1.3 61.9 + - - +
209B ARG* 3.3 0.4 - - - -
210B GLY 4.2 3.1 + - - -
211B HIS* 3.8 17.3 + - - +
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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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146A PHE* 4.1 22.2 - - + -
183B LEU* 3.6 37.9 - - + +
186B VAL* 4.0 18.4 - - + -
187B SER* 4.1 4.0 - - - +
190B TRP* 3.9 32.1 - - + -
204B VAL 4.0 7.4 - - - +
205B ALA 3.4 14.6 - - - +
206B ASP 3.1 1.0 - - - -
207B GLN* 1.3 76.6 - - - +
209B ARG* 1.3 67.4 + - - +
211B HIS* 3.2 19.3 + - + +
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Residues in contact with ARG 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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180B ASP* 4.7 8.1 - - - +
183B LEU* 3.8 18.9 - - - +
184B ASP* 2.9 36.4 + - + +
187B SER* 3.1 30.4 + - - +
188B THR* 3.0 27.5 + - - +
191B GLU* 3.2 27.5 + - - -
206B ASP* 3.2 28.0 + - - +
208B VAL* 1.3 80.8 - - - +
210B GLY* 1.3 59.3 + - - +
211B HIS 3.4 1.7 + - - -
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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