Contacts of the helix formed by residues 184 - 188 (chain A) in PDB entry 3SMT
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 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 3.4 2.6 - - + -
183A ASP* 1.3 82.0 - - - +
185A PRO* 1.4 67.9 - - - +
186A LEU* 3.1 7.8 - - - +
187A TYR* 2.8 34.3 + - - +
188A PHE* 3.5 3.2 - - - -
208A GLN* 4.9 0.7 - - - -
248A SER* 3.1 24.0 + - - +
251A MSE 3.9 20.0 - - - -
252A THR* 3.5 32.1 - - + -
322A ILE 4.1 4.3 - - - +
323A HIS 4.2 2.0 - - - +
325A GLY* 4.0 12.1 - - - +
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Residues in contact with PRO 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 4.8 4.0 + - - -
53A ARG* 5.2 0.3 + - - -
183A ASP 4.5 0.7 - - - +
184A THR* 1.4 80.2 - - - +
186A LEU* 1.3 54.4 + - - +
187A TYR 3.0 1.1 - - - -
188A PHE* 3.0 44.4 + - + +
193A VAL* 4.7 4.0 - - - +
196A LEU* 6.0 0.7 - - + -
205A VAL* 3.8 38.4 - - + +
208A GLN* 3.4 16.4 - - - +
209A TYR* 5.1 4.1 - - - -
321A VAL* 3.5 17.0 - - + +
322A ILE* 3.4 34.5 - - + +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ARG* 5.2 0.9 + - - -
184A THR* 2.9 8.9 + - - +
185A PRO* 1.3 76.1 - - - +
187A TYR* 1.4 57.8 + - + +
188A PHE 3.5 2.4 - - - +
208A GLN* 3.6 24.0 + - + +
209A TYR* 4.2 33.6 - - + -
212A THR* 3.6 33.0 - - + +
240A TYR* 4.4 4.9 + - - +
244A ARG* 3.0 39.7 + - + -
247A VAL* 3.9 22.9 - - + -
248A SER* 3.5 19.7 - - - +
251A MSE 4.3 10.5 - - + -
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Residues in contact with TYR 187 (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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180A SER 4.5 1.9 + - - -
181A GLU* 3.9 16.4 - - + -
182A TYR* 3.2 47.8 - - + +
184A THR* 2.8 21.0 + - - +
186A LEU* 1.4 77.2 - - - +
188A PHE* 1.3 66.0 + - - +
189A GLU* 3.8 5.0 + - - +
241A GLU 4.8 0.5 + - - -
244A ARG* 3.5 42.3 + - + +
245A TRP* 3.3 32.2 + - - +
248A SER* 3.5 24.0 - - - -
459A ARG* 3.1 33.0 + - - +
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Residues in contact with PHE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ARG* 2.8 31.9 + - - -
183A ASP 3.2 23.3 - - - -
184A THR 3.5 4.9 - - - -
185A PRO* 3.0 32.8 + - + +
186A LEU 4.7 0.7 - - - +
187A TYR* 1.3 82.1 - - - +
189A GLU* 1.3 56.9 + - - +
192A GLU* 3.4 28.9 - - + +
193A VAL* 3.6 19.3 - - + -
196A LEU* 4.9 8.1 - - + -
321A VAL* 4.5 6.3 - - + -
459A ARG* 3.4 43.5 - - + +
462A MSE 3.7 21.3 - - + -
463A ALA* 4.1 14.1 - - + -
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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