Contacts of the strand formed by residues 251 - 255 (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 GLY 251 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224D VAL 3.5 2.4 + - - +
225D TRP* 3.4 15.9 - - - -
226D LEU* 3.0 22.6 + - - +
249D LEU* 3.6 3.1 - - - +
250D THR* 1.3 84.2 + - - +
252D VAL* 1.3 67.9 + - - +
275D VAL* 3.8 7.6 - - - +
276D PRO 3.4 12.8 - - - -
278D LYS* 4.0 5.8 - - - -
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Residues in contact with VAL 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D LEU* 3.3 20.2 - - + +
228D LEU* 3.8 21.1 - - + -
249D LEU* 4.6 0.4 - - + -
251D GLY* 1.3 78.8 - - - +
253D ILE* 1.3 73.4 + - - +
254D VAL* 3.8 17.0 - - + -
269D ILE* 4.4 4.0 - - + -
273D LEU* 3.9 20.2 - - + -
275D VAL* 3.5 23.1 - - + +
276D PRO 3.0 9.4 + - - +
277D ILE* 3.3 13.1 - - + +
278D LYS* 2.7 33.8 + - - +
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Residues in contact with ILE 253 (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* 6.2 0.4 - - + -
118D THR* 3.5 35.0 - - + -
122D LEU* 3.8 30.7 - - + -
225D TRP* 4.0 20.9 - - + -
226D LEU 2.9 10.4 + - - +
227D VAL* 3.3 9.4 - - + +
228D LEU 2.9 26.0 + - - +
252D VAL* 1.3 76.9 - - - +
254D VAL* 1.3 63.8 + - - +
255D THR* 3.9 11.3 + - + -
278D LYS* 4.5 1.3 - - + -
279D PHE* 3.4 34.1 - - + +
281D GLY 4.9 0.4 - - - +
289D LEU* 4.3 6.7 - - + -
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Residues in contact with VAL 254 (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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228D LEU* 3.1 11.2 - - + +
229D ASP 4.1 0.9 - - - -
230D ALA* 3.8 27.4 - - + +
252D VAL* 3.8 11.2 - - + -
253D ILE* 1.3 76.2 - - - +
255D THR* 1.3 62.0 + - - +
257D LEU* 3.4 10.5 - - + +
265D VAL* 5.2 0.4 - - + -
266D LEU* 3.7 33.9 - - + -
269D ILE* 3.9 19.1 - - + -
277D ILE* 3.7 24.0 - - + -
279D PHE 3.3 7.4 + - - +
280D VAL* 3.5 1.0 - - - -
281D GLY 2.9 20.8 + - - -
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Residues in contact with THR 255 (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 2.7 23.3 + - - +
118D THR* 3.3 26.0 - - - +
121D LYS* 5.8 0.2 - - - +
227D VAL* 3.5 18.8 - - + -
228D LEU 2.7 16.7 + - - -
229D ASP* 3.5 7.3 - - - -
230D ALA* 2.9 26.0 + - - +
253D ILE* 4.5 6.3 - - + -
254D VAL* 1.3 75.9 - - - +
256D LYS* 1.3 70.5 + - - +
257D LEU 3.3 2.6 + - - -
281D GLY* 4.0 7.9 - - - +
1001D GDP 3.8 18.2 - - - +
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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