Contacts of the strand formed by residues 129 - 135 (chain C) in PDB entry 5Z58
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 ILE 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C LEU 3.4 21.5 - - - +
123C MET* 4.3 2.9 - - - +
126C SER* 4.3 18.4 - - - +
127C GLU* 3.4 2.8 - - - +
128C LEU* 1.3 80.3 - - - +
130C ARG* 1.3 62.6 + - - +
131C ASN* 5.3 0.2 - - - +
198C TYR* 5.6 1.1 - - - -
199C LEU* 2.7 38.8 - - + +
201C ASN* 4.4 7.2 - - - +
440C SER* 4.0 8.3 + - - -
441C PRO* 3.7 28.5 - - + +
546C ALA 5.1 0.9 - - - +
547C GLY* 3.8 26.5 - - - +
548C ASN* 3.3 24.2 - - - +
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Residues in contact with ARG 130 (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* 1.3 75.6 - - - +
131C ASN* 1.3 62.5 + - - +
132C VAL* 4.4 5.2 - - + -
198C TYR* 5.6 2.2 - - + +
199C LEU 2.7 8.9 + - - -
200C PHE* 3.2 31.7 - - + -
201C ASN* 2.7 31.5 + - - -
434C CYS 4.9 7.0 - - - +
435C VAL* 5.5 4.0 - - + +
438C ILE* 4.5 14.8 - - + -
440C SER* 4.9 4.9 - - - +
441C PRO* 4.9 2.7 - - - -
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Residues in contact with ASN 131 (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* 5.3 0.5 - - - +
130C ARG* 1.3 72.2 - - - +
132C VAL* 1.3 64.5 + - - +
201C ASN* 3.1 33.7 + - - +
222C SER* 4.1 2.0 - - - -
223C ASP* 2.4 43.3 + - - +
224C GLY 3.5 21.6 + - - -
438C ILE* 4.0 9.4 - - - +
441C PRO* 4.2 8.7 - - - +
495C ARG* 3.6 9.3 - - - +
547C GLY 3.9 4.2 - - - +
549C TRP* 3.2 37.1 + - + -
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Residues in contact with VAL 132 (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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130C ARG* 4.4 2.5 - - + -
131C ASN* 1.3 82.4 - - - +
133C THR* 1.3 66.4 + - - +
200C PHE* 3.7 24.5 - - + -
201C ASN 2.9 6.6 + - - +
202C ILE* 3.5 8.8 - - + +
203C MET 3.2 22.9 + - - -
222C SER* 5.0 0.2 - - - -
224C GLY 3.8 3.4 - - - -
225C VAL 4.5 2.5 - - - -
226C VAL* 2.7 42.0 - - + +
430C PHE* 4.0 11.7 - - + -
434C CYS* 3.2 31.6 - - + -
438C ILE* 4.6 8.5 - - + -
549C TRP* 4.9 0.7 - - - -
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Residues in contact with THR 133 (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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132C VAL* 1.3 83.3 + - - +
134C LEU* 1.3 65.6 + - - +
135C CYS* 4.6 2.9 - - + -
203C MET* 3.8 21.1 + - + +
205C THR* 4.3 15.7 - - + +
215C VAL* 5.7 2.2 - - + -
218C GLY 5.1 2.2 + - - -
219C LEU* 4.5 8.3 - - + +
222C SER* 3.8 14.0 + - - -
224C GLY 3.6 8.5 + - - -
225C VAL* 3.3 26.8 - - + +
226C VAL* 2.1 50.0 + - - +
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Residues in contact with LEU 134 (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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133C THR* 1.3 72.3 - - - +
135C CYS* 1.3 64.9 + - - +
142C LYS* 4.0 30.5 + - + +
145C PHE* 4.2 13.9 - - + -
146C VAL* 3.4 33.0 - - + -
202C ILE* 4.8 12.7 - - + +
203C MET 4.0 6.4 + - - +
204C ASP* 4.9 10.8 - - + +
205C THR* 3.6 18.9 + - - +
226C VAL* 2.9 30.7 - - + -
228C PHE* 5.6 3.8 - - + +
256C CYS* 5.6 4.0 - - + -
430C PHE* 4.0 20.2 - - + -
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Residues in contact with CYS 135 (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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133C THR* 4.6 6.1 - - + -
134C LEU* 1.3 76.6 - - - +
136C GLY* 1.3 52.7 + - - +
142C LYS* 3.3 19.0 - - - +
205C THR* 4.4 6.5 - - - +
215C VAL* 5.9 1.6 - - + -
225C VAL* 4.2 12.6 - - + -
226C VAL 2.5 12.4 + - - -
227C LEU* 2.8 50.5 - - - -
228C PHE* 2.3 38.9 + - - +
242C LEU* 4.1 22.9 - - + -
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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