Contacts of the strand formed by residues 158 - 165 (chain A) in PDB entry 4BYI
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 ILE 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A LEU* 3.8 30.7 - - + -
150A ALA 3.5 4.5 - - - +
151A ARG* 3.7 31.9 - - + -
156A LYS 3.5 6.2 + - - +
157A PHE* 1.3 89.8 - - - +
159A LEU* 1.3 63.1 - - - +
212A TYR* 3.8 24.3 + - + +
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Residues in contact with LEU 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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133A PHE* 4.1 22.9 - - + -
149A LEU* 3.8 9.0 - - - +
150A ALA* 3.0 48.1 + - + +
152A GLU* 4.6 6.7 - - + +
157A PHE* 3.6 33.2 - - + +
158A ILE* 1.3 74.3 - - - +
160A ALA* 1.3 65.7 + - - +
161A LEU* 4.5 4.5 - - + +
197A TYR* 4.3 7.9 - - + -
209A ILE* 3.7 29.2 - - + -
210A LEU 3.3 13.5 - - - +
212A TYR* 3.6 13.0 - - - +
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Residues in contact with ALA 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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1A FH3 3.4 42.8 - - + +
139A LEU* 4.3 7.2 - - + -
147A VAL* 4.3 2.9 - - + -
148A TYR 3.5 8.3 - - - +
159A LEU* 1.3 75.5 - - - +
161A LEU* 1.3 60.6 + - - +
208A LEU 3.5 0.7 - - - +
209A ILE* 3.6 1.6 - - - -
210A LEU* 2.6 49.7 + - + +
211A GLU 3.9 2.7 - - - +
212A TYR* 3.8 2.3 - - - +
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Residues in contact with LEU 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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130A LEU* 4.4 22.4 - - + -
133A PHE* 4.5 21.5 - - + -
135A ILE* 4.5 13.7 - - + -
146A ASN 3.9 0.3 - - - +
147A VAL* 3.3 4.4 - - - -
148A TYR* 2.9 44.3 + - + +
150A ALA* 4.1 14.1 - - + -
159A LEU* 4.2 3.3 + - + -
160A ALA* 1.3 73.4 - - - +
162A LYS* 1.3 60.1 + - - +
163A VAL* 3.6 11.7 + - + -
200A PHE* 4.6 2.2 - - + -
207A TYR* 4.0 21.5 - - + -
208A LEU 3.4 21.8 - - - +
209A ILE* 3.8 20.2 - - + -
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Residues in contact with LYS 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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1A FH3 5.9 5.1 - - + +
144A PHE* 3.7 42.5 - - - -
145A GLY 5.0 3.7 + - - +
146A ASN 3.9 4.0 - - - +
147A VAL* 4.2 24.2 - - + +
160A ALA 4.0 0.8 + - - -
161A LEU* 1.3 70.1 - - - +
163A VAL* 1.3 61.6 + - - +
164A LEU* 3.8 20.9 - - + +
181A GLU* 5.0 9.2 - - - +
206A VAL 3.5 1.7 - - - +
207A TYR* 3.2 5.0 - - - -
208A LEU* 2.6 61.3 + - + -
210A LEU* 3.6 24.8 - - + +
274A ASP* 5.3 7.6 + - - -
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Residues in contact with VAL 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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135A ILE* 5.6 3.6 - - + -
145A GLY* 3.1 24.8 - - - -
146A ASN 2.9 18.3 + - - +
148A TYR* 4.0 27.8 - - + +
161A LEU* 4.2 9.6 - - + +
162A LYS* 1.3 74.3 - - - +
164A LEU* 1.3 64.5 + - - +
165A PHE* 5.2 8.4 - - + -
205A ARG* 3.7 31.6 - - + -
206A VAL 3.6 2.5 - - - -
207A TYR* 3.5 30.1 - - + -
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Residues in contact with LEU 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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144A PHE* 3.7 27.6 - - + +
145A GLY* 5.2 0.4 - - - +
162A LYS* 3.8 35.0 - - + +
163A VAL* 1.3 76.9 - - - +
165A PHE* 1.3 62.5 + - - +
169A LEU* 3.9 33.7 - - + -
178A LEU* 4.6 13.5 - - + -
181A GLU* 6.0 0.4 - - - +
205A ARG* 3.4 9.2 - - - +
206A VAL* 2.8 45.9 + - + +
208A LEU* 4.0 23.1 - - + -
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Residues in contact with PHE 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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143A LYS 5.0 3.6 - - - -
144A PHE 3.6 15.8 + - - +
145A GLY* 4.6 12.1 - - - -
146A ASN* 5.5 5.6 - - - -
163A VAL* 5.2 7.0 - - + -
164A LEU* 1.3 73.0 - - - +
166A LYS* 1.3 54.4 + - - +
167A ALA* 3.1 4.3 - - + +
168A GLN* 3.0 22.7 + - + +
169A LEU* 2.6 38.6 + - - +
204A THR* 4.4 6.7 - - - +
205A ARG* 3.8 31.2 - - + -
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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