Contacts of the strand formed by residues 199 - 205 (chain C) in PDB entry 5ZR1
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 LEU 199 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C ARG* 3.7 10.3 + - - -
125C TYR* 3.6 4.7 - - + +
127C VAL* 5.0 6.3 - - + -
150C LEU* 4.3 17.3 - - + -
188C VAL* 5.1 6.1 - - + -
191C PHE* 3.6 50.3 - - + -
198C ASP* 1.3 74.3 - - - +
200C ALA* 1.3 66.3 + - - +
201C MET* 3.6 40.6 - - + +
231C HIS* 3.0 16.1 + - - +
232C VAL* 3.5 38.6 - - + -
233C LYS* 3.5 3.0 + - - +
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Residues in contact with ALA 200 (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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124C ARG* 3.5 22.4 - - - +
125C TYR 2.7 17.5 + - - +
126C ASN* 3.4 24.9 - - - +
127C VAL 3.4 14.3 + - - +
199C LEU* 1.3 77.3 - - - +
201C MET* 1.3 61.4 + - - +
202C VAL* 4.5 6.5 - - + +
233C LYS* 3.5 16.8 - - + -
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Residues in contact with MET 201 (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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127C VAL* 3.6 18.4 - - + -
129C ILE* 3.7 9.0 - - + -
147C MET* 3.9 12.1 - - + -
150C LEU* 3.7 25.4 - - + -
185C LEU* 5.9 0.2 - - - -
188C VAL* 4.4 14.8 - - + -
199C LEU* 3.6 24.5 - - + +
200C ALA* 1.3 73.6 - - - +
202C VAL* 1.3 63.5 + - - +
203C PHE* 3.5 32.3 - - + -
223C LEU* 5.1 2.7 - - + -
226C ALA* 6.2 0.4 - - - -
232C VAL* 5.7 0.2 - - - -
233C LYS 3.1 9.9 + - - +
234C ILE* 3.6 29.1 - - + +
235C SER* 3.1 21.7 + - - -
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Residues in contact with VAL 202 (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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91C LEU* 4.5 12.1 - - + -
118C LEU* 4.2 20.4 - - + -
126C ASN* 5.9 0.7 - - - +
127C VAL 3.0 13.6 + - - +
128C LEU* 3.6 20.8 - - + +
129C ILE* 2.7 34.8 + - - +
200C ALA* 4.5 5.8 - - + +
201C MET* 1.3 79.3 - - - +
203C PHE* 1.3 61.3 + - - +
235C SER* 3.3 24.5 - - - +
237C ILE* 3.8 24.9 - - + -
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Residues in contact with PHE 203 (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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129C ILE* 3.3 23.6 - - + -
131C LEU* 4.0 13.2 - - + -
146C SER* 3.4 27.1 - - - -
147C MET* 5.2 0.4 - - + -
201C MET* 3.5 36.3 - - + -
202C VAL* 1.3 76.1 - - - +
204C ASN* 1.3 57.3 + - - +
205C PHE* 3.9 11.4 - + + -
219C PHE* 3.8 12.8 - + - -
223C LEU* 3.6 32.1 - - + -
234C ILE* 3.6 23.8 - - + -
235C SER 2.7 9.7 + - - +
236C LEU* 3.5 16.6 - - + -
237C ILE* 2.7 36.6 + - - +
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Residues in contact with ASN 204 (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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114C THR* 4.6 6.5 + - - +
116C ILE* 3.4 28.9 - - + +
128C LEU* 4.0 10.9 - - + +
129C ILE 2.8 8.2 + - - +
130C GLU* 3.4 35.5 + - + +
131C LEU* 3.0 23.9 + - - +
203C PHE* 1.3 73.1 - - - +
205C PHE* 1.3 61.6 + - - +
206C LYS* 3.5 14.2 + - - +
237C ILE* 3.6 13.3 - - + +
239C ASN* 2.9 25.8 + - - +
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Residues in contact with PHE 205 (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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131C LEU* 3.5 27.6 - - + +
142C MET* 3.7 25.6 - - + -
203C PHE* 3.9 17.0 - - + -
204C ASN* 1.3 70.6 - - - +
206C LYS* 1.3 63.8 + - - +
207C ASP 3.9 0.4 - - - -
208C VAL* 4.4 18.5 - - + +
211C ILE* 5.2 3.8 - - + -
216C LEU* 4.2 16.6 - - + -
219C PHE* 4.3 14.8 - + - -
220C ILE* 5.2 3.1 - - + -
236C LEU* 3.8 28.7 - - + -
237C ILE 2.9 21.2 + - - +
238C PHE* 3.6 29.8 - + + -
239C ASN* 2.9 27.4 + - - +
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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