Contacts of the strand formed by residues 147 - 153 (chain H) in PDB entry 1BEY
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 GLY 147 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132H LEU* 3.5 28.0 + - - -
146H LEU* 1.3 78.2 - - - +
148H CYS* 1.3 73.8 + - - -
162H TRP* 3.5 5.8 - - - -
188H SER 2.9 14.6 - - - -
189H VAL* 3.6 9.6 - - - -
219H VAL* 3.6 8.7 - - - +
118L PHE* 4.5 1.3 - - - -
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Residues in contact with CYS 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H VAL* 3.9 10.8 - - + -
130H PHE 3.8 6.7 - - - +
131H PRO* 5.2 3.1 - - - -
132H LEU* 3.9 7.1 - - - +
147H GLY* 1.3 83.1 - - - -
149H LEU* 1.3 60.2 + - - +
150H VAL* 3.9 5.0 + - + +
162H TRP* 4.0 12.1 - - + -
187H SER* 3.2 24.9 - - - -
188H SER* 2.6 17.7 + - - +
189H VAL* 4.7 0.4 - - - +
204H CYS* 2.0 51.4 - - - -
206H VAL* 5.2 0.2 - - + -
217H LYS* 5.1 3.6 - - - -
219H VAL* 4.5 7.2 - - - -
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Residues in contact with LEU 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H SER 2.9 2.9 - - - +
129H VAL* 2.8 10.9 - - - -
130H PHE* 2.5 49.9 + - + +
132H LEU* 3.8 13.2 - - + +
148H CYS* 1.3 73.2 - - - +
150H VAL* 1.3 52.3 + - - +
151H LYS* 3.5 28.5 - - + -
185H SER* 4.4 9.0 - - - +
186H LEU 3.8 8.1 - - - +
187H SER* 3.5 22.2 - - - +
124L GLN* 3.8 11.9 - - - +
131L SER* 3.2 28.5 - - - +
133L VAL* 4.5 13.2 - - + -
178L THR* 4.6 6.5 - - + +
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Residues in contact with VAL 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H PRO* 3.7 13.0 - - + -
128H SER 3.1 4.7 - - - +
129H VAL* 3.5 7.9 - - + -
148H CYS* 3.9 6.0 + - + +
149H LEU* 1.3 67.3 - - - +
151H LYS* 1.3 58.4 + - - +
153H TYR* 3.5 26.7 - - + -
158H VAL* 3.9 4.5 - - + -
160H VAL* 4.8 5.6 - - + -
185H SER* 3.7 3.3 - - - -
186H LEU* 3.1 49.4 + - + +
188H SER* 5.5 1.1 - - - +
206H VAL* 3.1 52.5 - - + -
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Residues in contact with LYS 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H PRO* 4.7 0.9 - - - -
128H SER* 2.3 56.5 + - - +
130H PHE* 3.9 13.5 - - + -
149H LEU* 3.5 18.6 - - + -
150H VAL* 1.3 68.6 - - - +
152H ASP* 1.3 85.0 + - - +
153H TYR* 4.1 0.7 - - - -
179H GLN* 2.9 28.7 + - - +
185H SER* 3.5 11.9 - - - +
124L GLN* 3.3 29.4 - - + +
129L THR* 4.8 10.3 - - + +
131L SER* 3.4 17.9 - - - -
178L THR* 5.7 0.9 - - - -
180L THR* 4.1 17.3 + - - +
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Residues in contact with ASP 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H LYS* 3.6 12.3 - - - +
126H GLY 3.4 14.0 - - - +
128H SER* 4.9 2.1 + - - +
151H LYS* 1.3 102.8 + - - +
153H TYR* 1.3 60.3 + - - +
179H GLN* 2.5 28.1 + - - -
181H SER* 3.1 10.7 + - - -
183H LEU* 3.5 20.0 - - + +
184H TYR 3.3 14.9 + - - -
185H SER* 4.0 1.2 + - - -
129L THR* 5.7 2.8 - - - +
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Residues in contact with TYR 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H LYS* 3.1 26.0 - - - +
127H PRO* 3.0 31.0 - - + -
150H VAL* 3.5 26.0 - - + -
152H ASP* 1.3 74.1 - - - +
154H PHE* 1.3 72.8 + - - +
155H PRO 4.5 1.1 - - - -
156H GLU* 4.0 19.8 + - + -
158H VAL* 2.7 43.5 - - + +
176H ALA* 4.5 1.4 - - - +
183H LEU* 4.0 3.1 - - - +
184H TYR* 3.2 49.7 + + + +
185H SER 4.7 0.2 - - - -
186H LEU* 3.7 13.3 + - - +
208H HIS* 4.0 12.3 - - - +
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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