Contacts of the helix formed by residues 192 - 197 (chain L) in PDB entry 6AHU
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 192 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L TYR* 3.7 14.9 + - - -
86L PHE* 4.1 5.6 - - - -
183L TRP* 5.9 1.3 - - - -
185L LYS* 6.3 4.0 - - - +
191L SER* 1.3 77.4 - - - +
193L MET* 1.3 64.9 + - - +
194L MET* 3.6 14.3 + - + +
195L SER* 2.9 44.8 + - - +
196L TYR* 3.9 3.1 + - - +
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Residues in contact with MET 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L TYR* 3.6 37.4 + - + -
82L PHE* 5.8 0.4 - - + -
86L PHE* 3.8 24.3 - - + -
92L CYS* 4.7 7.9 - - - -
181L LEU* 3.7 28.7 - - + -
182L ALA* 4.0 17.9 - - - +
183L TRP* 3.9 29.1 - - + +
191L SER 4.0 0.4 + - - -
192L THR* 1.3 74.7 + - - +
194L MET* 1.3 63.9 + - - +
195L SER 3.2 0.9 - - - -
196L TYR 3.4 1.0 + - - +
197L PHE* 3.2 39.4 + - + -
202L ILE* 3.8 10.1 - - + +
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Residues in contact with MET 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L TYR* 3.6 37.0 - - + +
192L THR* 3.3 12.3 + - + +
193L MET* 1.3 79.3 - - - +
195L SER* 1.3 59.7 + - - +
197L PHE 4.1 1.6 - - - +
198L SER* 4.0 19.1 + - - -
202L ILE* 3.7 38.4 - - + +
204L GLU* 4.8 13.2 - - + +
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Residues in contact with SER 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L SER* 4.6 7.3 - - - -
192L THR* 2.9 34.5 + - - +
194L MET* 1.3 79.9 - - - +
196L TYR* 1.3 61.9 + - - +
198L SER* 4.1 12.5 + - - -
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Residues in contact with TYR 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L GLU* 3.0 28.4 + - + +
79L THR* 3.3 20.4 + - - +
81L GLU* 3.7 30.5 - - + +
82L PHE* 3.4 33.2 + + + +
85L THR* 5.1 6.7 - - + -
86L PHE* 4.2 20.0 - + + -
192L THR 4.6 2.0 - - - +
193L MET 3.4 6.1 + - - +
194L MET 3.4 0.4 - - - -
195L SER* 1.3 83.4 + - - +
197L PHE* 1.3 85.6 + + + +
198L SER* 3.1 8.6 + - - -
199L LYS* 4.9 1.4 + - - +
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Residues in contact with PHE 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L VAL* 4.7 6.7 - - + -
72L LEU* 3.7 37.5 - - + -
76L GLU* 3.9 15.9 - - + -
77L LEU* 4.5 3.4 - - + -
82L PHE* 3.7 25.6 - + - -
86L PHE* 4.9 0.4 - + - -
181L LEU* 4.0 18.6 - - + -
193L MET* 3.2 37.6 + - + +
194L MET 4.1 3.8 - - - -
196L TYR* 1.3 98.6 - + - +
198L SER* 1.3 61.3 + - - +
199L LYS 3.3 3.1 - - - +
200L TYR* 3.4 20.0 - + + +
202L ILE* 3.4 35.9 - - + +
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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