Contacts of the strand formed by residues 128 - 136 (chain A) in PDB entry 2W8B
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 VAL 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ALA* 3.8 27.8 - - + -
117A GLN* 4.2 7.9 - - + -
118A LEU 3.5 6.7 - - - +
119A VAL* 4.5 3.4 - - + -
126A GLY 3.5 6.3 + - - +
127A THR* 1.3 80.0 - - - +
129A LEU* 1.3 61.9 + - - +
130A ALA* 3.5 23.5 - - - +
131A GLN* 3.8 31.4 + - + +
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP 5.3 0.7 - - - +
98A ALA* 5.0 2.7 - - + -
118A LEU* 2.8 31.9 + - + +
119A VAL 4.5 1.6 - - - -
120A ASP* 3.7 50.5 - - + +
124A ALA* 5.7 1.1 - - + -
127A THR* 4.0 13.0 - - + +
128A VAL* 1.3 73.0 - - - +
130A ALA* 1.3 63.0 + - - +
155A LYS* 3.6 33.5 + - + +
156A LEU* 4.2 15.0 - - + -
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 3.4 17.0 - - + +
117A GLN* 3.5 0.3 - - - -
118A LEU* 2.8 35.1 + - + -
128A VAL* 3.4 5.7 - - - +
129A LEU* 1.3 82.4 - - - +
131A GLN* 1.3 65.1 + - - +
151A GLU* 5.0 4.9 - - + +
155A LYS* 4.3 20.2 - - + -
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 3.4 22.5 + - - +
117A GLN* 3.8 19.6 + - + +
128A VAL* 3.8 18.9 + - + +
130A ALA* 1.3 80.2 - - - +
132A ASN* 1.3 68.4 + - - +
151A GLU* 4.1 2.1 - - - +
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Residues in contact with ASN 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL 4.6 0.2 - - - -
115A ALA* 3.2 6.3 - - - +
116A TYR* 3.1 48.4 + - + +
117A GLN* 4.9 0.7 + - - -
131A GLN* 1.3 79.8 - - - +
133A SER* 1.3 82.3 + - - +
134A TYR* 3.4 19.0 - - - +
151A GLU* 2.7 26.9 + - - +
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASN* 4.3 14.7 + - - +
114A VAL 3.3 8.2 + - - -
115A ALA* 3.7 16.6 - - - +
132A ASN* 1.3 91.3 + - - +
134A TYR* 1.3 70.4 + - - +
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Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TYR 3.5 1.4 - - - +
113A ASN* 3.3 4.9 - - - -
114A VAL* 2.7 54.7 + - + +
116A TYR* 3.4 15.6 - + - -
132A ASN* 3.4 27.8 - - + -
133A SER* 1.3 81.0 + - - +
135A LYS* 1.3 60.1 + - - +
136A VAL* 3.8 9.3 + - + +
144A ALA* 3.8 41.1 - - + -
147A THR* 3.5 26.8 - - + +
148A ALA* 3.6 14.1 + - + -
151A GLU* 2.6 25.8 + - - -
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASN* 3.9 16.8 - - - +
109A ASP* 2.7 30.5 + - - -
111A SER* 2.8 30.1 + - - +
112A TYR 3.2 4.5 - - - -
113A ASN* 4.0 8.7 - - - +
134A TYR* 1.3 72.9 - - - +
136A VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 3.4 5.3 - - - -
112A TYR* 2.8 32.7 + - - +
114A VAL* 4.4 4.5 - - + -
134A TYR* 4.5 9.2 - - + +
135A LYS* 1.3 79.1 - - - +
137A ASN* 1.3 72.2 + - - +
140A TRP* 3.9 28.3 - - + +
141A LEU* 3.8 23.8 - - + -
143A TYR* 5.1 7.2 - - + -
144A ALA* 4.1 21.1 - - + +
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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