Contacts of the strand formed by residues 223 - 229 (chain D) in PDB entry 2IYL
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 GLU 223 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D GLU 4.1 3.3 - - - +
100D PRO* 3.6 18.3 - - + +
101D LYS* 2.9 38.2 + - - +
102D GLY 4.8 0.9 - - - +
104D VAL 3.3 4.7 + - - +
105D VAL* 3.4 18.7 - - + -
106D LEU 2.9 23.5 + - - -
221D PRO* 3.7 3.1 - - - +
222D LYS* 1.3 86.1 - - - +
224D VAL* 1.3 68.0 + - - +
225D TRP* 2.9 30.5 + - + +
250D THR* 2.6 35.0 + - - +
278D LYS* 4.2 10.7 + - - -
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Residues in contact with VAL 224 (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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106D LEU* 3.3 27.8 - - + +
108D VAL* 4.4 5.6 - - + -
210D LYS* 4.6 5.4 - - - +
221D PRO* 4.2 17.5 - - + +
222D LYS 5.6 0.2 - - - -
223D GLU* 1.3 80.3 - - - +
225D TRP* 1.3 62.5 + - - +
247D VAL* 3.7 37.2 - - + +
248D GLY 3.5 21.5 - - - +
249D LEU* 3.5 14.2 - - + +
250D THR* 2.8 37.9 + - + +
251D GLY 3.5 1.4 + - - +
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Residues in contact with TRP 225 (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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98D VAL* 4.6 3.4 - - + -
99D GLU 5.1 0.7 - - - -
100D PRO* 3.9 23.1 - - + -
105D VAL* 3.6 24.0 - - + -
106D LEU 2.7 11.1 + - - +
107D VAL* 3.3 11.2 - - + +
108D VAL* 2.8 28.5 + - - +
122D LEU* 4.1 16.8 - - + -
126D TYR* 4.1 3.8 - - - -
189D PHE* 4.4 4.9 - + - -
223D GLU* 2.9 41.2 + - + -
224D VAL* 1.3 73.0 - - - +
226D LEU* 1.3 63.0 + - - +
227D VAL* 3.8 0.6 + - - -
250D THR* 3.3 17.4 + - - -
251D GLY* 3.4 17.3 - - - +
253D ILE* 4.0 22.7 - - + -
278D LYS* 3.6 30.9 - - + +
279D PHE* 4.0 29.4 - + - -
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Residues in contact with LEU 226 (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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108D VAL* 3.4 14.5 - - + +
109D GLY* 3.9 7.9 - - - -
224D VAL 4.1 0.8 + - - -
225D TRP* 1.3 73.5 - - - +
227D VAL* 1.3 69.5 + - - +
228D LEU* 3.6 26.0 - - + -
240D ALA* 3.6 24.0 - - + -
243D PHE* 3.8 33.0 - - + -
249D LEU* 3.8 25.3 - - + +
251D GLY 3.0 8.8 + - - +
252D VAL* 3.3 7.2 - - + +
253D ILE* 2.9 24.9 + - - +
273D LEU* 3.8 14.6 - - + -
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Residues in contact with VAL 227 (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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107D VAL* 3.5 30.5 - - + -
108D VAL 2.9 13.0 + - - +
109D GLY* 4.2 3.6 - - - -
110D VAL 5.0 0.3 + - - -
113D VAL* 3.3 35.9 - - + +
114D GLY 4.1 4.0 - - - -
115D LYS* 4.3 7.6 - - + -
118D THR* 3.9 24.0 - - + +
225D TRP 4.5 0.7 - - - +
226D LEU* 1.3 83.7 - - - +
228D LEU* 1.3 64.7 + - - +
253D ILE* 3.3 11.7 - - + +
255D THR* 3.5 30.1 - - + -
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Residues in contact with LEU 228 (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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113D VAL* 4.5 4.5 - - + -
226D LEU* 3.6 23.8 - - + -
227D VAL* 1.3 77.2 - - - +
229D ASP* 1.3 60.1 + - - +
232D THR 5.7 4.0 - - - +
237D LEU* 4.0 15.9 - - + +
240D ALA* 4.2 11.4 - - + -
252D VAL* 3.8 11.4 - - + -
253D ILE 2.9 9.4 + - - +
254D VAL* 3.1 9.7 - - + -
255D THR* 2.7 34.8 + - - -
269D ILE* 3.8 34.8 - - + -
273D LEU* 3.9 13.9 - - + -
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Residues in contact with ASP 229 (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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112D GLY 4.4 1.9 - - - +
113D VAL* 4.0 19.8 - - + +
228D LEU* 1.3 78.7 - - - +
230D ALA* 1.3 66.2 + - - +
231D VAL* 3.0 41.7 + - - +
232D THR* 3.5 36.6 + - + +
233D GLY* 3.8 3.5 + - - -
254D VAL* 4.1 2.2 - - - +
255D THR* 3.5 8.7 + - - +
256D LYS* 2.9 34.2 + - - +
269D ILE* 5.1 1.2 - - - +
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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