Contacts of the strand formed by residues 126 - 132 (chain C) in PDB entry 3W58
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 PHE 126 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C VAL* 4.0 26.7 - - + -
20C ARG 4.2 1.1 - - - -
21C GLY* 3.4 38.4 - - - -
22C GLU 3.5 10.5 - - - -
23C VAL* 3.9 22.0 - - + -
30C PHE* 3.3 46.0 - + + -
31C VAL 5.5 0.4 - - - +
32C LEU* 4.5 9.2 - - + -
85C ALA* 3.8 14.1 - - + -
86C GLU* 5.6 0.2 - - - -
87C VAL* 5.8 4.5 - - + -
122C ALA* 4.7 16.7 - - + +
123C ASP 4.7 4.0 - - - +
124C GLY 3.0 8.1 + - - +
125C ASP* 1.3 73.3 - - - +
127C LYS* 1.3 66.0 + - - +
128C ILE* 3.8 15.9 + - + -
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Residues in contact with LYS 127 (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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21C GLY* 4.2 1.3 - - - -
22C GLU* 3.0 33.7 + - + +
124C GLY 5.0 5.4 - - - +
125C ASP* 5.4 1.1 - - - -
126C PHE* 1.3 80.6 - - - +
128C ILE* 1.3 62.2 + - - +
129C LYS* 3.0 23.8 - - + +
203C SO4 3.4 28.7 + - - +
205C GOL 3.7 19.7 - - - +
10D ASN* 5.4 5.2 - - - +
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Residues in contact with ILE 128 (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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4C LEU* 3.8 23.7 - - + +
19C VAL* 3.8 22.7 - - + -
20C ARG 3.8 3.8 - - - +
21C GLY* 4.1 0.9 - - - -
32C LEU* 5.7 2.0 - - + -
120C MET* 3.7 26.7 - - + -
122C ALA* 3.5 27.6 - - + +
126C PHE* 3.8 14.2 + - + -
127C LYS* 1.3 72.1 - - - +
129C LYS* 1.3 62.8 + - - +
130C CYS 3.7 8.7 - - - +
131C VAL* 3.3 27.8 - - + -
205C GOL 3.1 33.5 + - - +
133D PHE* 3.7 5.0 - - + -
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Residues in contact with LYS 129 (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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20C ARG* 2.9 10.0 + - + +
21C GLY* 3.9 10.1 - - - -
22C GLU* 3.7 32.1 + - + +
84C VAL* 6.4 1.1 - - + -
127C LYS* 3.0 30.8 - - + +
128C ILE* 1.3 76.5 - - - +
130C CYS* 1.3 63.5 + - + +
201C SO4 6.1 0.7 - - - +
203C SO4 3.3 13.9 + - - -
205C GOL 2.9 35.6 + - - -
15D GLU* 5.3 1.0 + - - -
132D ALA* 3.2 2.3 - - - +
133D PHE* 2.8 53.5 + - - +
134D ASP* 5.5 0.3 - - - +
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Residues in contact with CYS 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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18C ARG 3.9 0.6 - - - +
19C VAL* 3.7 0.2 - - - -
20C ARG* 2.8 57.0 + - + +
128C ILE* 3.7 1.4 - - - +
129C LYS* 1.3 82.9 - - + +
131C VAL* 1.3 71.6 + - - +
132C ALA* 6.0 2.0 - - - -
130D CYS* 5.8 0.2 - - - -
131D VAL 3.3 5.2 - - - -
132D ALA* 3.9 6.3 - - + -
204D BME 3.7 35.2 - - - -
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Residues in contact with VAL 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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4C LEU* 4.2 6.1 - - + -
17C LEU* 4.0 5.4 - - + -
18C ARG 3.2 9.6 - - - +
19C VAL* 4.5 5.8 - - + -
120C MET* 3.9 25.4 - - + -
128C ILE* 3.3 32.5 - - + -
130C CYS* 1.3 76.5 - - - +
132C ALA* 1.3 61.8 + - - +
133C PHE* 3.4 39.2 + - + -
130D CYS* 3.1 6.7 - - - +
131D VAL* 2.9 37.6 + - + +
133D PHE* 5.7 0.7 - - + -
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Residues in contact with ALA 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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16C CYS 3.7 2.0 - - - +
17C LEU* 3.3 9.9 - - - +
18C ARG* 2.8 58.7 + - + +
130C CYS* 6.0 2.5 - - - -
131C VAL* 1.3 73.0 - - - +
133C PHE* 1.3 62.2 + - - +
134C ASP* 4.7 4.3 - - + +
129D LYS 3.5 7.0 - - - +
130D CYS* 4.0 6.3 - - + -
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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