Contacts of the strand formed by residues 129 - 137 (chain C) in PDB entry 4IYM
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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422A ARG* 4.4 0.8 - - - +
124C GLY* 3.2 3.8 - - - -
125C ALA* 2.8 34.3 + - + -
126C GLY* 2.9 17.1 + - - +
127C PRO* 3.4 32.1 - - + +
128C GLY* 1.3 79.0 - - - +
130C ASP* 1.3 71.5 + - - +
131C MSE 5.4 8.3 - - + -
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Residues in contact with ASP 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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422A ARG* 2.8 52.1 + - - +
121C PHE* 4.1 26.0 - - + -
122C THR 3.5 7.2 - - - +
123C GLU* 3.4 5.8 - - - +
124C GLY 3.1 13.9 + - - -
128C GLY 4.1 1.0 + - - -
129C ILE* 1.3 81.2 - - - +
131C MSE 1.3 62.9 + - - +
132C TYR* 4.6 12.5 - - + -
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Residues in contact with MSE 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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121C PHE* 3.7 0.3 - - - -
122C THR* 2.7 42.6 + - - +
125C ALA* 3.9 27.4 - - + -
129C ILE* 4.4 8.0 + - + -
130C ASP* 1.3 76.5 - - - +
132C TYR* 1.3 65.3 + - - +
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Residues in contact with TYR 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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121B PHE* 3.4 38.8 - + + -
132B TYR* 6.6 0.2 - + - -
120C GLU 3.3 13.0 - - - +
121C PHE* 3.5 33.2 - + + -
130C ASP* 4.6 10.1 - - + -
131C MSE 1.3 88.0 - - - +
133C SER* 1.3 65.0 + - - +
134C ILE* 4.6 11.9 - - + +
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Residues in contact with SER 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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121B PHE* 3.7 11.6 - - - +
119C SER* 2.5 26.6 + - - -
120C GLU* 2.9 34.7 + - - +
132C TYR* 1.3 73.2 - - - +
134C ILE* 1.3 68.0 + - - +
135C ARG* 6.1 0.7 - - - -
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Residues in contact with ILE 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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121B PHE* 3.7 26.0 - - + -
123B GLU* 3.6 49.4 - - + +
130B ASP* 5.7 1.1 - - - +
119C SER* 3.3 4.9 - - - +
132C TYR* 4.6 12.3 - - + +
133C SER* 1.3 81.8 - - - +
135C ARG* 1.3 70.3 + - - +
136C GLN* 3.6 21.8 + - + +
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Residues in contact with ARG 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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123B GLU* 5.5 0.2 - - - +
116C LEU 3.4 20.9 + - - -
117C GLN* 3.3 46.4 + - + +
118C LYS 3.2 21.9 + - - -
119C SER* 4.0 13.2 + - - +
133C SER* 6.1 0.7 - - - -
134C ILE* 1.3 78.8 - - - +
136C GLN* 1.3 62.1 + - - +
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Residues in contact with GLN 136 (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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123B GLU* 2.9 38.5 + - - +
117C GLN* 4.8 3.1 - - - -
134C ILE* 3.6 26.6 + - + +
135C ARG* 1.3 74.5 - - - +
137C PRO* 1.3 81.2 - - + +
138C VAL* 3.5 4.3 + - - +
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Residues in contact with PRO 137 (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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123B GLU* 6.0 0.2 - - - +
52C GLN* 3.7 17.0 - - - +
56C ALA* 3.9 17.9 - - + +
117C GLN* 4.9 1.1 - - - +
135C ARG 4.7 1.1 - - - +
136C GLN* 1.3 96.2 - - + +
138C VAL* 1.3 61.6 + - - +
139C GLY 3.9 0.9 - - - +
164C CYS* 3.7 21.0 - - + +
165C GLY* 3.8 16.2 - - - +
166C ASN* 3.3 17.7 - - - +
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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