Contacts of the strand formed by residues 270 - 274 (chain A) in PDB entry 2G1Y
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 LYS 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A HIS* 3.3 44.6 - - + -
266A HIS* 4.0 4.2 - - - -
267A LEU 3.0 26.6 + - - +
268A GLY 4.9 1.8 - - - +
269A GLY* 1.3 85.6 - - - +
271A GLU* 1.3 65.1 + - - +
272A TYR* 3.2 26.9 - - + +
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Residues in contact with GLU 271 (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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202A GLY 5.1 0.7 - - - +
204A SER* 4.0 5.4 + - - -
264A SER* 3.0 27.6 - - - +
265A PHE 3.6 4.4 + - - -
266A HIS* 2.7 45.6 + - + +
270A LYS* 1.3 78.7 - - - +
272A TYR* 1.3 63.8 + - - +
273A THR* 3.7 13.4 + - - +
318A PHE* 5.6 0.3 - - - -
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Residues in contact with TYR 272 (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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186A HIS* 3.3 33.0 + + - +
188A ILE* 5.0 1.4 - - + +
264A SER* 3.5 0.3 - - - -
265A PHE* 2.9 49.2 + - + +
267A LEU* 3.7 27.5 + - + -
270A LYS* 3.2 30.3 - - + -
271A GLU* 1.3 72.5 - - - +
273A THR* 1.3 60.2 + - - +
314A PHE* 3.6 25.9 - + + -
318A PHE* 3.4 39.7 - + + -
331A PHE* 3.3 36.9 + + + +
332A ALA* 5.8 0.4 - - - -
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Residues in contact with THR 273 (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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262A ASP* 3.7 36.1 - - + +
263A ILE 3.5 3.1 - - - +
264A SER* 3.0 19.3 + - - +
271A GLU* 3.7 12.0 + - - +
272A TYR* 1.3 71.7 - - - +
274A LEU* 1.3 68.9 + - - +
275A THR* 5.5 1.1 - - - +
317A LYS* 2.8 29.2 + - - +
318A PHE* 4.0 5.4 - - - -
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Residues in contact with LEU 274 (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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227A ILE* 3.5 32.3 - - + -
262A ASP* 3.3 7.4 - - - +
263A ILE* 2.8 36.5 + - + +
265A PHE* 4.2 13.7 - - + -
273A THR* 1.3 78.5 - - - +
275A THR* 1.3 63.1 + - - +
278A ASP* 3.7 13.9 - - + +
279A TYR* 4.5 14.4 - - + -
295A ILE* 6.0 0.9 - - + -
313A THR* 3.9 24.0 - - + +
314A PHE* 4.6 4.9 - - + -
317A LYS* 3.5 33.2 - - + -
318A PHE* 3.9 13.7 - - + -
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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