Contacts of the strand formed by residues 128 - 136 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D ALA* 4.1 26.2 - - + -
117D GLN* 4.3 7.9 - - + -
118D LEU 3.5 7.6 - - - +
119D VAL* 4.7 2.2 - - + +
126D GLY 4.7 4.0 - - - +
127D THR* 1.3 76.4 - - - +
129D LEU* 1.3 61.1 + - - +
130D ALA 3.4 24.5 - - - +
131D GLN* 3.7 32.9 + - + +
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Residues in contact with LEU 129 (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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35D ARG* 5.7 1.1 - - - +
97D ASP 5.4 0.4 - - - +
98D ALA* 4.6 6.7 - - + -
118D LEU* 2.8 28.3 + - + +
120D ASP* 3.8 47.3 - - + +
124D ALA* 5.8 1.6 - - + -
127D THR* 4.6 5.8 - - - +
128D VAL* 1.3 74.2 - - - +
130D ALA* 1.3 64.9 + - - +
155D LYS* 3.7 31.3 + - + +
156D LEU* 4.1 24.0 - - + -
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Residues in contact with ALA 130 (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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116D TYR* 3.5 18.3 - - + +
118D LEU* 2.7 35.7 + - + +
128D VAL* 3.4 5.8 - - - +
129D LEU* 1.3 81.3 - - - +
131D GLN* 1.3 66.4 + - - +
151D GLU* 5.3 2.7 - - + +
155D LYS* 4.4 19.7 - - + -
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Residues in contact with GLN 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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116D TYR* 3.3 23.4 + - - +
117D GLN* 3.9 18.3 + - + +
128D VAL* 3.7 23.4 - - + +
130D ALA* 1.3 81.3 - - - +
132D ASN* 1.3 71.2 + - - +
151D GLU* 4.2 1.6 - - - +
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Residues in contact with ASN 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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114D VAL 4.7 0.2 - - - -
115D ALA* 3.2 5.7 - - - +
116D TYR* 3.1 40.2 + - + +
117D GLN* 5.0 0.5 + - - -
131D GLN* 1.3 80.3 + - - +
133D SER* 1.3 81.3 + - - +
134D TYR* 3.6 16.5 - - - +
151D GLU* 3.0 35.4 + - - +
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Residues in contact with SER 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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113D ASN* 4.4 13.2 - - - +
114D VAL 3.3 9.7 + - - -
115D ALA* 3.8 13.7 - - - +
132D ASN* 1.3 90.3 + - - +
134D TYR* 1.3 72.0 + - - +
135D LYS 4.4 0.2 + - - -
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Residues in contact with TYR 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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112D TYR 3.4 1.2 - - - +
113D ASN* 3.3 5.2 - - - -
114D VAL* 2.7 52.3 + - + +
116D TYR* 3.5 14.3 - + - -
132D ASN* 3.8 17.9 - - + -
133D SER* 1.3 81.2 + - - +
135D LYS* 1.3 64.0 + - - +
136D VAL* 3.6 6.6 + - + +
144D ALA* 3.8 39.5 - - + -
147D THR* 3.5 26.0 - - + +
148D ALA* 3.6 15.2 + - + -
151D GLU* 2.6 35.5 + - - -
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Residues in contact with LYS 135 (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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107D ASN* 3.7 19.7 - - - +
109D ASP* 2.9 21.5 + - - -
111D SER* 2.8 35.4 + - - +
112D TYR 3.3 3.1 - - - -
113D ASN* 3.9 9.4 - - - +
134D TYR* 1.3 73.7 - - - +
136D VAL* 1.3 64.0 + - - +
137D ASN* 5.4 0.8 + - - -
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Residues in contact with VAL 136 (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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111D SER* 3.5 3.3 - - - -
112D TYR* 2.8 34.3 + - - +
114D VAL* 4.3 2.5 - - + -
134D TYR* 4.3 10.5 - - + +
135D LYS* 1.3 78.9 - - - +
137D ASN* 1.3 69.7 + - - +
140D TRP* 3.8 24.5 - - + +
141D LEU* 3.8 27.1 - - + -
143D TYR* 5.4 5.4 - - + -
144D ALA* 4.0 24.2 - - + +
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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