Contacts of the strand formed by residues 140 - 146 (chain E) in PDB entry 3WBR
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 TYR 140 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97E ILE* 3.6 24.5 - - + +
134E LEU* 3.8 26.2 - - + -
135E LYS* 2.9 34.3 + - - +
138E SER* 3.3 35.4 + - - -
139E SER* 1.3 77.1 + - - +
141E PHE* 1.3 60.9 + - - +
182E ILE* 3.0 7.0 - - - -
183E ILE* 2.7 48.4 + - + +
191E TRP* 4.3 1.1 - + - -
202E GLN* 4.7 0.2 - - - -
203E LYS* 3.2 32.0 - - + +
204E SER 3.9 13.5 - - - -
205E ILE* 3.8 25.4 - - + -
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Residues in contact with PHE 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E GLN 3.2 25.8 - - - -
104E TRP* 3.4 36.8 - + + -
107E SER* 3.9 7.0 - - - -
118E LEU* 4.3 8.2 - - + +
119E VAL* 4.6 0.5 - - - +
140E TYR* 1.3 75.6 - - - +
142E LEU* 1.3 63.9 + - - +
180E CYS* 3.8 18.8 - - + -
181E ALA 3.6 9.0 - - - -
182E ILE* 3.5 21.5 - - + +
196E ILE* 3.8 11.9 - - + -
198E CYS 3.7 15.0 - - - -
200E VAL 3.3 20.0 - - - -
202E GLN* 3.6 19.9 - - + +
203E LYS 2.7 13.8 + - - +
204E SER* 4.2 7.9 - - - -
205E ILE* 3.7 21.3 + - - +
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TRP* 4.8 2.7 - - + -
104E TRP* 2.8 32.4 + - - -
118E LEU* 4.0 5.4 - - - +
119E VAL* 3.7 24.5 - - + +
121E ILE* 3.8 14.8 - - + -
141E PHE* 1.3 76.6 - - - +
143E GLY* 1.3 52.5 + - - +
144E LEU* 3.0 16.5 + - + +
181E ALA* 3.0 21.4 + - + +
182E ILE 4.1 9.2 - - - +
183E ILE* 3.6 33.2 - - + +
193E TRP* 3.6 46.4 - - + +
205E ILE* 4.6 1.6 - - + -
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Residues in contact with GLY 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D GLN 3.6 0.5 - - - +
155D TRP* 3.2 11.8 - - - -
156D VAL* 2.8 33.2 + - - +
104E TRP* 4.0 8.2 - - - -
118E LEU* 3.6 25.5 - - - +
119E VAL 2.8 22.8 + - - -
142E LEU* 1.3 69.9 - - - +
144E LEU* 1.3 57.2 + - - +
145E SER 4.2 0.2 + - - -
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Residues in contact with LEU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D TRP* 3.8 13.5 - - + -
154D GLN 3.4 13.9 - - - +
155D TRP* 3.7 26.2 - - + -
161D TYR* 3.7 29.6 - - + -
168D TRP* 3.7 23.3 - - + -
104E TRP* 3.9 3.9 + - - -
142E LEU* 3.0 6.3 + - + +
143E GLY* 1.3 77.3 - - - +
145E SER* 1.3 64.6 + - - +
180E CYS* 3.9 0.5 - - - -
181E ALA* 3.0 44.0 + - + +
193E TRP* 3.7 30.7 - - + -
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Residues in contact with SER 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D TRP* 3.5 10.9 - - - -
154D GLN* 2.8 39.5 + - - +
104E TRP* 3.8 22.1 - - - -
144E LEU* 1.3 77.2 - - - +
146E ASP* 1.3 63.2 + - - +
147E PRO* 4.0 4.2 - - - +
179E ARG 3.3 15.5 - - - -
180E CYS* 3.9 15.0 - - - -
198E CYS* 5.0 0.4 - - - -
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Residues in contact with ASP 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ARG* 2.7 59.0 + - + +
152D HIS* 4.1 16.7 + - - +
153D TRP* 3.7 6.6 - - + -
154D GLN* 5.4 0.2 + - - -
176D LEU* 5.1 0.7 - - - +
145E SER* 1.3 76.6 - - - +
147E PRO* 1.4 66.5 - - - +
148E GLY* 2.8 26.4 + - - +
176E LEU* 5.0 5.4 - - - +
178E GLU* 3.2 3.3 - - - +
179E ARG* 2.9 32.4 + - + +
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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