Contacts of the strand formed by residues 140 - 146 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97G ILE* 3.4 21.5 - - + -
98G SER 5.0 0.2 - - - -
134G LEU* 3.6 34.0 - - + -
135G LYS* 2.7 45.0 + - - -
138G SER* 3.2 28.2 - - - -
139G SER* 1.3 77.2 + - - +
141G PHE* 1.3 62.7 + - - +
182G ILE* 3.0 6.7 - - - -
183G ILE* 2.7 48.1 + - + +
191G TRP* 4.4 1.1 - + - -
203G LYS* 3.3 29.2 - - + +
204G SER* 3.9 12.8 - - - -
205G ILE* 3.7 25.8 - - + -
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Residues in contact with PHE 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G GLN 3.3 24.7 - - - -
104G TRP* 3.3 42.4 - + + -
107G SER* 3.8 7.4 - - - -
118G LEU* 4.2 7.9 - - + +
140G TYR* 1.3 74.7 - - - +
142G LEU* 1.3 61.0 + - - +
180G CYS* 3.8 17.9 - - + -
181G ALA 3.6 6.5 - - - -
182G ILE* 3.5 21.7 - - + +
196G ILE* 3.8 12.1 - - + -
197G HIS 4.6 0.2 - - - -
198G CYS 3.7 13.7 - - - -
200G VAL 3.2 23.6 - - - -
202G GLN* 3.6 17.6 - - + +
203G LYS 2.9 14.0 + - - +
204G SER* 4.3 6.7 - - - -
205G ILE* 3.5 24.6 + - - +
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Residues in contact with LEU 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C TRP* 4.7 2.9 - - + -
104G TRP* 2.8 31.0 + - - -
118G LEU* 4.0 4.8 - - - +
119G VAL* 4.0 20.2 - - + +
121G ILE* 3.8 21.3 - - + -
141G PHE* 1.3 77.7 - - - +
143G GLY* 1.3 52.9 + - - +
144G LEU* 3.1 13.0 + - + +
181G ALA* 2.9 29.7 + - + +
182G ILE 4.4 2.7 - - - +
183G ILE* 3.6 33.2 - - + +
193G TRP* 3.7 47.3 - - + +
205G ILE* 4.5 1.8 - - + -
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Residues in contact with GLY 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C GLN 3.7 0.5 - - - +
155C TRP* 3.4 10.9 - - - -
156C VAL* 2.8 36.0 + - - +
104G TRP* 4.1 8.9 - - - -
118G LEU* 3.5 26.5 - - - +
119G VAL 2.8 20.8 + - - -
142G LEU* 1.3 68.9 - - - +
144G LEU* 1.3 55.7 + - - +
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Residues in contact with LEU 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C TRP* 3.7 26.0 - - + -
154C GLN 3.4 18.8 - - - +
155C TRP* 3.6 24.5 - - + +
161C TYR* 3.7 18.4 - - + -
168C TRP* 3.7 28.9 - - + -
104G TRP* 4.0 0.5 + - - -
142G LEU* 3.1 7.7 + - + +
143G GLY* 1.3 77.3 - - - +
145G SER* 1.3 62.6 + - - +
180G CYS* 3.7 0.9 - - - -
181G ALA* 2.9 42.5 + - + -
193G TRP* 3.8 23.8 - - + -
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Residues in contact with SER 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C TRP* 3.6 9.5 - - - -
154C GLN* 2.8 41.1 + - - +
156C VAL* 6.0 0.3 - - - -
104G TRP* 3.7 24.3 - - - -
143G GLY 4.2 0.2 - - - -
144G LEU* 1.3 77.0 - - - +
146G ASP* 1.3 61.8 + - - +
147G PRO* 3.9 10.7 - - - +
179G ARG 3.3 14.4 - - - -
180G CYS* 3.8 15.5 - - - -
198G CYS* 4.9 0.2 - - - -
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Residues in contact with ASP 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ARG* 3.1 57.2 + - + +
152C HIS* 4.0 18.3 + - - +
153C TRP* 3.9 6.9 - - + -
154C GLN* 4.9 1.0 + - - -
176C LEU* 5.4 0.2 - - - +
145G SER* 1.3 73.2 - - - +
147G PRO* 1.3 66.7 - - - +
148G GLY* 2.9 21.0 + - - +
176G LEU* 4.6 6.9 - - - +
178G GLU* 3.2 2.1 - - - +
179G ARG 2.7 34.6 + - - +
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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