Contacts of the strand formed by residues 155 - 161 (chain A) in PDB entry 3BU0
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 PHE 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A THR* 3.6 20.2 - - + -
115A TYR 3.4 10.8 - - - -
116A GLY* 4.1 0.4 - - - -
120A LEU* 4.2 16.8 - - + -
121A THR 5.1 0.7 - - - -
122A TYR* 3.5 43.7 - + + -
129A LEU 5.0 0.2 - - - -
131A PRO* 3.9 26.7 - - + -
134A TRP* 3.6 6.3 - - - -
153A PHE* 3.6 0.7 - - - +
154A ASN* 1.3 81.3 - - - +
156A VAL* 1.3 86.7 + - - +
157A LEU* 3.9 11.4 - - + -
253A PHE* 3.3 8.5 - - - +
254A ARG* 2.9 37.5 + - - +
256A ILE* 3.5 31.4 - - + -
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Residues in contact with VAL 156 (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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113A ALA 3.9 0.3 - - - +
114A THR* 3.4 4.9 - - - -
115A TYR* 2.7 58.3 + - + +
134A TRP* 3.9 13.7 - - + -
138A LEU* 4.1 12.8 - - + -
155A PHE* 1.3 81.9 - - - +
157A LEU* 1.3 63.4 + - - +
158A ILE* 4.0 7.5 + - + +
251A LEU* 3.8 26.5 - - + -
252A THR 3.5 12.3 - - - +
253A PHE* 3.6 28.0 - - + -
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Residues in contact with LEU 157 (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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112A GLN* 4.3 21.1 - - + +
113A ALA 3.6 10.1 - - - +
114A THR* 3.9 13.7 - - + -
122A TYR* 3.4 32.5 - - + +
124A PHE* 5.8 0.7 - - + -
129A LEU* 4.7 3.6 - - + -
155A PHE* 3.9 14.4 - - + -
156A VAL* 1.3 71.9 - - - +
158A ILE* 1.3 66.2 + - - +
159A ASN* 3.4 11.6 + - - +
250A ASN* 3.5 2.4 + - - +
251A LEU* 3.5 0.7 - - - -
252A THR* 2.8 47.5 + - - +
254A ARG* 3.6 12.1 - - - +
301A AKG 3.1 28.0 - - - +
7B 2YR 5.9 0.7 - - - +
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Residues in contact with ILE 158 (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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85A LEU* 5.3 0.4 - - + -
89A VAL* 3.9 12.8 - - + -
91A TYR* 3.7 28.0 - - + +
111A LYS 3.6 0.5 - - - +
112A GLN* 3.1 9.4 - - - +
113A ALA* 2.8 41.8 + - + +
115A TYR* 3.7 33.0 - - + -
138A LEU* 3.9 23.3 - - + -
156A VAL* 4.4 14.1 - - + -
157A LEU* 1.3 76.4 - - - +
159A ASN* 1.3 63.9 + - - +
249A VAL* 3.7 20.2 - - + -
250A ASN 3.2 4.3 - - - +
251A LEU* 4.5 7.0 - - + -
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Residues in contact with ASN 159 (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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110A ARG* 2.9 27.5 + - - -
111A LYS 3.4 2.0 - - - -
112A GLN* 3.1 16.1 + - - +
157A LEU* 3.4 18.0 + - - +
158A ILE* 1.3 76.2 - - - +
160A ARG* 1.3 59.4 + - - +
161A TYR* 3.4 33.2 - - + +
249A VAL* 3.6 0.7 - - - -
250A ASN* 2.8 41.5 + - + +
301A AKG 2.5 37.4 + - + +
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Residues in contact with ARG 160 (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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86A GLU* 2.7 39.6 + - - -
91A TYR* 3.5 47.3 - - + +
110A ARG* 3.4 7.1 - - - +
111A LYS* 2.8 57.6 + - + +
158A ILE 4.1 0.4 - - - -
159A ASN* 1.3 73.0 - - - +
161A TYR* 1.3 63.4 + - - +
162A LYS* 3.6 28.5 + - - +
166A ASP* 3.9 1.7 - - - +
247A PRO* 3.6 19.4 - - - +
248A ARG 3.3 11.2 - - - +
249A VAL* 3.9 6.6 - - + +
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Residues in contact with TYR 161 (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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110A ARG* 3.7 13.5 - - + -
159A ASN* 3.4 35.5 - - + +
160A ARG* 1.3 72.6 - - - +
162A LYS* 1.3 63.3 + - - +
163A ASP* 3.2 2.9 + - - -
166A ASP* 3.5 8.3 - - + -
167A HIS* 3.5 43.3 - - - -
168A ILE* 3.4 16.4 - - + +
193A ARG* 3.7 18.2 - - - +
238A LEU* 3.6 15.9 - - + -
246A ALA 4.1 0.5 - - - +
247A PRO* 3.1 0.5 - - - +
248A ARG* 2.8 72.7 + - + +
250A ASN* 4.4 0.4 - - + -
301A AKG 2.5 23.8 + - - +
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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