Contacts of the strand formed by residues 157 - 164 (chain A) in PDB entry 1BOO
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 VAL 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A GLY* 4.7 8.5 + - - -
108A ARG* 5.6 1.2 + - - -
132A TYR* 4.0 31.6 - - + -
133A TRP 3.3 7.9 - - - +
134A PHE* 4.0 20.4 - - + -
138A LYS* 5.0 0.4 + - - -
155A ASP* 4.0 9.5 + - - +
156A ALA* 1.3 84.7 - - + +
158A ASN* 1.3 69.4 + - - +
159A THR* 4.3 4.3 + - + +
222A LEU* 5.4 5.4 - - + -
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Residues in contact with ASN 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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96A ASP* 3.6 18.6 - - - +
97A PHE 3.1 8.6 - - - +
98A GLY* 3.0 24.7 + - - -
99A GLY 5.2 0.2 - - - +
132A TYR* 3.5 5.0 - - - -
133A TRP* 2.9 60.7 + - + +
135A ASN* 5.1 4.2 - - - +
138A LYS* 3.1 32.9 + - - +
156A ALA 4.8 1.6 + - - -
157A VAL* 1.3 77.3 - - - +
159A THR* 1.3 62.1 + - - +
160A VAL* 3.3 4.5 + - - +
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Residues in contact with THR 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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95A VAL 3.6 2.6 - - - +
97A PHE* 3.1 36.4 + - - +
98A GLY 5.8 0.2 - - - -
112A ASN* 2.9 34.6 + - - +
113A PHE* 3.9 13.5 - - + -
131A PHE 4.1 4.7 - - - -
132A TYR* 4.1 13.5 - - + -
157A VAL* 5.3 3.4 - - + +
158A ASN* 1.3 71.4 - - - +
160A VAL* 1.3 61.3 + - - +
161A TRP* 3.5 32.8 + - + -
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Residues in contact with VAL 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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51A MET* 5.1 1.6 - - + -
94A VAL* 3.8 27.6 - - + -
95A VAL 3.4 12.1 - - - +
96A ASP* 4.0 20.2 - - + +
131A PHE* 2.9 45.1 + - + +
132A TYR 4.8 0.2 - - - -
133A TRP* 3.9 25.1 - - + +
158A ASN 3.8 10.3 - - - +
159A THR* 1.3 72.0 - - - +
161A TRP* 1.3 59.8 + - - +
223A LEU* 5.4 1.6 - - + -
254A LEU* 4.8 10.5 - - + -
258A PHE* 4.1 16.8 - - + -
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Residues in contact with TRP 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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93A PHE 3.5 1.7 - - - +
94A VAL* 3.3 3.5 - - - -
95A VAL 2.9 37.0 + - - +
97A PHE* 3.8 29.6 - + - -
112A ASN 2.9 22.2 + - - -
113A PHE* 3.6 33.0 - + - -
115A VAL* 5.2 0.2 - - + -
116A LEU* 3.8 32.3 - - + +
127A LEU* 4.3 7.9 - - + -
129A GLU 4.7 0.2 - - - -
130A ASP* 3.8 26.9 - - + -
132A TYR* 3.9 16.8 - + - -
159A THR* 3.5 30.3 - - + -
160A VAL* 1.3 80.7 - - - +
162A TRP* 1.3 60.3 + - - +
163A PHE* 3.4 36.2 + + + -
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Residues in contact with TRP 162 (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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92A SER* 2.9 27.6 + - - -
94A VAL* 4.1 22.2 - - + +
127A LEU* 3.5 8.3 - - - +
128A ALA* 3.2 39.7 + - + +
129A GLU* 3.3 51.6 + - + +
131A PHE* 3.8 24.5 - + + -
160A VAL* 3.8 1.8 + - - +
161A TRP* 1.3 70.7 - - - +
163A PHE* 1.3 68.7 + - - +
169A PRO* 3.9 15.6 - - + +
171A SER* 3.5 24.5 - - - -
173A ILE* 6.5 0.4 - - + -
258A PHE* 4.7 3.6 - + + -
261A MET* 4.5 9.2 - - - -
262A LEU* 3.3 24.8 - - + +
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Residues in contact with PHE 163 (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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92A SER* 3.4 0.9 - - - -
93A PHE* 2.9 49.9 + + + +
95A VAL* 3.9 19.7 - - + -
115A VAL* 4.9 6.3 - - + -
116A LEU* 3.7 26.2 - - + -
119A MET* 3.7 46.7 - - + -
120A ILE* 4.0 6.1 - - + -
125A PHE* 3.7 20.4 - - + -
126A PHE 3.3 14.6 - - - +
127A LEU* 4.7 3.4 - - + -
161A TRP* 3.5 41.3 - + + -
162A TRP* 1.3 84.1 - - - +
164A SER* 1.3 62.3 + - - +
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Residues in contact with SER 164 (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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91A GLY 3.6 5.2 - - - -
92A SER* 4.1 1.1 - - - +
93A PHE 4.7 0.2 - - - +
125A PHE* 3.7 8.6 - - - -
126A PHE* 3.0 33.6 + - - +
128A ALA* 3.4 18.6 + - - +
163A PHE* 1.3 77.1 - - - +
165A LYS* 1.3 64.3 + - - +
166A THR 3.0 16.4 + - - -
167A GLU* 4.9 0.3 - - - -
169A PRO* 3.3 36.4 - - - +
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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