Contacts of the strand formed by residues 139 - 146 (chain A) in PDB entry 3WYR
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 GLU 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ARG* 2.7 70.5 + - + +
137A GLU 3.4 8.1 - - - +
138A GLY* 1.3 90.5 - - - +
140A ALA* 1.3 58.5 + - - +
141A HIS* 2.8 24.2 + - + +
142A GLU* 4.5 2.6 - - - +
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Residues in contact with ALA 140 (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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138A GLY 3.8 4.2 + - - -
139A GLU* 1.3 67.4 - - - +
141A HIS* 1.3 58.4 + - - +
142A GLU* 4.0 13.8 - - - +
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Residues in contact with HIS 141 (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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134A LEU 4.3 1.2 - - - +
135A SER* 4.7 3.8 - - - -
136A ARG* 4.8 2.8 + - - +
139A GLU* 2.8 22.6 + - + +
140A ALA* 1.3 75.1 + - - +
142A GLU* 1.3 78.9 + - - +
143A LEU* 3.9 20.9 - - + +
191B PRO* 6.1 6.7 - - + -
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Residues in contact with GLU 142 (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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16A ALA* 5.9 0.5 - - - +
17A VAL* 3.9 22.9 - - - +
95A MET* 4.3 6.2 - - - +
133A HIS* 5.1 1.3 - - + -
134A LEU 3.6 4.9 - - - +
135A SER* 3.7 27.9 - - - +
139A GLU 4.5 1.6 - - - +
140A ALA* 4.0 10.0 - - - +
141A HIS* 1.3 99.8 + - - +
143A LEU* 1.3 63.5 + - - +
144A ARG* 3.4 41.7 + - - +
183A TRP* 3.8 19.7 - - + -
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Residues in contact with LEU 143 (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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133A HIS* 3.2 9.0 - - - +
134A LEU* 2.9 48.7 + - + +
135A SER* 5.5 0.9 - - - -
136A ARG* 6.1 2.5 - - + +
141A HIS* 3.9 20.2 - - + +
142A GLU* 1.3 79.0 - - - +
144A ARG* 1.3 61.7 + - - +
145A LEU* 6.1 0.2 - - + -
159A PHE* 3.7 24.1 - - + -
160A PRO 5.8 2.0 - - - +
161A LEU* 4.1 26.5 - - + -
170A TYR* 6.2 3.1 - - + -
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Residues in contact with ARG 144 (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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93A VAL* 5.4 1.2 - - - +
95A MET* 3.5 30.1 - - - -
131A ILE* 4.4 6.5 - - + -
132A TYR 3.7 2.0 - - - -
133A HIS* 3.2 30.9 + - + +
142A GLU* 3.4 38.4 + - - +
143A LEU* 1.3 78.3 - - - +
145A LEU* 1.3 73.6 + - - +
146A PRO* 4.9 0.3 - - - +
159A PHE* 3.9 0.9 - - - -
181A TYR* 5.4 6.9 - - - -
183A TRP* 3.7 8.3 - - - -
189B PRO* 6.5 2.2 - - - -
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Residues in contact with LEU 145 (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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131A ILE* 3.4 8.0 - - - +
132A TYR* 2.8 34.3 + - - +
143A LEU* 6.1 0.2 - - + -
144A ARG* 1.3 84.3 - - - +
146A PRO* 1.3 75.2 - - + +
157A ALA* 4.1 8.3 - - + -
158A ASP 3.3 37.9 - - - +
159A PHE* 3.5 31.0 - - + +
160A PRO* 5.3 4.7 - - + -
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Residues in contact with PRO 146 (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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130A ASP* 3.3 14.6 - - - +
131A ILE* 4.4 4.5 - - + -
144A ARG 4.9 0.2 - - - +
145A LEU* 1.3 97.7 - - + +
147A ALA* 1.3 66.4 + - - +
148A VAL* 4.2 9.1 - - + +
157A ALA* 3.8 12.2 - - - +
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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