Contacts of the helix formed by residues 173 - 177 (chain D) in PDB entry 1C72
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 CYS 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D LEU* 5.0 5.8 - - - -
131D PRO* 5.0 8.1 - - - -
134D LEU* 4.0 20.4 - - - -
170D VAL* 3.2 33.2 + - + +
171D PRO 3.3 1.2 - - - +
172D ASP* 1.3 79.3 - - - +
174D PRO* 1.3 74.1 - - - +
175D GLU* 3.2 15.5 - - - -
176D LEU* 3.0 33.7 + - + +
177D GLN* 3.6 6.9 - - - +
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Residues in contact with PRO 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D ASP 3.2 7.8 - - - +
173D CYS* 1.3 88.7 - - - +
175D GLU* 1.3 81.8 + - - +
176D LEU 3.1 5.2 - - - -
177D GLN* 3.1 32.1 + - + +
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Residues in contact with GLU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PRO* 3.3 24.0 - - + +
134D LEU* 4.1 25.1 - - + +
135D ARG* 3.6 41.8 + - - +
138D SER* 4.8 4.9 + - - -
173D CYS* 3.2 3.5 - - - -
174D PRO* 1.3 104.2 - - - +
176D LEU* 1.3 59.6 + - - +
177D GLN 3.4 5.8 - - - +
180D LEU* 3.8 18.7 - - - +
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Residues in contact with LEU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D LEU* 3.9 21.3 - - + -
163D LEU* 4.1 34.5 - - + +
166D GLN* 4.3 5.6 - - + +
167D ARG* 3.5 44.0 + - + +
170D VAL* 3.6 25.1 - - + +
171D PRO 4.9 0.2 - - - +
173D CYS* 3.0 19.1 + - + +
175D GLU* 1.3 79.6 - - - +
177D GLN* 1.3 57.9 + - - +
180D LEU* 3.9 9.0 - - + -
181D SER* 2.9 33.2 + - - -
184D LEU* 5.0 5.8 - - + +
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Residues in contact with GLN 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ARG* 3.1 34.9 + - - +
171D PRO 4.5 2.8 - - - +
172D ASP 5.0 1.9 - - - +
173D CYS 3.6 14.0 - - - +
174D PRO* 3.1 21.4 + - + +
175D GLU* 4.0 6.2 - - - +
176D LEU* 1.3 79.9 - - - +
178D GLY* 1.3 61.7 + - - +
179D ASN* 5.5 0.3 - - - +
180D LEU* 5.1 1.1 + - - +
181D SER* 3.2 10.4 + - - +
185D GLN* 6.1 0.2 - - - +
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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