Contacts of the helix formed by residues 176 - 182 (chain A) in PDB entry 6TOS
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 MET 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A TYR* 3.3 12.9 - - + -
127A ALA* 3.6 38.4 - - + +
128A VAL* 3.7 17.3 - - + +
131A SER* 3.6 24.9 - - - +
172A SER 3.3 19.9 + - - +
173A LEU 4.1 0.2 + - - -
174A ALA 3.2 1.0 - - - -
175A ILE* 1.4 84.0 - - + +
177A VAL* 1.4 63.6 + - - +
178A PRO* 3.4 2.2 - - - -
179A GLN* 3.2 20.1 + - - +
180A ALA 3.3 4.0 + - - -
215A TYR* 4.7 5.4 - - - -
219A PHE* 3.6 28.0 - - + -
223A THR* 3.8 14.6 - - + -
404B PGW 4.0 12.8 - - + -
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Residues in contact with VAL 177 (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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124A TYR* 3.8 4.7 - - + -
173A LEU 3.4 19.5 - - - +
174A ALA 3.2 11.2 + - - +
176A MET* 1.4 75.2 - - - +
178A PRO* 1.4 63.7 - - - +
180A ALA* 2.9 6.1 + - - +
181A ALA* 2.9 20.6 + - - +
413A SOG 3.7 50.5 - - + +
145B TRP* 3.9 13.0 - - + -
150B HIS* 6.1 0.9 - - + -
237B GLN* 4.7 6.1 - - - +
404B PGW 3.3 33.4 - - + +
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Residues in contact with PRO 178 (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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174A ALA 4.0 0.9 - - - +
175A ILE* 3.3 21.5 - - - +
176A MET 3.5 0.7 - - - -
177A VAL* 1.4 88.3 - - + +
179A GLN* 1.4 59.2 + - - +
181A ALA* 3.3 7.0 + - + +
182A VAL* 3.2 24.2 + - - +
215A TYR* 4.2 20.2 - - + -
230B LEU* 4.1 5.6 - - + -
233B MET* 3.7 25.8 - - + -
404B PGW 3.5 49.1 - - + +
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Residues in contact with GLN 179 (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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123A PRO 4.3 13.2 - - - +
124A TYR* 5.2 0.9 - - - -
127A ALA* 4.1 23.3 - - + -
176A MET* 3.2 15.3 + - - +
178A PRO* 1.4 74.2 - - - +
180A ALA* 1.4 65.0 + - - +
182A VAL* 3.4 14.4 - - - +
183A MET* 3.2 43.2 - - - +
204A GLU* 3.1 24.6 + - - +
215A TYR* 2.7 44.4 + - - +
401A NRE 3.6 31.1 + - + +
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Residues in contact with ALA 180 (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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120A LYS* 2.9 39.1 + - - +
124A TYR* 3.9 30.7 - - + +
176A MET 3.3 1.6 + - - -
177A VAL* 2.9 10.1 + - - +
179A GLN* 1.4 76.5 - - - +
181A ALA* 1.4 60.3 + - - +
183A MET* 3.3 9.8 + - - +
413A SOG 4.0 29.4 - - + +
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Residues in contact with ALA 181 (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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120A LYS* 3.2 13.5 + - - +
177A VAL 2.9 11.2 + - - +
178A PRO 3.3 10.3 + - - +
180A ALA* 1.4 76.4 - - - +
182A VAL* 1.3 56.9 + - - +
184A GLU* 4.0 6.4 - - - +
408A SOG 4.0 18.6 + - - +
413A SOG 3.6 21.2 + - - +
404B PGW 3.5 36.8 - - - +
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Residues in contact with VAL 182 (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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178A PRO 3.2 13.8 + - - +
179A GLN* 3.4 21.3 - - - +
181A ALA* 1.3 73.3 - - - +
183A MET* 1.3 63.2 + - - +
184A GLU* 3.4 1.7 + - - +
204A GLU* 3.3 25.5 - - + -
205A ARG* 2.8 48.5 + - - +
206A TRP* 3.8 37.0 - - + -
215A TYR* 5.6 0.7 - - + -
408A SOG 4.6 7.6 - - - -
404B PGW 3.6 16.2 - - + +
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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