Contacts of the helix formed by residues 175 - 183 (chain R) in PDB entry 5M32
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 GLU 175 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172R SER 4.7 1.2 + - - +
173R ALA* 4.4 0.4 - - - +
174R SER* 1.3 80.2 - - - +
176R GLY* 1.3 62.0 + - - +
177R ALA 3.4 0.7 - - - -
178R GLN* 3.9 1.8 - - - +
179R SER* 2.9 31.2 + - - -
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Residues in contact with GLY 176 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173R ALA* 4.8 2.2 - - - +
174R SER 4.8 0.4 - - - +
175R GLU* 1.3 76.9 - - - +
177R ALA* 1.3 60.3 + - - +
179R SER* 2.9 19.6 + - - -
180R SER* 2.9 17.7 + - - -
203R LYS* 4.2 9.9 + - - -
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Residues in contact with ALA 177 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ILE* 4.9 5.8 - - + +
169R ALA* 4.4 7.9 - - + -
173R ALA* 3.3 35.7 + - + +
175R GLU 3.4 0.2 - - - -
176R GLY* 1.3 73.7 - - - +
178R GLN* 1.3 60.5 + - - +
180R SER* 2.7 21.9 + - - -
181R LEU* 2.9 18.2 + - - +
200R ILE* 3.8 20.7 - - + +
201R ILE* 6.4 1.1 - - + -
203R LYS* 5.6 1.8 - - - +
204R GLN* 5.5 3.4 - - + -
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Residues in contact with GLN 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167R ALA 3.3 14.4 + - - -
168R ARG* 3.5 20.8 - - - +
169R ALA* 2.8 39.0 + - + +
173R ALA 4.2 0.8 + - - -
174R SER 3.3 26.7 - - - +
175R GLU* 3.5 3.4 + - - +
176R GLY 3.3 0.4 - - - -
177R ALA* 1.3 79.3 - - - +
179R SER* 1.3 58.3 + - - +
181R LEU* 3.3 5.2 + - - +
182R GLN* 2.9 27.4 + - + +
54S SER 6.2 0.2 - - - -
55S GLU* 3.0 40.6 + - - +
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Residues in contact with SER 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R GLU 2.9 16.7 + - - -
176R GLY* 2.9 17.3 + - - -
178R GLN* 1.3 73.9 - - - +
180R SER* 1.3 64.1 + - - +
182R GLN* 3.4 21.4 + - - +
183R GLU* 3.8 12.0 + - - +
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Residues in contact with SER 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176R GLY 2.9 7.8 + - - -
177R ALA* 2.7 28.4 + - - -
179R SER* 1.3 78.8 + - - +
181R LEU* 1.3 59.8 + - - +
183R GLU* 3.3 28.2 - - - +
184R VAL* 3.3 15.1 - - - +
200R ILE* 3.4 24.8 - - - +
203R LYS* 3.3 28.9 + - - -
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Residues in contact with LEU 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ILE* 4.8 11.2 - - + -
39R GLY 4.5 3.6 - - - +
40R ILE* 3.8 30.1 - - + -
167R ALA* 3.7 39.4 - - + +
168R ARG 3.7 15.5 - - - +
169R ALA* 4.5 3.8 - - + +
177R ALA 2.9 19.3 + - - +
178R GLN* 3.3 9.6 + - - +
180R SER* 1.3 74.7 + - - +
182R GLN* 1.3 62.6 + - - +
183R GLU 3.2 0.8 + - - -
184R VAL* 3.7 22.9 + - + +
185R TYR* 4.0 11.9 + - + +
196R LYS 5.3 0.9 - - - +
197R SER* 5.6 1.6 - - - -
200R ILE* 4.8 13.2 - - + -
55S GLU* 4.0 6.5 - - - +
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Residues in contact with GLN 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178R GLN* 2.9 16.5 + - + +
179R SER* 3.5 14.0 + - - +
180R SER 3.2 0.8 - - - -
181R LEU* 1.3 79.1 - - - +
183R GLU* 1.3 64.1 + - - +
184R VAL 4.0 0.2 + - - -
185R TYR 4.8 5.9 - - - +
55S GLU* 3.4 35.7 - - - +
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Residues in contact with GLU 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179R SER 4.0 10.1 - - - +
180R SER* 3.3 22.0 - - - +
182R GLN* 1.3 88.5 - - - +
184R VAL* 1.3 66.4 + - + +
185R TYR 3.7 1.6 - - - -
186R HIS* 6.0 0.2 + - - -
203R LYS* 5.8 0.3 + - - -
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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