Contacts of the strand formed by residues 223 - 228 (chain A) in PDB entry 4MYF
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 THR 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A MET* 3.8 2.2 - - - +
133A GLY 3.2 4.9 - - - +
135A ILE* 4.2 4.3 - - + -
216A PHE* 4.0 23.1 - - + -
219A THR* 2.8 41.2 + - + +
220A GLY 2.9 17.7 + - - -
222A ASN* 1.3 72.4 - - - +
224A PHE* 1.3 74.9 + - - +
225A PHE 3.7 2.6 + - - +
265A THR* 2.8 20.9 + - - -
266A VAL* 3.5 7.6 - - + -
267A MET 3.0 24.3 + - - -
268A MET 3.7 2.9 + - - -
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Residues in contact with PHE 224 (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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117A SER* 3.5 25.6 - - - -
120A ASN* 3.7 9.4 - - + -
121A GLY* 3.7 20.4 - - - -
124A MET* 3.8 17.6 - - + +
133A GLY 2.8 14.5 + - - +
134A VAL* 3.8 22.2 - - + +
135A ILE* 3.0 29.5 + - - +
158A PHE* 4.6 4.7 - + - -
161A LEU* 4.7 0.9 - - + -
223A THR* 1.3 70.5 - - - +
225A PHE* 1.3 62.5 + - - +
226A SER* 3.6 13.5 - - - -
268A MET* 3.6 24.7 - - + -
270A ASP* 3.3 50.5 - - - -
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Residues in contact with PHE 225 (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* 3.7 18.2 - - + -
137A VAL* 4.1 16.2 - - + -
212A LEU* 3.9 25.4 - - + -
216A PHE* 3.8 10.8 - + + -
223A THR 3.7 1.4 + - - -
224A PHE* 1.3 71.1 - - - +
226A SER* 1.3 58.2 + - - +
227A PHE* 3.6 25.8 - + + -
256A MET* 4.2 9.4 - - + -
257A CYS* 4.2 5.8 - - - -
260A ALA* 3.6 24.7 - - + -
266A VAL* 3.8 17.3 - - + -
268A MET 3.1 15.0 + - - +
269A MET* 3.1 63.7 - - + +
270A ASP 3.2 2.9 + - - -
294A PHE* 5.4 0.2 - + - -
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Residues in contact with SER 226 (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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117A SER* 3.2 17.0 + - - -
135A ILE 3.0 18.3 + - - +
136A ASN* 3.6 2.7 + - - +
137A VAL* 2.8 31.8 + - - +
158A PHE* 3.5 19.3 - - - -
224A PHE* 3.6 16.1 - - - -
225A PHE* 1.3 72.5 - - - +
227A PHE* 1.3 60.5 + - - +
228A ASP 3.8 0.8 + - - -
270A ASP* 2.7 21.9 + - - -
272A SER* 5.3 0.2 + - - -
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Residues in contact with PHE 227 (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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137A VAL* 3.3 18.2 - - + -
225A PHE* 3.6 25.8 - + + -
226A SER* 1.3 73.4 - - - +
228A ASP* 1.3 67.8 + - - +
229A VAL 3.4 2.0 + - - -
231A SER* 3.2 22.9 - - - -
232A LEU* 3.6 13.7 - - + -
248A LEU* 4.2 3.1 - - + -
253A ALA* 3.9 19.3 - - + -
256A MET* 4.0 21.3 - - + -
257A CYS* 3.9 13.9 - - - -
269A MET* 4.0 11.2 - - + -
270A ASP* 3.0 17.9 + - - +
271A MET* 3.2 8.3 - - + +
272A SER* 3.0 21.6 + - - -
290A MET* 3.5 30.1 - - + -
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Residues in contact with ASP 228 (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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114A ASN* 2.8 14.6 + - - +
136A ASN* 4.5 3.4 - - - +
137A VAL 2.8 17.4 + - - +
138A ASP* 3.7 4.9 - - + +
226A SER* 3.8 1.6 + - - -
227A PHE* 1.3 71.0 - - - +
229A VAL* 1.3 59.7 + - - +
230A ASP* 2.9 22.8 + - - +
231A SER* 2.8 30.3 + - - -
272A SER* 3.7 7.6 - - - +
273A GLU* 3.2 12.1 - - - +
400A MN 2.2 35.3 + - - +
401A MN 2.2 19.9 + - - -
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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