Contacts of the helix formed by residues 141 - 148 (chain C) in PDB entry 5I75
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 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B TYR* 4.1 5.5 - - - +
148B PRO* 2.9 54.9 + - - +
149B LEU* 5.2 1.2 - - - +
150B ALA* 5.4 3.6 - - - -
139C PRO 3.4 4.3 + - - -
140C PRO* 1.3 77.4 - - - +
142C SER* 1.3 64.0 + - - +
143C GLU 3.9 0.6 + - - -
144C GLN* 3.4 15.4 + - - +
145C LEU* 3.2 21.2 + - - +
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Residues in contact with SER 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C SER* 1.3 73.1 - - - +
143C GLU* 1.3 66.2 + - - +
144C GLN 3.1 0.4 - - - -
145C LEU* 3.1 15.3 + - - +
146C THR* 2.9 33.3 + - - -
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Residues in contact with GLU 143 (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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146B VAL 3.7 4.3 - - - +
147B TYR* 3.7 10.0 - - + -
148B PRO* 3.2 38.1 - - + +
233B LYS* 3.2 44.2 + - - +
234B LYS 5.4 2.4 - - - +
141C SER* 3.3 1.2 + - - -
142C SER* 1.3 82.9 + - - +
144C GLN* 1.3 60.4 + - - +
146C THR* 3.6 14.6 + - - -
147C SER* 3.7 14.6 + - - -
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Residues in contact with GLN 144 (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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147B TYR* 3.5 44.7 - - + +
149B LEU* 5.3 2.6 - - - +
166B LEU* 4.1 14.2 - - - +
168B LYS* 6.2 1.6 - - - +
140C PRO* 4.2 10.2 - - + +
141C SER* 3.4 13.6 + - - +
142C SER 3.1 0.4 - - - -
143C GLU* 1.3 78.9 - - - +
145C LEU* 1.3 63.5 + - - +
146C THR 3.2 0.4 - - - -
147C SER* 3.3 4.2 + - - -
148C GLY 3.1 14.9 + - - -
149C GLY* 3.1 26.1 + - - +
150C ALA* 3.6 8.4 - - - +
151C SER* 3.2 42.2 + - - +
200C THR* 5.6 0.8 - - - +
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Residues in contact with LEU 145 (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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140C PRO* 4.4 10.3 - - + +
141C SER 3.2 14.7 + - - +
142C SER* 3.1 16.5 + - - +
144C GLN* 1.3 73.9 - - - +
146C THR* 1.3 66.1 + - - +
148C GLY* 3.3 7.7 + - - +
149C GLY 3.5 17.0 - - - +
150C ALA* 3.9 16.6 - - + -
203C LYS* 3.6 32.9 + - + +
206C TYR* 4.0 23.1 - - + +
207C GLU* 5.5 5.4 - - - +
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Residues in contact with THR 146 (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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142C SER* 2.9 18.3 + - - -
143C GLU* 3.7 9.6 + - - -
144C GLN 3.2 0.4 - - - -
145C LEU* 1.3 78.2 - - - +
147C SER* 1.3 61.4 + - - +
148C GLY* 3.4 0.5 + - - -
203C LYS* 5.1 2.8 + - - -
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Residues in contact with SER 147 (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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147B TYR* 2.9 30.3 + - - -
143C GLU 3.7 8.6 + - - -
144C GLN* 3.3 9.0 + - - -
146C THR* 1.3 78.1 - - - +
148C GLY* 1.3 58.9 + - - +
149C GLY 5.1 0.7 - - - -
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Residues in contact with GLY 148 (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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144C GLN 3.1 3.2 + - - -
145C LEU 3.3 9.3 + - - -
146C THR 3.2 3.2 - - - -
147C SER* 1.3 79.8 - - - +
149C GLY* 1.3 58.6 + - - +
202C THR* 4.9 2.6 - - - -
203C LYS* 4.0 31.2 + - - +
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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