Contacts of the helix formed by residues 199 - 210 (chain B) in PDB entry 3O7O
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 VAL 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B PHE* 2.8 39.6 + - + +
98B VAL* 4.0 4.0 - - + -
118B THR* 5.7 0.2 - - + -
197B PHE* 3.6 22.4 + - + -
198B ASP* 1.3 70.0 - - - +
200B ARG* 1.4 62.1 + - - +
202B PHE* 2.9 24.8 + - + -
203B LEU* 3.0 19.2 + - + +
224B PHE* 3.6 32.5 - - + -
227B TRP* 3.7 28.7 - - + -
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Residues in contact with ARG 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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90B VAL* 2.9 35.2 + - - +
93B MET* 3.3 29.8 + - + +
94B LYS 3.5 15.5 - - - +
95B SER* 4.2 3.6 - - - -
96B PHE* 4.5 3.1 + - + +
198B ASP* 3.0 23.4 + - - +
199B VAL* 1.4 76.7 - - - +
201B HIS* 1.4 53.2 + - + +
203B LEU* 3.1 29.8 + - + +
204B ASP* 2.9 71.2 + - - +
220B GLU* 2.8 32.2 + - - -
257B ARG* 4.5 10.6 - - - +
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Residues in contact with HIS 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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157B ILE* 3.7 27.7 - - + +
158B PRO* 3.9 38.0 - - + +
198B ASP* 3.2 36.0 + - + +
200B ARG* 1.4 75.5 - - + +
202B PHE* 1.4 58.0 + - - +
204B ASP* 3.6 14.2 + - - +
205B ALA* 3.2 27.0 + - - +
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Residues in contact with PHE 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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136B ILE* 4.7 5.8 - - + -
138B VAL* 3.6 30.5 - - + -
157B ILE* 3.6 33.2 - - + -
170B TRP* 3.7 45.3 - + - -
184B PHE* 3.6 36.8 - + + -
197B PHE* 3.8 32.3 - + + -
198B ASP 4.2 7.4 - - - -
199B VAL* 2.9 16.1 + - + +
201B HIS* 1.4 73.9 - - - +
203B LEU* 1.3 61.5 + - + +
205B ALA 3.6 0.3 + - - -
206B ALA* 3.0 31.2 + - - +
227B TRP* 5.9 0.2 - - + -
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Residues in contact with LEU 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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90B VAL* 4.1 14.1 - - + -
93B MET* 3.8 35.0 - - + -
118B THR* 4.8 1.6 - - + -
120B LEU* 4.2 12.6 - - + -
136B ILE* 3.9 25.1 - - + -
199B VAL* 3.0 20.8 + - + +
200B ARG* 3.1 31.3 + - - +
202B PHE* 1.3 74.6 - - + +
204B ASP* 1.3 58.8 + - - +
206B ALA* 3.5 0.6 + - - -
207B GLY* 3.0 24.6 + - - -
219B PHE* 3.3 15.7 - - + -
220B GLU* 5.1 0.2 - - - +
224B PHE* 3.9 23.3 - - + -
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Residues in contact with ASP 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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200B ARG* 2.9 57.9 + - - +
201B HIS* 3.7 15.1 + - - +
202B PHE 3.4 0.2 - - - -
203B LEU* 1.3 74.3 - - - +
205B ALA* 1.4 57.2 + - - +
207B GLY* 3.3 3.0 + - - -
208B LYS* 3.0 30.0 + - - +
220B GLU* 5.8 0.2 - - - -
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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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155B PHE* 3.7 33.1 - - + -
157B ILE* 4.4 5.4 - - + -
184B PHE* 3.6 27.4 - - + -
201B HIS 3.2 14.3 + - - +
202B PHE 4.0 0.2 - - - +
203B LEU 3.5 0.2 - - - -
204B ASP* 1.4 76.9 - - - +
206B ALA* 1.3 57.3 + - - +
208B LYS* 3.4 5.5 + - - +
209B ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 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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136B ILE* 3.6 23.8 - - + -
182B LEU* 3.6 26.0 - - + -
184B PHE* 3.7 8.6 - - + -
202B PHE 3.0 19.0 + - - +
203B LEU 3.9 2.9 - - - +
205B ALA* 1.3 73.5 - - - +
207B GLY* 1.3 60.1 + - - +
209B ALA* 3.4 2.7 + - - +
210B LEU* 2.9 34.8 + - - +
219B PHE* 4.1 6.5 - - + -
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Residues in contact with GLY 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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203B LEU 3.0 17.8 + - - -
204B ASP* 3.8 1.8 - - - -
206B ALA* 1.3 75.5 - - - +
208B LYS* 1.3 56.7 + - - +
210B LEU* 3.7 1.8 - - - -
211B SER* 3.0 28.2 + - - -
219B PHE* 3.7 30.3 - - - +
220B GLU* 5.7 0.2 - - - -
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Residues in contact with LYS 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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153B GLU* 4.2 15.4 + - - +
155B PHE* 4.4 18.1 - - + -
204B ASP 3.0 16.9 + - - +
205B ALA* 3.5 7.2 - - - +
207B GLY* 1.3 74.9 - - - +
209B ALA* 1.4 58.4 + - - +
211B SER* 2.6 29.9 + - - +
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Residues in contact with ALA 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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152B ILE* 4.2 9.1 - - + +
153B GLU* 4.2 17.9 - - - +
155B PHE* 4.6 1.5 - - + -
172B LEU* 3.5 29.2 - - + -
174B LEU* 4.8 4.8 - - + +
182B LEU* 4.7 4.5 - - + -
205B ALA 2.9 18.4 + - - +
206B ALA* 3.7 5.2 - - - +
208B LYS* 1.4 74.7 - - - +
210B LEU* 1.3 63.7 + - - +
211B SER 3.7 0.5 + - - -
212B SER* 4.8 2.6 + - - -
213B SER* 5.6 0.3 + - - -
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Residues in contact with LEU 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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134B VAL* 3.9 39.3 - - + -
174B LEU* 4.0 19.7 - - + -
176B GLU* 5.9 0.2 - - - +
180B ASP* 3.3 26.0 - - - +
182B LEU* 4.0 11.7 - - + -
206B ALA 2.9 19.8 + - - +
207B GLY 3.7 3.8 - - - +
209B ALA* 1.3 75.7 - - - +
211B SER* 1.4 56.6 + - - +
212B SER 3.0 11.7 + - - -
213B SER* 3.0 32.5 + - - +
216B VAL* 3.8 20.5 - - + +
219B PHE* 4.2 16.4 - - + -
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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