Contacts of the helix formed by residues 173 - 178 (chain C) in PDB entry 1D7W
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 ALA 173 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASP* 2.9 16.7 + - - -
171C VAL 3.8 0.4 - - - -
172C ASP* 1.3 79.1 - - - +
174C SER* 1.3 55.8 + - - +
175C MET* 3.0 13.2 - - - -
176C VAL* 2.9 22.7 + - + +
177C TYR* 3.1 19.3 - - + -
284C VAL* 3.8 28.7 - - + -
285C GLY* 4.2 5.5 - - - -
288C VAL* 4.1 16.8 - - + +
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Residues in contact with SER 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE 5.3 0.2 - - - -
95A HIS 4.8 1.0 + - - -
96A ASP* 3.2 10.7 + - - -
167C LEU* 4.8 3.5 - - - +
168C THR* 3.3 8.0 + - - -
172C ASP* 3.2 16.3 + - - -
173C ALA* 1.3 76.2 - - - +
175C MET* 1.3 56.6 + - - +
176C VAL 3.1 1.6 - - - -
177C TYR* 4.3 2.7 - - - +
178C GLY* 2.8 41.2 + - - +
179C SER* 3.4 22.4 + - - -
236C GLY* 3.6 4.3 - - - +
1600C CA 2.5 23.4 - - - -
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Residues in contact with MET 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TRP* 5.8 0.2 - - + -
92A LEU* 3.6 48.9 - - + +
93A LEU* 4.8 1.1 - - - +
95A HIS* 3.5 25.7 + - + +
96A ASP* 3.7 19.3 + - + +
173C ALA* 3.0 22.5 - - - -
174C SER* 1.3 79.0 + - - +
176C VAL* 1.4 64.5 + - + +
236C GLY* 3.1 16.2 + - - -
237C ASP* 3.1 13.1 + - + +
250C HIS* 3.0 41.2 + - + +
253C LEU* 4.2 11.2 - - + -
288C VAL* 4.3 14.8 - - + -
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ALA* 2.9 17.4 + - + +
175C MET* 1.4 89.4 - - + +
177C TYR* 1.3 84.1 + - + +
178C GLY 3.6 0.4 - - - -
187C LEU* 3.8 10.0 - - - +
197C LEU* 3.8 24.1 - - + +
235C ALA* 4.5 0.6 - - - -
236C GLY* 3.5 12.9 + - - +
250C HIS* 5.0 7.9 - - - +
253C LEU* 3.9 46.4 - - + +
254C LEU* 4.9 2.5 - - + +
284C VAL* 4.7 1.8 - - + -
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Residues in contact with TYR 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.5 1.8 - - + -
172C ASP 4.2 3.1 - - - -
173C ALA* 3.1 29.8 + - + +
174C SER* 4.7 2.0 - - - -
176C VAL* 1.3 95.3 - - + +
178C GLY* 1.4 62.3 + - - +
184C ALA* 3.3 22.5 - - - +
187C LEU* 3.3 18.5 - - - +
197C LEU* 4.1 11.7 - - + -
257C HIS* 2.9 40.6 + + - +
277C TYR* 3.6 31.3 + + - +
281C ARG* 3.2 43.1 - - + +
284C VAL* 3.2 34.5 - - + +
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Residues in contact with GLY 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.4 19.3 - - - +
174C SER* 2.8 28.3 + - - -
177C TYR* 1.4 76.7 - - - +
179C SER* 1.3 63.1 + - - -
180C GLU 3.7 2.9 - - - -
183C LEU* 4.0 11.9 - - - -
236C GLY* 3.4 19.4 - - - -
281C ARG* 5.5 1.0 + - - -
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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