Contacts of the strand formed by residues 128 - 134 (chain B) in PDB entry 4U2M
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 ALA 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B PRO* 3.5 14.9 - - - +
111B LEU* 3.7 28.3 - - + +
114B LEU* 4.2 14.4 - - + -
126B GLY* 3.8 0.6 - - - -
127B THR* 1.3 80.7 - - - +
129B ASP* 1.3 63.2 + - - +
132C ILE* 4.1 19.5 - - + -
133C GLN 3.3 9.0 - - - +
134C PHE* 4.6 12.3 - - + -
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU 3.3 8.5 - - - +
85B SER* 3.3 12.6 - - - -
86B PRO* 3.1 25.8 - - - +
128B ALA* 1.3 74.9 - - - +
130B SER* 1.3 64.2 + - - +
132C ILE* 3.3 4.9 - - - +
133C GLN* 2.8 52.4 + - + +
135C THR* 3.8 20.7 - - - +
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Residues in contact with SER 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LEU 3.6 1.9 - - - +
83B SER* 3.5 1.4 - - - -
84B LEU* 2.7 43.4 + - - +
111B LEU* 3.9 20.1 - - - +
114B LEU* 6.1 0.2 - - - -
128B ALA 4.2 0.2 + - - -
129B ASP* 1.3 77.6 - - - +
131B CYS* 1.3 58.5 + - - +
132B ILE* 3.5 15.6 - - - +
130C SER* 2.8 27.0 + - - -
131C CYS 3.4 4.8 + - - -
132C ILE* 3.8 8.7 - - - +
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Residues in contact with CYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS* 4.7 15.5 - - - -
82B LEU 3.5 3.4 - - - -
83B SER* 3.9 20.0 - - - +
130B SER* 1.3 72.5 - - - +
132B ILE* 1.3 64.1 + - - +
133B GLN* 4.1 2.7 + - - +
129C ASP 3.9 0.3 - - - +
130C SER* 3.5 1.4 - - - -
131C CYS* 2.9 46.0 + - + +
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ALA 3.5 1.4 - - - +
81B LYS* 3.3 3.8 - - - -
82B LEU* 2.8 45.4 + - + +
84B LEU* 4.1 16.4 - - + -
107B ALA* 3.6 32.1 - - + +
110B ALA* 6.2 0.7 - - + -
111B LEU* 6.2 0.4 - - + -
130B SER* 3.5 23.3 - - - +
131B CYS* 1.3 75.0 - - - +
133B GLN* 1.3 62.9 + - - +
134B PHE* 3.6 28.7 + - + -
114C LEU* 4.5 10.8 - - + -
128C ALA* 4.0 13.9 - - + -
129C ASP 3.3 10.5 - - - +
130C SER* 3.8 8.1 - - - +
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B THR 5.7 0.9 - - - +
80B ALA* 3.5 12.8 - - + +
81B LYS* 4.5 7.6 - - + +
131B CYS* 4.1 2.4 + - - +
132B ILE* 1.3 74.9 - - - +
134B PHE* 1.3 66.6 + - - +
135B THR* 3.4 15.3 + - + +
128C ALA* 3.3 3.5 - - - -
129C ASP* 2.8 54.8 + - + +
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Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PHE* 3.5 28.0 - + + -
80B ALA* 2.9 24.4 + - - +
82B LEU* 4.4 12.1 - - + -
103B ASP* 3.9 39.7 - - + -
104B ILE* 5.7 0.2 - - + -
107B ALA* 4.5 7.9 - - + -
132B ILE* 3.6 29.4 - - + -
133B GLN* 1.3 71.0 - - - +
135B THR* 1.3 65.0 + - - +
136B ARG 3.2 2.5 - - - +
137B HIS* 3.2 30.2 + - + +
138B ALA 4.7 0.3 + - - -
114C LEU* 4.6 10.8 - - + -
127C THR* 3.9 10.1 - - - +
128C ALA* 4.5 14.4 - - + -
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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