Contacts of the strand formed by residues 247 - 251 (chain D) in PDB entry 3HYW
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 PHE 247 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D THR* 3.5 22.0 - - + -
132D THR* 4.2 2.7 - - + -
135D LYS* 3.7 43.3 - - + +
136D LEU* 3.5 36.6 - - + -
139D LEU* 3.9 27.6 - - + -
145D PRO 3.3 3.4 + - - +
146D VAL* 3.4 22.4 - - + -
147D VAL 3.0 22.9 + - - -
148D ILE* 4.9 0.4 - - + -
163D PHE* 3.9 26.0 - + - -
167D LEU* 4.2 4.7 - - + -
245D ALA* 4.2 0.2 - - - +
246D LYS* 1.3 80.1 - - + +
248D THR* 1.3 77.4 + - - +
249D MET* 4.0 1.8 - - + -
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Residues in contact with THR 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ASN 4.2 1.7 + - - -
120D SER* 2.6 35.0 + - - -
121D THR* 2.7 30.0 + - - -
135D LYS* 3.6 8.5 + - - +
147D VAL 3.1 11.7 - - - +
226D ILE* 3.5 11.8 - - + +
227D GLU 5.5 1.3 - - - +
231D VAL* 3.7 18.2 - - + -
245D ALA* 3.6 24.0 - - + +
246D LYS 5.4 0.4 - - - -
247D PHE* 1.3 88.3 - - - +
249D MET* 1.3 55.6 + - - +
250D PHE* 4.1 7.4 - - - -
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Residues in contact with MET 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D THR* 3.3 27.1 - - - +
122D SER* 3.9 10.3 - - - -
123D ILE* 4.0 15.5 - - + -
132D THR* 4.6 0.2 - - + -
147D VAL 3.2 6.1 + - - -
148D ILE* 3.3 21.0 - - + +
149D GLY 3.2 21.3 + - - -
160D ALA* 4.1 4.5 - - + -
163D PHE* 3.7 53.2 - - + -
247D PHE* 4.0 3.2 - - + -
248D THR* 1.3 72.7 - - - +
250D PHE* 1.3 63.5 + - - +
251D MET* 3.2 35.9 - - + -
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Residues in contact with PHE 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLN* 3.8 22.9 + - + +
120D SER* 3.6 12.2 + - - +
121D THR 3.1 17.1 + - - +
122D SER* 3.9 6.4 - - - -
147D VAL* 3.7 40.6 - - + -
148D ILE 4.1 1.1 - - - -
149D GLY* 3.3 36.1 - - - -
150D ALA* 3.5 9.9 - - - -
151D ILE* 4.2 7.4 - - + -
185D ILE* 3.8 5.6 - - + -
223D VAL* 3.6 28.9 - - + -
226D ILE* 3.7 25.1 - - + -
231D VAL* 4.1 8.7 - - + -
248D THR* 4.1 3.1 - - - -
249D MET* 1.3 82.9 - - - +
251D MET* 1.3 62.3 + - - +
252D PRO* 3.4 8.5 - - - +
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Residues in contact with MET 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLN* 3.6 3.7 + - - -
123D ILE* 3.8 20.4 - - + +
124D CYS* 4.4 16.4 - - - -
149D GLY 2.9 13.9 + - - +
150D ALA* 4.3 3.8 - - + -
151D ILE* 3.4 15.6 + - - +
154D VAL* 3.4 29.4 - - + +
156D CSS 3.6 24.2 - - + +
159D PRO* 4.3 10.3 - - - -
160D ALA* 3.7 28.9 - - + +
249D MET* 3.2 43.3 - - + -
250D PHE* 1.3 71.7 - - - +
252D PRO* 1.3 67.5 - - + +
254D PHE* 6.4 0.4 - - - -
441D FAD 5.8 1.1 - - - -
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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