Contacts of the helix formed by residues 87 - 93 (chain C) in PDB entry 5C51
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 SER 87 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C LEU* 4.5 3.4 - - - -
84C GLN 4.5 8.0 + - - -
86C LEU* 1.3 90.0 - - - +
88C ARG* 1.3 62.6 + - - +
89C ASP* 3.9 7.6 + - - +
90C SER* 2.8 35.3 + - - -
91C LEU* 3.2 11.6 + - - +
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Residues in contact with ARG 88 (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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67C GLU* 2.9 54.8 + - - +
70C LEU* 3.9 17.0 - - + +
87C SER* 1.3 74.5 - - - +
89C ASP* 1.3 58.4 + - - +
91C LEU* 3.7 5.9 - - - +
92C LEU* 2.9 39.9 + - + +
293C PHE* 6.4 0.4 - - - -
295C TRP* 3.4 71.3 - - + +
351C TYR* 3.9 20.1 + - - +
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Residues in contact with ASP 89 (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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87C SER* 3.2 8.1 + - - +
88C ARG* 1.3 80.3 - - - +
90C SER* 1.3 57.3 + - - +
92C LEU* 3.7 10.3 + - - +
93C SER* 3.1 25.6 + - - -
295C TRP* 5.1 7.7 - - + -
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Residues in contact with SER 90 (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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85C GLN* 3.3 30.6 + - - -
87C SER* 2.8 41.8 + - - -
89C ASP* 1.3 77.3 - - - +
91C LEU* 1.3 60.8 + - - +
93C SER* 2.9 25.9 + - - +
95C CYS* 3.2 23.7 - - - +
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Residues in contact with LEU 91 (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 LEU* 5.3 7.9 - - + -
79C LEU* 4.2 36.6 - - + -
85C GLN 4.2 10.1 - - - +
86C LEU* 4.1 12.8 - - - +
87C SER 3.2 21.2 + - - +
88C ARG* 3.7 7.0 - - - +
89C ASP 3.3 0.2 - - - -
90C SER* 1.3 82.9 + - - +
92C LEU* 1.3 61.8 + - + +
93C SER 3.0 11.9 - - - +
95C CYS 6.0 0.2 - - - +
96C HIS* 3.8 29.0 + - + +
97C PRO 5.6 0.9 - - - +
98C GLY 5.6 0.4 - - - +
99C PHE* 4.8 1.8 - - + -
344C ARG* 4.9 2.3 + - - -
347C LEU* 4.0 33.4 - - + +
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Residues in contact with LEU 92 (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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88C ARG* 2.9 31.1 + - + +
89C ASP* 3.9 11.4 - - - +
91C LEU* 1.3 77.3 - - - +
93C SER* 1.3 60.9 + - - +
216C HIS* 5.2 3.5 + - - -
293C PHE* 4.6 18.6 - - + -
295C TRP* 4.4 19.5 - - + +
298C GLU* 3.5 33.7 - - + +
344C ARG* 2.7 50.4 + - - +
347C LEU* 4.5 15.5 - - + -
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Residues in contact with SER 93 (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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89C ASP 3.1 18.7 + - - -
90C SER* 2.9 22.5 - - - +
91C LEU 3.0 11.3 - - - +
92C LEU* 1.3 78.8 - - - +
94C GLY* 1.3 68.7 + - - +
95C CYS* 3.1 12.6 + - - +
96C HIS* 4.3 3.5 + - - -
216C HIS* 4.6 4.7 - - - -
218C VAL* 3.2 30.9 - - - +
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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