Contacts of the strand formed by residues 143 - 150 (chain B) in PDB entry 2AW9
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 LYS 143 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B SER* 6.2 0.4 - - - +
111B ALA* 5.9 3.8 - - + -
139B VAL* 3.4 1.9 - - - -
140B LYS* 2.8 36.6 + - - +
141B ASP* 2.9 19.4 + - + +
142B GLY* 1.3 80.3 - - - +
144B LEU* 1.3 66.9 + - - +
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Residues in contact with LEU 144 (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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104B LEU* 4.4 7.2 - - + -
107B ALA* 3.8 32.1 - - + -
108B ILE* 3.8 29.8 - - + +
111B ALA* 3.7 21.5 - - + +
112B PHE* 3.9 16.9 - - + -
137B LEU* 4.0 13.0 - - + -
138B VAL 3.2 13.7 - - - +
139B VAL* 3.7 23.3 - - + -
142B GLY 4.2 0.4 + - - -
143B LYS* 1.3 76.8 - - - +
145B ASP* 1.3 62.4 + - - +
169B ILE* 4.0 17.0 - - + -
207B TYR* 4.2 7.9 - - + -
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Residues in contact with ASP 145 (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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112B PHE* 4.0 6.6 - - - -
121B LYS* 3.3 21.8 + - - -
137B LEU* 3.6 5.0 - - - +
138B VAL* 2.9 45.1 + - + +
140B LYS* 5.3 7.2 - - + -
143B LYS 3.8 1.9 + - - +
144B LEU* 1.3 75.3 - - - +
146B VAL* 1.3 85.8 + - - +
147B VAL* 4.1 9.0 - - + +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.6 25.3 - - + -
118B PHE* 4.0 22.4 - - + -
121B LYS* 3.7 27.3 + - + +
122B PHE* 3.9 17.0 - - + +
125B ALA* 3.6 27.1 - - + +
136B TRP 3.3 11.2 - - - +
137B LEU* 4.4 1.8 - - + -
145B ASP* 1.3 85.8 + - - +
147B VAL* 1.3 73.2 - - - +
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Residues in contact with VAL 147 (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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125B ALA* 4.5 7.7 - - - +
135B ALA* 3.4 3.3 - - - +
136B TRP* 2.6 46.7 + - + +
138B VAL* 3.9 35.4 - - + -
145B ASP* 4.1 14.6 - - + +
146B VAL* 1.3 82.6 - - - +
148B SER* 1.3 58.6 + - - +
155B PRO* 4.2 4.5 - - + -
164B VAL* 4.1 36.8 - - + -
165B SER 5.0 3.1 - - - +
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Residues in contact with SER 148 (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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125B ALA* 4.1 21.9 + - - +
129B ARG* 2.8 31.4 + - - +
134B TRP 3.1 16.4 - - - -
135B ALA* 4.2 2.7 - - - -
136B TRP* 4.0 1.6 - - - -
147B VAL* 1.3 77.0 - - - +
149B THR* 1.3 70.4 + - - +
162B ALA 4.6 1.7 - - - +
164B VAL* 3.5 17.0 - - - +
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Residues in contact with THR 149 (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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129B ARG* 3.3 14.2 + - - +
133B GLY* 3.1 20.4 - - - -
134B TRP* 3.0 15.4 + - - +
136B TRP* 3.1 23.8 + - + +
148B SER* 1.3 81.6 - - - +
150B ALA* 1.3 59.3 + - - +
153B ASP* 2.7 38.1 + - - +
154B ASN 4.2 0.2 - - - +
155B PRO* 4.0 8.5 - - + -
162B ALA* 4.3 10.5 - - + +
164B VAL* 3.9 17.7 - - + -
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Residues in contact with ALA 150 (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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129B ARG* 3.5 20.9 - - - +
132B SER 3.7 4.5 - - - +
149B THR* 1.3 71.6 - - - +
151B ASN* 1.3 82.0 + - - +
153B ASP* 2.9 36.8 + - - +
162B ALA 5.1 2.0 + - - -
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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