Contacts of the strand formed by residues 141 - 148 (chain D) in PDB entry 2BG9
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 ASN 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140D GLN* 1.2 88.0 + - - +
142D CYS* 1.3 65.1 + - - +
143D THR* 3.0 6.6 + - - +
182D ARG* 2.9 29.7 - - - +
204D HIS* 3.3 14.1 + - + -
205D PHE 2.8 10.1 - - - +
206D ILE* 3.2 29.3 - - + +
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Residues in contact with CYS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D CYS* 2.1 50.0 - - - -
129D GLU* 3.6 19.3 - - - +
130D ILE* 5.8 0.7 - - + -
134D HIS* 6.4 0.7 - - + -
140D GLN* 3.6 5.3 + - - +
141D ASN* 1.3 68.0 - - - +
143D THR* 1.3 57.7 + - - +
144D MET* 3.2 25.9 + - - -
203D TYR 3.4 0.2 - - - +
204D HIS* 3.2 5.9 - - - -
205D PHE* 3.0 36.7 + - + -
207D MET* 4.6 6.0 - - + +
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Residues in contact with THR 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ASN* 2.8 40.8 + - - +
128D CYS* 3.9 3.5 - - - +
129D GLU* 4.6 19.1 - - + -
141D ASN* 3.0 6.3 + - - +
142D CYS* 1.3 68.0 - - - +
144D MET* 1.3 64.5 + - - +
145D LYS* 4.6 4.5 + - - +
202D THR* 4.4 9.2 - - - +
203D TYR 3.6 5.6 - - - -
204D HIS* 3.6 23.1 - - - -
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Residues in contact with MET 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D VAL* 5.3 11.0 - - + -
92D LEU* 4.7 10.5 - - - -
95D ASN* 2.9 31.2 - - - +
126D SER* 4.5 9.9 - - - +
128D CYS* 3.5 7.6 - - - -
142D CYS* 3.2 28.7 + - - -
143D THR* 1.3 73.3 + - - +
145D LYS* 1.3 51.4 + - - +
146D LEU* 3.3 8.5 - - + -
202D THR* 4.1 1.6 - - - -
203D TYR* 2.4 67.6 + - + -
205D PHE* 2.9 40.8 - - + -
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Residues in contact with LYS 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LEU* 3.4 1.4 - - - +
93D TYR* 2.8 52.4 + - + +
94D ASN* 4.9 4.3 + - - +
95D ASN* 4.4 2.5 + - - +
143D THR* 4.0 7.0 + - - +
144D MET* 1.3 71.0 - - - +
146D LEU* 1.3 72.2 + - - +
186D HIS* 5.2 6.8 + - - +
188D VAL* 4.4 11.1 - - - +
190D TYR* 6.0 1.1 - - - -
198D TYR* 6.0 0.4 - - - -
200D ASP* 2.4 36.8 + - + +
201D ILE 3.1 2.0 - - - +
202D THR* 2.7 36.7 + - + +
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Residues in contact with LEU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D LEU* 5.3 6.1 - - + -
90D LEU* 6.2 0.7 - - + -
91D VAL 3.8 7.4 - - - +
92D LEU* 3.1 41.3 - - + -
93D TYR* 3.9 0.9 - - - -
100D PHE* 5.7 2.5 - - + -
124D PHE* 5.3 2.7 - - + -
144D MET* 3.1 17.3 - - + +
145D LYS* 1.3 99.7 - - - +
147D GLY* 1.3 57.2 + - - +
200D ASP* 2.9 6.1 - - - -
201D ILE* 2.4 44.3 + - - +
203D TYR* 3.0 52.0 - - + +
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Residues in contact with GLY 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D LEU* 3.3 14.5 - - - +
91D VAL 3.4 16.8 + - - -
93D TYR* 3.0 24.5 - - - -
146D LEU* 1.3 76.3 - - - +
148D ILE* 1.3 71.2 + - - +
149D TRP* 4.2 0.5 - - - -
158D ILE* 4.0 5.2 - - - -
199D LEU 3.5 7.0 - - - -
200D ASP* 4.1 0.4 - - - -
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Residues in contact with ILE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ILE* 5.1 2.2 - - + -
88D PRO* 3.3 33.2 - - + -
89D ASP* 3.2 15.9 - - - +
90D LEU* 3.2 11.9 - - + +
93D TYR* 3.7 8.7 + - - -
147D GLY* 1.3 74.8 - - - +
149D TRP* 1.3 63.3 + - - +
151D TYR* 3.1 50.0 - - + +
156D VAL* 3.9 23.3 - - + +
158D ILE* 3.2 16.5 - - + +
198D TYR* 3.5 26.6 - - + -
199D LEU 4.0 2.0 + - - +
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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