Contacts of the helix formed by residues 170 - 174 (chain C) in PDB entry 2I6A
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 PHE 170 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ASN* 3.6 8.1 + - - +
38C GLN* 3.9 12.8 - - - -
65C SER* 3.7 21.5 - - - -
168C ALA* 4.4 4.9 - - + +
169C GLY* 1.3 77.3 - - - +
171C PHE* 1.3 61.6 + - - +
172C LEU 3.4 0.2 + - - -
173C THR* 3.3 23.1 + - - +
174C VAL* 4.4 0.3 + - - +
198C SER* 2.9 45.2 + - - -
199C ALA* 3.7 20.9 - - + -
201C PHE* 3.8 18.2 - + - -
202C ILE* 4.0 5.6 - - + -
500C 5I5 3.2 78.5 + + + +
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Residues in contact with PHE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C MET* 3.6 28.7 - - + -
13C GLY* 3.6 26.7 - - - -
14C ASN* 3.3 24.6 - - - +
66C THR* 6.0 0.2 - - - +
87C PHE 5.5 0.2 - - - -
141C ALA 4.5 1.3 - - - -
144C TYR* 3.7 32.8 - + + -
167C ILE* 3.6 19.1 - - + -
168C ALA* 3.0 14.0 + - + +
169C GLY 3.0 0.4 + - - -
170C PHE* 1.3 74.6 - - - +
172C LEU* 1.3 57.4 + - - +
173C THR 3.1 2.9 - - - -
174C VAL* 2.8 37.1 + - + +
175C SER* 3.0 31.2 + - - -
178C SER* 4.4 1.6 - - - -
179C VAL* 3.8 19.3 - - + -
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Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ALA 5.6 0.4 - - - +
169C GLY* 2.9 24.7 + - - +
171C PHE* 1.3 78.0 - - - +
173C THR* 1.3 56.0 + - - +
174C VAL 3.1 3.8 + - - -
176C PRO* 3.3 28.9 - - + +
179C VAL* 3.8 33.7 - - + -
195C LEU* 4.6 7.4 - - + -
202C ILE* 4.4 11.0 - - + -
206C TYR* 4.3 10.7 - - + +
209C SER* 4.3 13.6 + - - +
210C LEU* 3.2 52.5 - - + +
213C VAL* 3.9 15.5 - - + -
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Residues in contact with THR 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.8 8.4 - - + +
138C LEU* 3.7 19.8 - - - +
142C ASN* 3.6 11.8 + - - -
170C PHE 3.3 11.7 + - - +
171C PHE 3.1 1.2 - - - -
172C LEU* 1.3 74.7 - - - +
174C VAL* 1.3 56.5 + - - +
176C PRO* 5.2 0.4 - - - -
201C PHE* 4.0 9.4 - - + -
202C ILE* 3.5 20.0 - - + -
206C TYR* 3.1 53.1 - - + -
500C 5I5 5.5 0.7 + - - -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASN* 3.5 21.8 - - - +
138C LEU* 3.6 18.8 - - + -
141C ALA 3.3 20.6 - - - +
142C ASN* 3.4 37.0 + - - +
144C TYR* 4.2 13.9 - - + +
145C LYS* 5.4 5.7 + - - -
170C PHE 4.6 0.4 - - - +
171C PHE* 2.8 24.7 + - + +
172C LEU 3.0 0.4 - - - -
173C THR* 1.3 83.8 - - - +
175C SER* 1.3 59.1 + - - +
176C PRO* 3.8 5.5 - - - +
177C GLU* 4.8 0.9 - - - +
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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