Contacts of the helix formed by residues 193 - 204 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189C MET 5.6 1.7 + - - -
190C ASN* 3.4 29.6 + - + +
191C ASP 3.3 2.6 + - - +
192C ASN* 1.3 76.5 - - - +
194C HIS* 1.3 70.7 + - + +
195C GLY 3.4 1.8 - - - -
196C THR* 3.2 7.9 + - - -
197C ARG* 3.0 69.7 + - - +
355C ASP* 3.6 8.2 + - - +
356C LEU* 3.6 30.7 - - + -
520F PRO* 6.0 2.8 - - - +
521F HIS* 3.8 30.8 + - - -
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Residues in contact with HIS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ASP* 2.7 28.1 + - - +
154C ASP* 3.3 14.1 + - - +
191C ASP 4.3 0.9 + - - +
193C ARG* 1.3 84.1 - - + +
195C GLY* 1.3 62.5 + - - +
197C ARG* 3.3 9.2 + - - +
198C CYS* 3.2 29.4 + - - -
253C SER* 3.2 32.8 - - - -
364C HIS* 4.5 8.5 - + - -
368C SER* 2.7 30.9 + - - -
4J ARG* 3.5 34.2 - - + +
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Residues in contact with GLY 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ILE* 3.9 6.5 - - - +
153C ASP* 3.2 21.9 + - - -
154C ASP* 2.6 23.2 + - - -
155C GLY 3.3 14.4 - - - -
156C ILE* 4.9 0.7 - - - +
194C HIS* 1.3 73.6 - - - +
196C THR* 1.3 56.8 + - - +
198C CYS* 3.4 3.8 + - - +
199C ALA* 3.0 29.3 + - - +
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Residues in contact with THR 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C GLY 3.6 2.9 + - - -
156C ILE* 3.7 5.2 - - - +
157C GLU* 3.0 39.7 + - + +
160C HIS* 4.3 2.9 - - + -
163C LEU* 4.2 9.0 - - + -
184C PRO* 4.0 8.3 - - - +
192C ASN 4.8 0.5 + - - -
193C ARG* 3.2 12.6 + - - -
195C GLY* 1.3 73.4 - - - +
197C ARG* 1.3 64.4 + - - +
199C ALA* 3.5 6.7 + - - +
200C GLY 3.2 9.0 + - - -
354C THR* 2.9 37.6 + - - +
355C ASP 4.1 16.6 - - - +
356C LEU* 4.2 5.9 - - - +
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Residues in contact with ARG 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ARG* 3.0 62.7 + - - +
194C HIS* 3.3 8.3 + - - +
196C THR* 1.3 76.8 - - - +
198C CYS* 1.3 63.0 + - - +
200C GLY 3.4 0.7 + - - -
201C GLU* 3.4 4.7 + - - +
353C THR* 2.7 33.0 + - + +
354C THR 3.2 18.8 - - - +
355C ASP* 2.7 37.6 + - - +
361C THR* 3.7 17.3 + - - +
363C SER* 3.5 24.4 + - - -
364C HIS* 3.7 33.0 + - + +
365C THR 5.2 0.4 - - - +
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Residues in contact with CYS 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ILE* 4.0 17.7 - - + -
153C ASP* 4.4 2.2 - - - -
194C HIS* 3.2 26.5 + - - +
195C GLY 3.7 6.7 - - - +
196C THR 3.3 0.2 - - - -
197C ARG* 1.3 80.4 - - - +
199C ALA* 1.3 63.0 + - - +
201C GLU* 3.2 25.5 + - - +
202C VAL* 3.5 4.0 + - - +
253C SER* 3.7 18.6 - - - +
364C HIS* 3.7 10.3 - - - -
368C SER 3.7 23.1 - - - -
372C PRO* 3.5 17.3 - - + +
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Residues in contact with ALA 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ILE* 3.8 21.7 - - + +
156C ILE* 3.7 31.0 - - + -
163C LEU* 4.2 8.2 - - + +
195C GLY 3.0 17.2 + - - +
196C THR 3.7 5.6 - - - +
197C ARG 3.3 0.2 - - - -
198C CYS* 1.3 76.3 - - - +
200C GLY* 1.3 63.7 + - - +
202C VAL* 3.0 13.3 + - - +
203C ALA* 3.0 13.0 + - - -
221C ILE* 4.1 10.0 - - + +
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Residues in contact with GLY 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C LEU* 4.0 11.2 - - - +
196C THR 3.2 8.7 + - - -
197C ARG 3.4 0.2 + - - -
198C CYS 3.3 0.6 - - - -
199C ALA* 1.3 78.4 - - - +
201C GLU* 1.3 62.3 + - - +
204C ALA* 3.0 32.9 + - - +
213C VAL 4.4 1.0 - - - +
214C GLY* 3.5 3.3 - - - -
353C THR* 3.3 17.5 - - - -
354C THR* 3.3 13.4 + - - -
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C GLN* 6.3 0.4 - - - +
123C TYR* 5.5 1.3 - - - +
197C ARG 3.6 9.0 - - - +
198C CYS* 3.2 9.7 + - - +
200C GLY* 1.3 76.0 - - - +
202C VAL* 1.3 57.5 + - - +
213C VAL 4.6 1.5 - - - +
214C GLY* 3.3 2.4 - - - -
215C VAL* 3.0 31.5 + - - +
351C ILE* 3.5 23.5 - - + +
352C VAL 5.1 2.2 - - - +
353C THR* 3.3 8.5 + - - +
364C HIS* 3.1 31.4 + - + -
369C ALA* 2.5 33.6 - - - +
372C PRO* 3.4 21.8 - - + +
373C LEU* 3.4 21.9 - - + +
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Residues in contact with VAL 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C VAL* 4.0 30.5 - - + -
151C ILE* 4.1 15.5 - - + -
198C CYS 3.7 13.7 - - - +
199C ALA 3.0 5.3 + - - +
201C GLU* 1.3 78.9 - - - +
203C ALA* 1.3 62.4 + - + +
214C GLY* 3.8 0.9 - - - -
215C VAL 3.2 2.2 + - - +
216C ALA* 2.8 34.4 + - + +
219C ALA* 5.5 0.4 - - + -
221C ILE* 4.1 7.4 - - + -
372C PRO* 3.2 32.1 - - + +
375C ALA* 4.3 4.3 - - + -
376C GLY* 3.9 19.7 - - - +
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Residues in contact with ALA 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ASP 4.1 1.7 - - - +
163C LEU* 4.2 6.3 - - - +
166C ASN* 2.9 19.6 + - - +
199C ALA 3.0 9.2 + - - -
202C VAL* 1.3 84.3 - - + +
204C ALA* 1.3 66.1 + - - +
205C VAL 3.4 0.7 + - - -
214C GLY* 4.1 1.1 - - - -
216C ALA 3.4 18.4 - - - +
219C ALA* 3.9 17.7 - - + +
221C ILE* 3.8 25.8 - - + -
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Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ASP* 3.3 26.9 - - - +
163C LEU* 4.3 4.3 - - - -
200C GLY* 3.0 28.2 + - - +
203C ALA* 1.3 76.6 - - - +
205C VAL* 1.3 66.9 + - - +
211C CYS* 6.5 0.2 - - - -
212C GLY 4.2 0.7 - - - +
213C VAL* 3.8 7.6 - - - +
214C GLY* 3.0 25.3 + - - +
217C TYR* 3.3 9.9 - - - +
353C THR* 6.2 1.3 - - - -
354C THR* 4.4 5.8 - - + +
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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