Contacts of the strand formed by residues 270 - 275 (chain G) in PDB entry 1RZR
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 270 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G LEU* 4.4 12.2 - - + +
175G SER* 5.2 4.9 - - - -
177G HIS* 3.1 37.0 + - + +
241G THR* 3.1 3.4 + - + +
242G ALA* 3.4 3.5 - - - +
243G ILE 3.3 22.4 + - - +
265G VAL 3.6 5.4 - - - -
266G PRO 3.9 11.7 - - - +
267G ASN 4.9 3.6 - - - +
269G LEU* 1.3 74.9 - - - +
271G ILE* 1.3 60.9 + - - +
330G SER 3.7 4.7 - - - +
331G THR* 2.4 41.3 + - - +
332G LYS* 3.4 20.2 + - - +
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Residues in contact with ILE 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243G ILE* 4.1 11.0 - - + -
245G VAL* 4.1 21.3 - - + -
251G ALA* 4.2 2.9 - - + +
254G VAL* 3.2 32.3 - - + +
255G ILE* 3.6 43.1 - - + +
258G ALA* 5.3 2.0 - - + -
265G VAL* 4.1 7.2 + - + -
269G LEU* 3.7 18.3 + - + +
270G GLU* 1.3 80.7 - - - +
272G ILE* 1.3 63.7 + - - +
287G LEU* 3.5 9.7 - - + +
288G THR 3.9 0.9 - - - +
330G SER* 2.4 37.4 + - - +
331G THR* 4.3 4.9 - - - +
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Residues in contact with ILE 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G ALA* 3.6 34.5 - - + +
171G SER* 4.9 6.7 - - - +
172G LEU* 4.0 23.8 - - + -
243G ILE 3.3 17.4 + - - +
244G PHE* 3.5 18.3 - - + -
245G VAL 3.0 22.2 + - - -
271G ILE* 1.3 78.6 - - - +
273G GLY* 1.3 65.7 + - - +
287G LEU* 4.2 0.2 - - - -
288G THR* 3.2 32.3 - - + +
289G SER* 4.6 1.1 - - - -
290G VAL* 4.7 1.1 - - + -
325G ILE* 4.1 14.6 - - + -
331G THR* 5.0 3.6 - - + -
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Residues in contact with GLY 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G PHE* 4.3 1.5 - - - -
245G VAL 3.5 10.1 - - - -
247G THR 3.8 9.2 - - - -
248G ASP* 3.5 7.0 - - - -
251G ALA* 3.9 10.3 - - - -
272G ILE* 1.3 76.3 - - - +
274G PHE* 1.3 62.2 + - - +
287G LEU* 3.5 6.1 - - - +
288G THR 2.9 11.8 + - - -
289G SER* 3.3 4.7 - - - -
290G VAL* 3.0 24.4 + - - +
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Residues in contact with PHE 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G ILE* 4.9 2.0 - - + -
161G TYR* 4.2 15.5 - + - -
164G ALA* 3.5 40.4 - - + -
165G ALA* 4.1 4.0 - - + -
196G LYS* 4.0 27.8 - - + -
244G PHE* 3.8 18.8 - + - -
245G VAL 3.4 14.0 + - - +
246G GLY 3.7 12.1 - - - +
247G THR* 3.5 3.9 + - - -
248G ASP* 2.6 28.8 + - - +
273G GLY* 1.3 73.3 - - - -
275G ASP* 1.3 96.0 + - - +
290G VAL* 3.8 25.4 - - + -
292G GLN* 4.0 24.9 - - + -
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Residues in contact with ASP 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G PHE* 3.1 34.4 - - - +
246G GLY 5.3 1.6 - - - +
247G THR* 5.1 7.7 + - - +
248G ASP* 4.0 2.8 + - + +
274G PHE* 1.3 94.8 - - - +
276G ASN* 1.3 70.3 + - - +
277G THR* 4.3 17.6 - - + +
290G VAL 2.9 11.4 + - - -
291G VAL* 4.5 0.5 - - - +
292G GLN* 3.1 45.9 + - - +
294G MSE 3.6 12.0 - - - +
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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