Contacts of the strand formed by residues 225 - 228 (chain A) in PDB entry 6IRT
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 LEU 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A TRP* 4.5 7.6 - - + -
220A TRP* 5.3 5.4 - - + -
224A ALA* 1.3 91.2 - - - +
226A TYR* 1.3 66.0 + - - +
257A VAL* 4.3 3.3 - - - +
258A LYS* 4.5 2.2 - - + -
259A GLY* 3.8 29.6 - - - +
261A VAL* 4.9 7.0 - - + -
306A ILE* 4.4 14.6 - - + -
376A LEU* 5.2 3.1 - - + -
378A ILE* 4.0 25.4 - - + -
400A LEU* 5.1 5.8 - - + -
464A THR* 4.2 15.9 - - + -
465A PRO 3.0 6.5 + - - -
466A VAL* 3.9 31.0 - - + -
467A PHE* 3.4 21.6 + - - +
524A PHE* 6.1 0.2 - - - -
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Residues in contact with TYR 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 1.3 80.5 - - - +
227A ARG* 1.3 65.5 + - - +
228A ILE* 3.2 31.0 + - + +
234A PHE* 4.3 6.4 - + - -
251A TYR* 4.5 1.9 + - - -
252A LEU* 4.0 18.6 - - + -
255A LEU* 4.1 12.7 - - + +
257A VAL* 4.0 21.8 - - + -
259A GLY 3.7 14.7 + - - +
260A LEU* 3.7 8.7 - - + +
261A VAL* 3.3 17.4 + - - +
467A PHE* 3.3 8.7 - - + -
468A SER 4.1 10.5 - - - -
469A TYR* 3.3 31.6 - - + +
470A GLY 3.4 1.9 + - - -
472A GLU* 2.7 41.5 + - - -
490A MET* 4.3 4.2 - - - +
524A PHE* 5.4 6.3 - + - -
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Residues in contact with ARG 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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226A TYR* 1.3 70.3 - - - +
228A ILE* 1.3 61.5 + - - +
229A GLY* 3.8 1.7 + - - +
261A VAL* 3.9 23.1 - - + -
347A GLN* 4.4 15.0 - - - +
349A ARG* 6.2 0.2 - - - +
402A THR* 4.5 7.1 + - - +
435A SER* 4.2 5.7 + - - -
437A SER* 2.9 26.9 + - - +
438A GLN* 3.0 30.7 + - - +
439A ALA* 3.8 4.5 + - - +
440A ARG 3.7 9.9 + - - -
466A VAL* 3.3 41.9 + - + +
467A PHE 2.5 16.3 + - - +
468A SER* 3.0 28.8 + - - +
469A TYR* 3.2 27.5 + - - -
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Residues in contact with ILE 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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226A TYR* 3.7 28.3 - - + +
227A ARG* 1.3 70.5 - - - +
229A GLY* 1.3 65.0 + - - +
230A ASP 4.9 0.7 - - - +
231A LEU* 3.8 26.1 - - + +
234A PHE* 4.3 33.0 - - + -
245A LEU* 4.8 7.0 - - + -
252A LEU* 4.5 7.2 - - + -
260A LEU* 3.8 37.7 - - + -
261A VAL* 3.1 22.2 + - - +
262A LEU* 4.9 5.6 - - + +
263A GLY 3.8 12.1 + - - +
469A TYR* 4.2 7.2 - - + -
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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