Contacts of the strand formed by residues 139 - 146 (chain F) 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 SER 139 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D MET* 3.5 17.1 - - - +
201D PRO* 3.7 14.7 - - - +
138F SER* 1.3 75.0 - - - +
140F TYR* 1.3 63.0 + - - +
182F ILE* 3.3 4.2 - - - +
183F ILE 3.5 5.3 + - - -
184F ASN* 3.0 29.2 + - - +
202F GLN* 2.8 29.5 + - - +
203F LYS* 3.2 25.1 + - - +
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Residues in contact with TYR 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F ILE* 3.3 23.2 - - + +
98F SER 4.7 0.2 - - - -
134F LEU* 3.8 33.3 - - + -
135F LYS* 2.7 46.1 + - - -
138F SER* 3.3 28.0 - - - -
139F SER* 1.3 75.6 + - - +
141F PHE* 1.3 62.3 + - - +
182F ILE* 3.1 6.6 - - - -
183F ILE* 2.8 46.7 + - + +
191F TRP* 4.7 0.9 - + - -
202F GLN* 4.8 0.2 - - - -
203F LYS* 3.1 29.8 - - + +
204F SER 3.8 13.7 - - - -
205F ILE* 3.7 24.5 - - + -
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Residues in contact with PHE 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F GLN 3.3 25.1 - - - -
104F TRP* 3.4 42.0 - + + -
107F SER* 4.0 7.6 - - - -
118F LEU* 4.0 15.3 - - + +
140F TYR* 1.3 73.5 - - - +
142F LEU* 1.3 62.8 + - - +
180F CYS* 3.9 19.3 - - + -
181F ALA 3.6 6.1 - - - -
182F ILE* 3.4 21.9 - - + +
196F ILE* 4.2 7.2 - - + -
197F HIS 4.4 2.2 - - - -
198F CYS 3.7 15.5 - - - -
200F VAL 3.3 20.4 - - - -
202F GLN* 3.6 18.8 - - + +
203F LYS 2.8 13.3 + - - +
204F SER* 4.4 1.6 - - - -
205F ILE* 3.7 22.9 + - - +
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F TRP* 2.8 25.3 + - - -
118F LEU* 3.9 5.0 - - - +
119F VAL* 3.8 18.8 - - + +
121F ILE* 3.7 22.2 - - + -
141F PHE* 1.3 76.1 - - - +
143F GLY* 1.3 58.4 + - - +
144F LEU* 3.0 11.6 + - + +
181F ALA* 2.9 29.1 + - + +
182F ILE 4.4 2.7 - - - +
183F ILE* 3.6 32.3 - - + +
193F TRP* 3.7 47.6 - - + +
205F ILE* 4.6 1.3 - - + -
155H TRP* 4.4 7.0 - - + -
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Residues in contact with GLY 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F TRP* 4.1 7.7 - - - -
118F LEU* 3.5 27.2 - - - +
119F VAL 2.9 20.3 + - - -
142F LEU* 1.3 69.8 - - - +
144F LEU* 1.3 56.5 + - - +
145F SER* 4.2 0.5 + - - -
154H GLN 3.7 0.5 - - - +
155H TRP* 3.3 11.8 - - - -
156H VAL* 2.8 34.8 + - - +
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Residues in contact with LEU 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F TRP* 3.9 4.9 + - - -
142F LEU* 3.0 5.4 - - + +
143F GLY* 1.3 77.7 - - - +
145F SER* 1.3 63.5 + - - +
180F CYS* 3.8 0.7 - - - -
181F ALA* 3.0 33.9 + - + +
193F TRP* 3.9 17.5 - - + -
153H TRP* 3.8 13.0 - - + -
154H GLN 3.4 20.4 - - - +
155H TRP* 3.5 34.8 - - + -
161H TYR* 3.7 26.5 - - + -
168H TRP* 3.7 34.8 - - + -
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Residues in contact with SER 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F TRP* 3.9 23.0 - - - -
144F LEU* 1.3 77.5 - - - +
146F ASP* 1.3 63.9 + - - +
147F PRO* 4.6 1.9 - - - +
179F ARG 3.3 13.5 - - - -
180F CYS* 3.9 15.5 - - - -
153H TRP* 3.6 9.0 - - - -
154H GLN* 2.8 45.5 + - - +
156H VAL* 6.2 0.2 - - - -
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Residues in contact with ASP 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F SER* 1.3 76.1 - - - +
147F PRO* 1.3 69.9 - - - +
148F GLY* 2.9 15.9 + - - +
176F LEU* 5.0 5.5 - - - +
178F GLU* 3.3 4.0 - - - +
179F ARG 2.8 31.1 + - - +
198F CYS* 5.1 0.2 - - - -
151H ARG* 2.7 56.8 + - + +
152H HIS* 3.8 20.1 + - - +
153H TRP* 3.7 7.7 - - + -
176H LEU* 5.3 0.3 - - - +
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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