Contacts of the helix formed by residues 176 - 181 (chain D) in PDB entry 4LOE
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 CYS 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D ARG 3.9 0.4 + - - -
175D ARG* 1.3 77.7 - - - +
177D PRO* 1.3 71.5 - - + +
178D HIS* 3.7 14.4 - - - -
179D HIS* 3.3 19.9 + - - -
180D GLU* 2.9 25.7 + - - +
238D CYS* 3.3 6.9 - - - -
242D CYS* 3.9 7.4 - - + -
243D MET 3.6 19.5 - - - +
244D GLY 3.6 5.4 - - - -
245D GLY* 3.8 10.8 - - - +
401D ZN 2.4 32.8 - - - -
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Residues in contact with PRO 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ARG 4.4 1.1 - - - +
176D CYS* 1.3 87.6 - - + +
178D HIS* 1.3 62.7 + - - +
180D GLU* 4.3 11.2 - - + +
181D ARG* 3.0 52.9 + - + +
243D MET 4.8 0.9 - - - +
244D GLY* 3.4 21.1 - - - +
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Residues in contact with HIS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D CYS* 3.3 10.8 - - - -
177D PRO* 1.3 80.6 - - - +
179D HIS* 1.3 92.8 + + - +
181D ARG* 3.6 15.1 + - - +
182D CYS* 3.4 26.4 + - + +
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Residues in contact with HIS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 3.8 28.8 - - + +
175D ARG* 2.8 40.7 + - - +
176D CYS* 3.3 4.4 + - - -
178D HIS* 1.3 101.3 + + - +
180D GLU* 1.3 65.6 + - - +
182D CYS* 3.2 22.5 + - - +
184D ASP* 5.2 0.2 - - - -
237D MET 3.7 8.9 + - - +
238D CYS* 3.5 5.7 - - - -
239D TYR* 4.2 11.2 - + - -
242D CYS* 3.3 13.5 - - - -
401D ZN 1.9 38.8 - - - -
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Residues in contact with GLU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D ARG* 6.2 0.3 - - - -
175D ARG* 4.0 13.2 + - + +
176D CYS 2.9 17.1 + - - +
177D PRO* 3.8 12.2 - - - +
179D HIS* 1.3 77.7 - - - +
181D ARG* 1.3 66.3 + - + +
182D CYS 3.4 5.7 + - - +
191D PRO* 3.6 45.0 - - + +
192D GLN* 3.3 33.7 + - + +
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Residues in contact with ARG 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D PRO* 3.0 47.0 + - + +
178D HIS* 4.0 11.4 + - - +
180D GLU* 1.3 84.3 - - + +
182D CYS* 1.3 60.9 + - - +
183D SER* 4.9 2.3 + - - -
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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