Contacts of the helix formed by residues 182 - 186 (chain A) in PDB entry 3A7H
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 THR 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ASP* 2.6 30.2 + - - -
146A LYS* 2.9 27.5 + - - +
181A GLY* 1.3 72.1 - - - -
183A PRO* 1.4 65.5 - - + -
184A PHE* 5.0 2.5 - - + -
185A TRP* 2.9 54.4 + - + +
186A MET* 3.4 9.2 + - - +
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Residues in contact with PRO 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A PHE* 5.9 2.0 - - + -
181A GLY 4.1 4.0 - - - +
182A THR* 1.4 89.6 - - + -
184A PHE* 1.3 77.3 + - + +
186A MET* 3.1 31.1 + - + +
191A ILE* 4.6 2.1 - - + +
224A PRO* 4.3 34.5 - - + +
227A VAL* 4.8 4.3 - - + -
228A LEU* 5.5 9.9 - - + +
231A ILE* 3.4 18.1 - - - +
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Residues in contact with PHE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A THR* 3.1 3.0 + - + -
183A PRO* 1.3 85.1 - - + +
185A TRP* 1.3 80.6 + + + +
186A MET 4.9 0.5 - - - +
203A TRP* 5.2 0.2 + - - -
207A ILE* 3.6 19.8 - - - +
217A PRO* 3.6 25.9 - - + +
218A PRO* 3.8 19.6 - - - +
219A HIS* 3.4 20.7 - - - -
220A SER* 3.8 15.7 - - - -
222A LEU 3.9 13.2 - - - -
224A PRO* 4.5 16.2 - - + -
227A VAL* 3.5 27.4 - - + -
231A ILE* 4.4 12.3 - - - +
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Residues in contact with TRP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ASP* 5.7 1.3 - - - +
145A ILE 3.6 26.7 - - - +
146A LYS* 3.4 24.8 - - + +
182A THR* 2.9 43.2 + - + +
184A PHE* 1.3 98.0 - + + +
186A MET* 1.3 59.5 + - - +
203A TRP* 3.7 5.0 - - - -
204A SER* 2.6 36.4 + - - +
207A ILE* 3.5 27.5 - - + +
208A THR* 3.8 11.7 + - - +
211A GLU* 3.0 40.2 + - - -
216A GLU* 5.9 0.2 - - - -
217A PRO* 3.6 26.8 - - + +
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Residues in contact with MET 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ARG 5.8 0.2 - - - +
179A PHE* 3.5 35.7 - - + -
180A VAL 3.9 18.6 - - - +
181A GLY* 4.1 6.1 - - - +
182A THR 3.4 18.2 - - - +
183A PRO* 3.1 29.3 + - - +
184A PHE 3.4 0.6 - - - +
185A TRP* 1.3 78.3 - - - +
187A ALA* 1.3 64.2 + - - +
190A VAL* 3.4 26.5 - - + -
191A ILE* 3.4 28.9 - - + +
203A TRP* 3.3 11.0 + - - -
204A SER* 4.6 1.1 - - - -
231A ILE* 3.5 17.7 - - - +
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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