Contacts of the helix formed by residues 193 - 204 (chain B) in PDB entry 4OMD
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 ARG 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B MET 5.5 2.1 + - - -
190B ASN* 3.4 29.6 + - + +
191B ASP 3.3 2.8 + - - +
192B ASN* 1.3 78.3 - - - +
194B HIS* 1.3 71.9 + - + +
195B GLY 3.4 1.3 - - - -
196B THR* 3.1 7.3 + - - -
197B ARG* 3.1 67.3 + - - +
355B ASP* 3.6 16.3 + - - +
356B LEU* 3.6 21.5 - - + -
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Residues in contact with HIS 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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153B ASP* 2.7 29.6 + - - -
154B ASP* 3.2 13.9 + - - +
191B ASP 4.3 0.6 + - - +
193B ARG* 1.3 84.5 - - + +
195B GLY* 1.3 62.8 + - - +
197B ARG* 3.2 9.9 + - - +
198B CYS* 3.2 25.5 + - - -
253B SER* 3.2 32.3 - - - -
364B HIS* 4.4 9.2 - + - -
368B SER* 2.8 31.9 + - - -
4I ARG* 3.5 34.5 - - + +
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Residues in contact with GLY 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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151B ILE* 3.9 5.5 - - - +
153B ASP* 3.3 23.7 + - - -
154B ASP* 2.7 18.2 + - - -
155B GLY 3.3 19.3 - - - -
156B ILE* 5.0 1.0 - - - +
194B HIS* 1.3 74.1 - - - +
196B THR* 1.3 56.5 + - - +
198B CYS* 3.4 3.0 + - - +
199B ALA* 3.0 29.0 + - - +
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Residues in contact with THR 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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154B ASP* 4.4 0.2 + - - -
155B GLY 3.6 2.7 + - - -
156B ILE* 3.8 5.6 - - - +
157B GLU* 3.2 38.0 + - + +
160B HIS* 4.3 3.1 - - + -
163B LEU* 4.3 9.2 - - + -
184B PRO* 4.0 9.0 - - - +
192B ASN 4.6 1.4 + - - -
193B ARG* 3.1 11.5 + - - -
195B GLY* 1.3 73.3 - - - +
197B ARG* 1.3 65.6 + - - +
199B ALA* 3.5 7.0 + - - +
200B GLY 3.2 8.8 + - - -
354B THR* 2.8 37.1 + - - +
355B ASP 4.0 17.0 - - - +
356B LEU* 4.2 7.6 - - - +
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Residues in contact with ARG 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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193B ARG* 3.1 61.1 + - - +
194B HIS* 3.2 9.2 + - - +
196B THR* 1.3 77.7 - - - +
198B CYS* 1.3 62.8 + - - +
200B GLY 3.4 1.0 + - - -
201B GLU* 3.4 4.3 + - - +
353B THR* 2.7 27.8 + - + +
354B THR 3.1 18.4 - - - +
355B ASP* 2.6 38.9 + - - +
361B THR* 3.6 22.2 + - + +
363B SER* 3.5 24.5 + - - -
364B HIS* 3.8 34.6 + - + +
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Residues in contact with CYS 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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151B ILE* 4.0 17.3 - - + -
153B ASP* 4.2 2.2 - - - -
194B HIS* 3.2 22.0 + - - +
195B GLY* 3.7 7.6 - - - +
197B ARG* 1.3 77.3 - - - +
199B ALA* 1.3 66.4 + - - +
201B GLU* 3.2 24.9 + - - +
202B VAL* 3.5 4.0 + - - +
251B SER* 5.8 0.2 - - - +
253B SER* 3.5 21.3 - - - -
364B HIS* 3.7 10.8 - - - -
368B SER 3.5 25.4 - - - -
372B PRO* 3.5 16.2 - - + +
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Residues in contact with ALA 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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151B ILE* 3.7 21.4 - - + +
156B ILE* 3.8 31.0 - - + -
163B LEU* 4.2 9.5 - - + +
195B GLY 3.0 17.4 + - - +
196B THR 3.7 5.4 - - - +
197B ARG 3.3 0.2 - - - -
198B CYS* 1.3 76.3 - - - +
200B GLY* 1.3 63.0 + - - +
202B VAL* 3.0 14.0 + - - +
203B ALA* 3.0 12.5 + - - -
221B ILE* 4.0 8.0 - - + +
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Residues in contact with GLY 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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163B LEU* 4.0 11.1 - - - +
196B THR 3.2 8.5 + - - -
197B ARG 3.4 0.2 + - - -
198B CYS 3.3 0.2 - - - -
199B ALA* 1.3 78.7 - - - +
201B GLU* 1.3 61.9 + - - +
204B ALA* 3.0 32.8 + - - +
213B VAL 4.4 1.2 - - - +
214B GLY* 3.5 2.9 - - - -
353B THR* 3.2 17.0 - - - -
354B THR* 3.4 13.4 + - - -
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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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121B GLN* 6.2 0.7 - - - +
123B TYR* 5.5 0.9 - - - +
197B ARG 3.6 8.5 - - - +
198B CYS* 3.2 8.9 + - - +
200B GLY* 1.3 76.7 - - - +
202B VAL* 1.3 57.7 + - - +
213B VAL 4.6 1.5 - - - +
214B GLY* 3.3 2.5 - - - -
215B VAL* 3.0 30.7 + - - +
351B ILE* 3.6 19.7 - - + +
352B VAL 5.2 2.0 - - - +
353B THR* 3.2 9.4 + - - +
364B HIS* 3.1 31.4 + - - -
369B ALA* 2.4 31.9 - - - +
372B PRO* 3.3 27.7 - - + +
373B LEU* 3.4 19.7 - - + +
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Residues in contact with VAL 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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149B VAL* 4.0 31.4 - - + -
151B ILE* 4.1 14.1 - - + -
198B CYS 3.8 12.6 - - - +
199B ALA 3.0 6.3 + - - +
201B GLU* 1.3 77.9 - - - +
203B ALA* 1.3 64.5 + - + +
214B GLY* 3.8 1.1 - - - -
215B VAL 3.2 2.0 + - - +
216B ALA* 2.8 34.0 + - + +
219B ALA* 5.5 0.2 - - + -
221B ILE* 4.3 5.2 - - + -
372B PRO* 3.1 33.0 - - + +
375B ALA* 4.2 4.9 - - + -
376B GLY* 4.0 18.2 - - - +
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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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149B VAL* 6.4 0.2 - - + -
162B ASP 4.2 1.9 - - - +
163B LEU* 4.2 6.6 - - - +
166B ASN* 3.0 18.7 + - - +
199B ALA 3.0 8.0 + - - -
202B VAL* 1.3 85.0 - - + +
204B ALA* 1.3 66.2 + - - +
205B VAL 3.4 0.7 + - - -
214B GLY* 4.1 0.9 - - - -
216B ALA 3.4 18.8 - - - +
219B ALA* 3.8 20.0 - - + +
221B ILE* 3.9 22.7 - - + -
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Residues in contact with ALA 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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162B ASP* 3.2 28.5 - - - +
163B LEU* 4.3 3.6 - - - -
200B GLY* 3.0 27.3 + - - +
203B ALA* 1.3 76.8 - - - +
205B VAL* 1.3 65.4 + - - +
212B GLY 4.3 0.7 - - - +
213B VAL* 3.8 7.6 - - - +
214B GLY* 3.0 25.8 + - - +
217B TYR* 3.3 9.7 - - - +
353B THR* 6.2 1.1 - - - -
354B THR* 4.3 6.1 - - + +
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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