Contacts of the strand formed by residues 151 - 156 (chain X) in PDB entry 2BOD
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 ALA 151 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105X LEU* 4.6 0.4 - - + -
108X ARG 4.7 2.2 - - - +
110X ALA* 3.5 11.4 - - + +
112X ILE* 3.9 27.6 - - + -
144X LEU 4.6 4.0 - - - +
145X LYS* 5.5 1.0 - - - +
148X SER* 3.2 29.2 + - - +
149X SER 4.4 3.6 - - - +
150X GLN* 1.3 79.4 - - - +
152X ARG* 1.3 62.3 + - - +
153X ILE* 3.9 18.0 + - + +
182X HIS* 5.6 0.5 - - - +
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Residues in contact with ARG 152 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X ALA 2.8 7.7 + - - -
111X TYR* 3.2 38.6 + - + -
112X ILE* 2.9 26.3 + - - +
150X GLN 4.2 7.4 - - - +
151X ALA* 1.3 72.8 - - - +
153X ILE* 1.3 62.0 - - - +
154X TYR* 3.4 35.4 - - + +
182X HIS* 3.7 34.3 + - + -
253X ASP* 4.7 6.0 + - - -
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Residues in contact with ILE 153 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X ILE* 3.6 7.2 - - + -
114X VAL* 3.8 22.2 - - + -
141X GLY* 3.8 10.5 - - - +
144X LEU* 4.0 16.8 - - + -
145X LYS* 3.1 50.5 - - + +
151X ALA* 3.9 19.3 + - + +
152X ARG* 1.3 74.6 - - - +
154X TYR* 1.3 63.0 + - - +
155X PHE* 4.2 2.7 - - + -
180X SER 3.9 15.0 - - - +
181X ALA* 3.5 14.0 - - + +
182X HIS* 2.8 32.7 + - - +
183X GLY 3.3 5.2 + - - -
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Residues in contact with TYR 154 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X TYR* 3.4 31.4 - + - -
112X ILE 2.9 16.2 + - - +
113X ILE* 3.5 14.5 - - + +
114X VAL* 2.9 26.4 + - - -
152X ARG* 3.4 30.7 - - + -
153X ILE* 1.3 74.5 - - - +
155X PHE* 1.3 65.5 + - - +
156X ASP 3.5 0.3 + - - -
182X HIS* 3.4 20.4 - + - -
183X GLY 3.4 6.7 - - - -
184X ILE 3.5 34.3 - - - -
185X ALA* 4.0 8.5 - - + +
214X ARG 4.1 7.9 - - - -
216X VAL* 3.7 22.0 - - + -
253X ASP* 2.7 29.9 + - - -
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Residues in contact with PHE 155 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X VAL* 4.1 9.6 - - + -
137X MET* 3.2 51.4 - - + -
141X GLY* 4.0 13.5 - - - -
153X ILE* 4.2 3.6 - - + -
154X TYR* 1.3 71.9 - - - +
156X ASP* 1.3 64.4 + - - +
157X ALA 3.3 0.5 + - - -
172X LEU* 3.9 25.1 - - + -
175X ALA* 3.6 29.4 - - + -
177X ILE* 4.0 26.0 - - + -
180X SER* 3.8 18.2 - - - -
181X ALA* 3.9 15.3 - - + -
183X GLY 2.9 11.4 + - - +
184X ILE* 3.1 7.8 - - - +
185X ALA 3.0 17.8 + - - -
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Residues in contact with ASP 156 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X ILE* 4.6 4.5 - - + +
114X VAL 3.1 23.2 + - - +
115X GLU 3.6 11.0 - - - +
116X PRO* 3.5 8.2 - - + +
117X ASP* 2.9 27.7 + - - +
119X ILE* 4.3 25.6 + - - +
120X SER* 5.5 0.5 + - - -
137X MET* 4.2 2.3 - - - +
154X TYR 3.5 2.2 + - - -
155X PHE* 1.3 72.8 - - - +
157X ALA* 1.3 59.6 + - - +
158X GLY* 3.1 18.0 + - - +
172X LEU* 4.6 0.3 - - - +
185X ALA* 3.6 14.5 - - - +
186X THR* 4.9 0.3 - - - -
188X THR* 2.8 32.9 + - - -
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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