Contacts of the strand formed by residues 224 - 229 (chain C) in PDB entry 4BUR
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 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C ARG* 3.1 19.0 - - - +
157C ALA 2.9 10.7 + - - +
158C ARG* 4.3 1.0 - - - +
159C VAL* 3.0 27.0 + - - +
212C VAL* 4.1 11.2 - - - -
217C LEU* 3.5 9.9 - - - +
223C GLY* 1.3 73.7 - - - -
225C VAL* 1.3 64.2 + - - -
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Residues in contact with VAL 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 6.0 2.2 - - + -
147C ALA* 4.0 19.5 - - + -
148C ARG* 5.4 0.9 - - + +
151C ARG* 3.9 26.7 - - + +
159C VAL* 3.5 11.9 - - + +
161C ILE* 4.1 23.3 - - + -
206C GLN* 5.3 12.1 - - - +
210C PHE 5.7 1.9 + - - +
211C TYR* 3.5 34.2 - - + -
212C VAL* 3.2 23.6 + - - +
224C GLY* 1.3 75.5 - - - +
226C ALA* 1.3 63.3 + - - +
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Residues in contact with ALA 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C VAL 2.9 7.5 + - - +
160C LEU* 3.5 5.8 - - + +
161C ILE* 3.0 27.7 + - - +
212C VAL* 3.2 23.3 - - + +
213C SER 3.4 19.3 - - - +
214C ALA* 3.9 10.3 - - - -
217C LEU* 4.0 16.4 - - + -
224C GLY 4.1 0.4 - - - -
225C VAL* 1.3 75.1 - - - +
227C VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C LEU* 4.9 0.2 - - - -
161C ILE* 3.6 27.6 - - + +
163C SER* 4.5 7.2 - - - -
167C GLU 5.2 0.2 - - - +
168C LEU* 3.8 19.3 - - + +
169C PRO* 4.3 15.0 - - + -
211C TYR* 3.5 37.8 - - + +
212C VAL 4.3 2.8 + - - -
214C ALA* 5.5 3.9 + - - +
225C VAL* 4.3 0.4 + - + -
226C ALA* 1.3 77.4 - - - +
228C LEU* 1.3 61.2 + - - +
229C THR* 3.3 30.8 + - + +
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Residues in contact with LEU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LYS* 4.3 25.1 - - + -
128C ALA* 3.8 24.9 - - + -
160C LEU* 4.2 13.5 - - + +
161C ILE 2.9 14.1 + - - +
162C VAL* 3.8 14.0 - - + -
163C SER 3.0 24.0 + - - +
214C ALA* 4.5 14.1 - - + -
226C ALA 4.1 1.8 - - - -
227C VAL* 1.3 69.7 - - - +
229C THR* 1.3 66.8 + - - +
231C LYS* 3.7 36.0 - - + +
245C LEU* 4.0 14.6 - - + -
251C ILE* 4.8 0.2 - - + -
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Residues in contact with THR 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C SER* 3.6 5.4 - - - +
165C ASP 3.5 8.7 - - - +
166C PRO* 3.8 20.7 + - - +
167C GLU 4.1 11.2 - - - +
168C LEU* 4.2 12.3 - - + -
227C VAL* 3.3 28.7 + - + +
228C LEU* 1.3 74.7 - - - +
230C GLY* 1.3 66.0 + - - +
231C LYS* 3.1 14.6 + - - +
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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