Contacts of the strand formed by residues 126 - 134 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D GLY* 5.2 2.4 - - - -
4D LEU 5.3 0.3 + - - -
19D VAL* 4.1 21.8 - - + -
20D ARG 4.3 0.7 - - - -
21D GLY* 3.3 45.1 - - - -
22D GLU 3.6 3.1 - - - -
23D VAL* 4.4 7.0 - - + -
30D PHE* 3.6 48.7 - + + -
32D LEU* 4.4 16.6 - - + -
85D ALA* 3.8 13.7 - - + -
87D VAL* 4.4 14.6 - - + -
122D ALA* 3.6 22.1 - - + +
123D ASP* 3.2 17.3 + - - +
124D GLY 3.2 0.8 - - - -
125D ASP* 1.3 78.9 - - - +
127D LYS* 1.3 58.7 + - - +
128D ILE* 3.2 16.5 + - + -
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Residues in contact with LYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLN* 6.1 1.6 - - - +
10C ASN* 5.4 8.1 - - - +
12C LYS* 5.0 12.5 - - - +
4D LEU 6.3 0.2 - - - +
21D GLY* 3.2 1.1 - - - -
22D GLU* 2.8 63.6 + - + +
24D ALA* 5.4 7.9 - - + +
25D PRO* 5.9 1.8 - - + -
124D GLY 3.9 17.0 - - - +
125D ASP 5.2 0.2 - - - -
126D PHE* 1.3 67.7 - - - +
128D ILE* 1.3 67.4 + - - +
129D LYS* 3.3 20.2 + - + +
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Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C PHE* 3.8 22.7 - - + +
4D LEU* 4.1 31.5 - - + +
19D VAL* 3.9 21.3 - - + -
20D ARG 3.5 6.5 - - - +
21D GLY* 3.9 0.9 - - - -
32D LEU* 4.3 6.5 - - + -
120D MET* 4.0 18.2 - - + -
122D ALA* 3.9 19.5 - - + -
126D PHE* 3.2 19.2 + - + +
127D LYS* 1.3 70.5 - - - +
129D LYS* 1.3 64.5 + - - +
130D CYS 3.8 10.3 - - - +
131D VAL* 3.8 25.4 - - + -
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Residues in contact with LYS 129 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C GLU* 5.1 3.0 + - - -
132C ALA* 3.5 1.6 - - - +
133C PHE* 2.7 35.0 + - - -
134C ASP* 2.5 38.5 + - - +
20D ARG* 2.7 18.6 + - + +
21D GLY* 4.2 1.8 - - - -
22D GLU* 4.1 26.6 + - + +
84D VAL* 4.6 14.4 - - + -
127D LYS* 3.4 32.4 - - + +
128D ILE* 1.3 76.6 - - - +
130D CYS* 1.3 59.4 + - + +
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Residues in contact with CYS 130 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C CYS* 5.8 0.2 - - - -
131C VAL 3.1 13.9 - - - +
132C ALA* 4.0 9.9 - - + -
133C PHE* 4.1 2.7 - - - -
19D VAL* 3.5 1.4 - - - -
20D ARG* 3.0 56.2 + - - +
128D ILE* 3.7 2.6 - - - +
129D LYS* 1.3 83.9 - - - +
131D VAL* 1.3 69.8 + - - +
204D BME 2.6 41.1 - - + -
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Residues in contact with VAL 131 (chain D).
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* 6.2 2.0 - - + -
130C CYS* 3.3 3.3 - - - -
131C VAL* 2.9 35.8 + - + +
133C PHE* 4.1 11.9 - - + -
4D LEU* 5.5 1.6 - - + -
9D LEU* 5.9 0.2 - - + -
17D LEU* 3.5 28.0 - - + -
18D ARG 3.2 6.7 - - - +
19D VAL* 4.3 3.4 - - + -
120D MET* 3.8 28.5 - - + -
128D ILE* 3.8 15.3 - - + -
130D CYS* 1.3 81.1 - - - +
132D ALA* 1.3 63.9 + - - +
133D PHE* 3.8 19.8 - - + -
204D BME 4.0 2.0 - - - -
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LYS 3.2 10.1 - - - +
130C CYS* 3.9 7.2 - - + -
16D CYS 3.5 0.7 - - - +
17D LEU* 3.5 8.0 - - - +
18D ARG* 2.9 43.7 + - + -
131D VAL* 1.3 76.4 - - - +
133D PHE* 1.3 64.5 + - - +
134D ASP* 4.1 8.1 - - - +
204D BME 3.5 26.7 - - + +
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Residues in contact with PHE 133 (chain D).
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* 4.4 20.6 - - + -
128C ILE* 3.7 15.7 - - + -
129C LYS* 2.8 46.3 + - - +
131C VAL* 5.7 0.7 - - + -
205C GOL 3.6 39.0 - - - +
9D LEU* 4.0 34.8 - - + -
11D LEU* 4.2 16.8 - - + -
15D GLU* 5.4 1.3 - - - +
16D CYS 3.4 5.4 - - - +
17D LEU* 3.5 22.7 - - + -
131D VAL* 3.8 26.0 - - + -
132D ALA* 1.3 73.7 - - - +
134D ASP* 1.3 66.5 + - - +
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Residues in contact with ASP 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LYS 5.5 0.2 - - - +
15D GLU* 3.3 19.7 - - - +
16D CYS* 2.9 41.1 + - + +
18D ARG* 3.1 37.8 + - - +
132D ALA* 4.8 5.0 - - - +
133D PHE* 1.3 82.4 + - - +
203D BME 4.5 3.4 - - - -
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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