Contacts of the strand formed by residues 225 - 230 (chain B) in PDB entry 3BDW
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 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ARG* 3.6 9.9 - - - +
138B ARG* 2.8 28.2 + - - +
143B SER* 4.2 0.7 + - - -
172B SER* 3.6 21.1 - - - +
174B TRP* 3.5 38.1 - - + +
210B VAL* 3.6 28.9 - - + -
212B GLN* 5.0 7.9 - - - +
219B ALA* 4.2 9.4 - - + -
223B SER* 3.9 16.4 - - - -
224B SER* 1.3 79.3 - - - +
226B ILE* 1.3 77.2 + - - +
227B TYR 3.6 0.7 + - - -
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Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 5.9 0.2 - - + -
135B LYS* 3.6 41.7 - - + +
136B GLU 3.8 5.2 - - - +
137B ARG* 3.7 24.7 - - + +
170B SER* 5.8 1.1 - - - -
172B SER* 3.4 28.5 + - - +
173B SER* 3.3 4.4 - - - -
174B TRP* 3.2 21.7 + - - -
225B ILE* 1.3 78.9 - - - +
227B TYR* 1.3 64.2 + - - +
228B HIS* 3.8 23.8 - - + +
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Residues in contact with TYR 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B TYR* 5.3 2.0 - + - -
134B GLY* 3.5 19.1 - - - -
136B GLU* 3.3 34.4 + - + -
138B ARG* 3.5 32.9 + - + -
143B SER* 3.3 36.6 - - - +
146B ALA* 3.5 26.5 - - + +
147B CYS* 3.7 17.9 - - - -
150B LYS* 3.1 28.9 + - - -
154B LEU* 3.8 7.4 - - + -
173B SER* 3.8 4.9 - - - -
174B TRP* 4.3 2.7 - - + +
226B ILE* 1.3 76.3 - - - +
228B HIS* 1.3 69.2 + - - +
229B CYS* 4.0 9.9 - - - -
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Residues in contact with HIS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TYR* 5.7 4.3 - - + -
132B TYR 3.2 9.9 - - - +
133B ILE* 3.5 17.2 - - + +
134B GLY 3.4 22.0 - - - -
147B CYS* 3.5 7.1 - - - -
154B LEU* 3.5 2.6 - - - +
155B LEU* 2.8 44.0 + - + +
166B LEU* 4.8 12.6 - - + +
170B SER* 3.2 41.2 + - - -
172B SER 4.4 0.4 - - - -
173B SER* 3.3 28.5 + - - +
226B ILE* 3.8 13.2 - - + +
227B TYR* 1.3 77.2 - - - +
229B CYS* 1.3 66.9 + - - +
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Residues in contact with CYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TRP* 4.1 12.6 - - + -
130B CYS 4.5 0.2 - - - -
131B TYR* 3.4 8.7 - - - +
132B TYR* 3.1 35.4 + - + -
147B CYS* 2.0 48.2 - - - -
150B LYS* 4.4 12.3 - - - -
152B SER* 3.4 17.3 - - - +
153B SER 3.3 4.7 - - - +
155B LEU* 4.7 0.9 - - - -
227B TYR* 4.0 13.7 - - - -
228B HIS* 1.3 76.6 - - - +
230B LYS* 1.3 61.8 + - - +
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Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B SER* 4.2 14.4 - - - -
130B CYS 3.3 11.7 - - - +
131B TYR* 3.6 20.2 - - + -
152B SER* 3.7 1.5 + - - -
153B SER* 2.8 36.2 + - - +
154B LEU 4.8 0.4 - - - +
155B LEU* 4.0 14.4 - - + -
156B SER* 3.1 36.2 + - - +
158B ASP* 2.4 34.4 + - - -
162B GLU* 2.8 26.0 + - - +
229B CYS* 1.3 76.5 - - - +
231B HIS* 1.3 73.4 + - - +
232B LYS* 4.2 2.3 + - - +
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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