Contacts of the strand formed by residues 163 - 169 (chain A) in PDB entry 4BU2
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A GLN* 3.5 15.5 - - - -
141A GLN* 3.8 1.8 - - - -
151A GLN* 3.6 4.1 + - - -
161A LEU 4.1 1.2 - - - -
162A VAL* 1.3 75.5 - - - +
164A SER* 1.3 63.9 - - - -
165A ASN* 5.7 0.2 - - - -
256A ILE* 3.5 3.5 - - - +
257A SER* 3.0 35.4 + - - -
405A MSE 3.9 17.5 - - - +
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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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139A GLN* 2.9 37.7 + - - +
140A PRO* 3.1 23.8 - - - +
141A GLN* 3.3 0.7 + - - -
151A GLN* 2.7 28.6 + - - +
163A GLY* 1.3 74.2 - - - -
165A ASN* 1.3 66.6 + - - +
254A VAL* 3.7 12.7 - - - +
255A THR 3.1 13.2 - - - -
256A ILE* 4.0 5.8 - - - -
257A SER* 5.0 0.2 - - - -
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Residues in contact with ASN 165 (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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136A GLN* 3.2 17.3 + - + +
137A PHE 3.5 4.8 - - - +
138A HIS* 2.9 37.8 + - - +
139A GLN* 4.3 9.7 + - - +
140A PRO* 4.3 0.2 - - - -
164A SER* 1.3 81.0 + - - +
166A VAL* 1.3 64.1 + - - +
167A TYR* 4.0 11.0 - - + -
254A VAL* 3.2 2.8 - - - +
255A THR* 2.7 36.5 + - - -
257A SER* 5.3 3.0 + - - -
902A EDO 3.5 31.6 + - - +
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Residues in contact with VAL 166 (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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81A PHE* 3.8 37.9 - - + -
135A ILE 3.6 0.7 - - - +
136A GLN* 3.2 9.0 - - - +
137A PHE* 2.9 41.8 + - + +
140A PRO* 3.7 29.8 - - + -
147A LEU* 5.3 0.2 - - + -
165A ASN* 1.3 76.8 - - - +
167A TYR* 1.3 64.1 + - - +
168A ILE* 4.1 17.3 - - + -
190A LEU* 5.4 0.2 - - + -
252A THR* 4.4 6.1 - - + -
253A HIS 3.4 10.3 - - - +
254A VAL* 3.8 14.8 - - + -
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Residues in contact with TYR 167 (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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134A THR* 4.2 18.2 - - + -
135A ILE 3.5 2.2 - - - -
136A GLN* 3.6 36.2 + - + -
165A ASN* 4.0 10.3 - - + -
166A VAL* 1.3 73.7 - - - +
168A ILE* 1.3 63.7 + - - +
169A THR* 4.2 1.1 - - - -
176A LEU* 4.3 11.8 - - + +
194A LYS* 4.9 1.9 + - - +
251A SER 3.6 1.0 - - - +
252A THR* 3.3 5.5 - - - -
253A HIS* 2.8 65.2 + + + +
255A THR* 3.4 22.7 - - - -
701A AKG 3.4 34.2 - - + +
902A EDO 2.8 32.5 + - - -
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Residues in contact with ILE 168 (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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81A PHE* 4.4 8.3 - - + -
83A LEU* 3.6 32.8 - - + -
86A LEU* 3.8 33.7 - - + -
133A ALA 4.2 0.5 - - - +
134A THR* 3.7 0.7 - - - +
135A ILE* 2.8 55.7 + - + +
137A PHE* 5.7 1.1 - - + -
166A VAL* 4.1 18.4 - - + -
167A TYR* 1.3 78.8 - - - +
169A THR* 1.3 67.6 + - - +
170A PRO* 4.5 0.9 - - + +
250A HIS* 4.1 7.2 - - + -
251A SER 3.3 8.1 - - - +
252A THR* 3.6 13.9 - - + +
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Residues in contact with THR 169 (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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133A ALA 3.6 4.0 - - - +
134A THR* 3.4 29.2 + - - +
167A TYR 4.2 0.4 - - - -
168A ILE* 1.3 76.7 + - - +
170A PRO* 1.3 76.1 - - + +
173A SER* 3.3 22.7 - - - +
174A GLN 4.0 6.5 - - - +
175A GLY* 4.9 0.2 - - - -
194A LYS* 2.8 23.3 + - - +
243A ASP* 6.2 0.2 - - - -
244A THR* 3.3 17.8 + - - +
250A HIS* 3.3 3.7 - - - +
251A SER 2.8 35.6 + - - -
701A AKG 4.7 0.2 + - - -
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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