Contacts of the strand formed by residues 140 - 146 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.5 20.9 - - + -
98A SER 4.4 0.2 - - - -
134A LEU* 3.7 34.2 - - + -
135A LYS* 2.7 45.2 + - - -
138A SER* 3.2 27.5 - - - -
139A SER* 1.3 76.6 + - - +
141A PHE* 1.3 62.3 + - - +
182A ILE* 3.1 6.6 - - - -
183A ILE* 2.7 47.8 + - + +
191A TRP* 4.5 0.9 - + - -
202A GLN* 4.5 0.4 - - - -
203A LYS* 3.2 32.1 - - + +
204A SER* 3.8 13.2 - - - -
205A ILE* 3.8 24.7 - - + -
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Residues in contact with PHE 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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102A GLN 3.3 19.3 - - - -
104A TRP* 3.2 48.0 - + + -
107A SER* 3.9 6.5 - - - -
118A LEU* 4.2 8.8 - - + +
140A TYR* 1.3 74.6 - - - +
142A LEU* 1.3 60.8 + - - +
180A CYS* 3.8 16.8 - - + -
181A ALA 3.6 6.5 - - - -
182A ILE* 3.4 22.2 - - + -
196A ILE* 3.8 12.6 - - + -
197A HIS 4.5 0.2 - - - -
198A CYS 3.7 14.1 - - - -
200A VAL 3.2 20.9 - - - -
202A GLN* 3.6 17.7 - - + +
203A LYS 2.9 12.6 + - - +
204A SER* 3.9 7.1 - - - -
205A ILE* 3.5 25.1 + - - +
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Residues in contact with LEU 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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104A TRP* 2.8 24.4 + - - -
118A LEU* 4.0 4.5 - - - -
119A VAL* 3.8 17.7 - - + +
121A ILE* 3.7 24.2 - - + -
141A PHE* 1.3 75.8 - - - +
143A GLY* 1.3 58.8 + - - +
144A LEU* 3.0 12.0 + - + +
181A ALA* 3.0 27.1 + - + +
182A ILE 4.2 7.4 - - - +
183A ILE* 3.6 26.2 - - + -
193A TRP* 3.7 45.8 - - + +
205A ILE* 4.6 2.0 - - + -
155B TRP* 4.7 7.0 - - + -
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Residues in contact with GLY 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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104A TRP* 4.2 5.6 - - - -
118A LEU* 3.4 27.3 - - - +
119A VAL 2.8 19.9 + - - -
142A LEU* 1.3 68.7 - - - +
144A LEU* 1.3 57.1 + - - +
154B GLN 3.6 0.5 - - - +
155B TRP* 3.3 10.7 - - - -
156B VAL* 2.8 38.2 + - - +
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Residues in contact with LEU 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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104A TRP* 4.0 0.9 + - - -
142A LEU* 3.0 8.6 + - + +
143A GLY* 1.3 78.1 - - - +
145A SER* 1.3 62.6 + - - +
180A CYS* 3.8 0.7 - - - -
181A ALA* 3.0 42.5 + - + +
193A TRP* 3.8 23.1 - - + -
153B TRP* 4.0 11.9 - - + -
154B GLN 3.4 15.9 - - - +
155B TRP* 3.6 34.3 - - + -
161B TYR* 3.7 26.2 - - + -
168B TRP* 3.8 28.7 - - + -
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Residues in contact with SER 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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104A TRP* 3.8 28.7 - - - -
143A GLY 4.2 0.2 - - - -
144A LEU* 1.3 77.5 - - - +
146A ASP* 1.3 65.5 + - - +
147A PRO* 3.9 8.3 - - - +
179A ARG 3.3 14.1 - - - -
180A CYS* 4.0 9.9 - - - -
198A CYS* 5.1 0.4 - - - -
153B TRP* 3.7 8.7 - - - -
154B GLN* 2.8 41.7 + - - +
156B VAL* 6.1 0.3 - - - -
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Residues in contact with ASP 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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145A SER* 1.3 75.5 - - - +
147A PRO* 1.3 65.6 - - - +
148A GLY* 2.9 20.1 + - - -
176A LEU* 4.1 10.4 - - - +
178A GLU* 3.1 5.0 - - - +
179A ARG 2.8 31.9 + - - +
198A CYS* 5.2 0.2 - - - -
151B ARG* 2.8 54.1 + - + +
152B HIS* 3.9 19.8 + - - +
153B TRP* 3.9 6.9 - - + -
154B GLN* 4.8 0.9 + - - -
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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