Contacts of the helix formed by residues 192 - 201 (chain C) in PDB entry 6DF3
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 GLU 192 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ARG* 3.3 4.0 - - - -
91C LEU* 2.8 31.4 + - - +
92C LEU* 2.7 38.1 + - + +
116C TYR* 4.3 6.9 + - - +
173C PHE* 5.2 0.2 - - - -
188C LYS* 3.0 20.6 + - - +
189C ALA* 3.9 7.9 - - - +
190C LEU 3.1 0.8 - - - -
191C GLY* 1.3 75.4 - - - +
193C VAL* 1.3 65.3 + - - +
194C ASP* 3.0 8.7 - - - -
195C ILE* 2.8 33.1 + - + +
196C LEU 3.4 6.1 + - - -
60L TYR* 2.7 28.3 + - - +
112L ARG* 4.2 4.7 - - - +
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Residues in contact with VAL 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C PHE* 3.7 20.9 - - + -
116C TYR* 3.7 29.6 - - + -
121C PHE* 4.3 15.7 - - + -
137C PHE* 4.3 3.4 - - + -
140C LEU* 4.1 15.3 - - + -
144C PHE* 4.7 8.5 - - + -
189C ALA 3.7 0.8 + - - +
190C LEU 3.2 19.0 + - - +
191C GLY 3.4 0.6 - - - -
192C GLU* 1.3 78.7 - - - +
194C ASP* 1.3 57.8 + - - +
196C LEU* 3.1 10.5 + - + +
197C LEU* 2.8 44.2 + - + +
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Residues in contact with ASP 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C TRP* 3.6 13.7 - - + -
73C PHE* 3.5 20.4 - - + -
77C LYS* 4.2 0.9 - - - +
81C GLN* 2.9 26.6 + - - +
191C GLY 3.3 13.7 - - - +
192C GLU* 3.3 6.2 - - - -
193C VAL* 1.3 78.8 - - - +
195C ILE* 1.3 73.7 + - - +
197C LEU* 4.4 2.0 - - - +
198C THR* 2.7 34.7 + - - -
91L LEU* 3.8 11.7 - - - +
112L ARG* 5.0 0.5 + - - -
114L SER* 5.1 0.2 - - - -
117L GLN* 3.0 31.8 + - - +
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Residues in contact with ILE 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ARG* 3.7 41.3 - - - +
92C LEU* 3.9 10.8 - - + +
97C LEU* 3.7 21.1 - - + -
192C GLU* 2.8 40.0 + - + +
194C ASP* 1.3 85.1 + - - +
196C LEU* 1.3 62.5 + - - +
198C THR* 3.6 6.1 - - - -
199C TRP* 3.1 22.5 + - - +
60L TYR* 4.4 2.7 - - + -
91L LEU* 3.8 25.4 - - + -
112L ARG* 5.8 0.4 - - - +
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Residues in contact with LEU 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 4.0 17.0 - - + +
97C LEU* 5.2 2.7 - - + -
109C VAL* 5.5 0.7 - - + -
112C LEU* 4.2 27.6 - - + -
113C LEU* 3.7 25.8 - - + -
116C TYR* 4.0 25.6 - - + -
144C PHE* 3.8 19.7 - - + -
192C GLU 3.4 1.8 + - - +
193C VAL* 3.1 12.5 + - - +
195C ILE* 1.3 79.2 - - - +
197C LEU* 1.3 62.3 + - - +
199C TRP* 3.3 13.7 + - + +
200C MET* 3.1 46.2 + - + +
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Residues in contact with LEU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LEU* 4.0 26.2 - - + +
70C TRP* 3.9 29.2 - - + -
73C PHE* 4.3 5.4 - - + -
140C LEU* 4.4 2.5 - - + -
144C PHE* 4.0 18.8 - - + -
193C VAL* 2.8 34.1 + - + +
194C ASP* 3.9 4.0 - - - +
196C LEU* 1.3 73.1 - - - +
198C THR* 1.3 63.9 + - - +
200C MET* 3.7 19.3 - - + -
201C GLN* 3.0 4.9 + - - +
302C GOL 2.8 60.5 + - - +
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Residues in contact with THR 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C TRP* 3.4 20.7 - - - -
194C ASP 2.7 22.3 + - - -
195C ILE* 3.6 7.4 - - - -
197C LEU* 1.3 77.9 - - - +
199C TRP* 1.3 65.5 + - - +
201C GLN* 3.6 14.0 - - - +
202C LYS* 3.8 18.6 + - - +
88L LEU 5.7 0.9 - - - +
116L LEU* 4.2 17.0 - - + -
117L GLN* 4.8 3.6 + - - -
208L TRP* 3.9 20.1 - - + -
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Residues in contact with TRP 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C PHE* 4.9 1.8 - + - -
97C LEU* 3.6 53.7 + - + -
100C VAL* 3.8 30.2 - - + +
105C SER* 3.9 22.0 - - - -
108C LEU* 4.1 11.7 - - + -
109C VAL* 3.8 28.7 - - + -
112C LEU* 4.6 9.2 - - + -
195C ILE 3.1 13.6 + - - +
196C LEU* 3.3 13.2 + - + +
198C THR* 1.3 77.6 - - - +
200C MET* 1.3 79.4 + - + +
202C LYS* 3.1 44.0 + - - +
203C PHE* 3.6 32.0 - + - -
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Residues in contact with MET 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C PHE* 3.4 14.0 - - + -
56C PHE* 4.1 12.5 - - + -
69C LEU* 4.9 0.2 - - + -
109C VAL* 3.7 25.8 - - + -
113C LEU* 4.2 15.5 - - - -
144C PHE* 4.1 15.9 - - + -
147C ILE* 4.4 14.4 - - + -
196C LEU* 3.1 22.7 + - + +
197C LEU* 3.7 17.7 - - + -
198C THR 3.5 0.2 - - - -
199C TRP* 1.3 92.1 - - + +
201C GLN* 1.3 53.7 + - - +
203C PHE* 3.0 28.6 + - - +
302C GOL 3.0 35.2 - - - +
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Residues in contact with GLN 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C PHE* 4.1 5.8 - - - -
66C PRO* 4.1 6.5 - - + -
70C TRP* 2.7 11.3 + - - -
197C LEU 3.0 7.1 + - - +
198C THR* 3.6 8.3 - - - +
200C MET* 1.3 72.9 - - - +
202C LYS* 1.3 60.7 + - - +
203C PHE 3.1 0.9 - - - -
204C TYR* 3.2 15.6 + - + +
302C GOL 2.1 50.5 + - - +
161L HIS* 3.5 17.1 - - + -
207L THR* 2.7 49.7 + - - +
208L TRP* 3.3 29.6 - - + +
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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