Contacts of the strand formed by residues 289 - 295 (chain A) in PDB entry 1RL3
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 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A GLY 4.0 0.8 - - - -
288A ASP* 1.3 89.2 - - - +
290A PHE* 1.3 60.8 + - - +
291A PHE* 2.9 43.2 - - + -
322A PHE 4.6 1.4 - - - +
323A GLY* 4.7 6.7 - - - -
327A LEU* 5.8 4.0 - - - +
347A LYS* 5.1 8.8 - - + +
348A LEU 3.1 12.3 - - - +
349A ASP* 4.8 8.7 - - + +
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Residues in contact with PHE 290 (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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253A ILE* 3.2 29.8 - - + -
254A LEU* 4.9 1.8 - - + -
269A LEU* 6.6 0.2 - - + -
289A GLU* 1.3 71.0 - - - +
291A PHE* 1.3 74.6 + - - +
292A ILE* 3.5 28.5 - - + -
321A TYR* 3.9 5.4 - + + -
322A PHE 3.4 12.3 - - - -
323A GLY* 4.9 3.1 - - - -
324A GLU* 3.4 35.9 - - + -
327A LEU* 6.0 2.2 - - + -
346A VAL 3.7 1.1 - - - +
347A LYS* 3.2 6.8 - - - -
348A LEU* 2.8 57.5 + - + +
353A PHE* 3.6 30.3 - + + +
357A LEU* 4.1 11.9 - - + -
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Residues in contact with PHE 291 (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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272A VAL* 4.1 18.6 - - + -
274A PHE* 3.9 27.1 - + - -
281A VAL* 4.1 24.5 - - + -
289A GLU* 2.9 47.8 - - + -
290A PHE* 1.3 81.0 - - - +
292A ILE* 1.3 74.1 + - - +
321A TYR* 3.3 16.4 - - - +
322A PHE* 3.2 50.8 + + + +
323A GLY* 5.7 0.2 - - - -
345A CYS* 4.3 13.2 - - - -
346A VAL 3.6 3.8 - - - -
347A LYS* 4.3 7.6 - - + -
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE* 3.3 33.7 - - + -
248A LEU* 4.4 8.5 - - + -
251A VAL* 4.3 17.3 - - + -
254A LEU* 4.2 22.9 - - + -
265A VAL* 5.6 1.1 - - + -
269A LEU* 5.2 6.7 - - + -
290A PHE* 3.5 27.8 - - + -
291A PHE* 1.3 87.6 - - - +
293A ILE* 1.3 56.9 + - - +
319A SER* 5.1 0.4 - - - -
320A ASP 3.6 13.5 - - - +
321A TYR* 4.2 4.7 - - + +
322A PHE* 5.7 0.4 - - - -
345A CYS* 2.7 26.8 - - - +
346A VAL* 3.2 27.5 + - + +
348A LEU* 6.2 0.4 - - + -
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Residues in contact with ILE 293 (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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247A PHE* 2.7 33.1 - - - -
292A ILE* 1.3 71.7 - - - +
294A LEU* 1.3 55.3 + - - +
295A GLU 4.8 0.4 - - - +
296A GLY 4.7 6.1 - - - +
316A LEU* 5.8 1.6 - - + -
317A GLY* 3.0 36.8 - - - +
318A PRO* 4.0 1.1 - - + -
319A SER 3.4 7.5 + - - +
320A ASP* 3.2 12.0 + - + +
321A TYR* 4.9 0.4 - - - +
322A PHE* 5.4 8.4 - - + -
343A LEU* 6.6 0.4 - - + -
344A LYS 3.7 2.0 - - - +
345A CYS* 3.6 8.1 - - + -
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Residues in contact with LEU 294 (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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244A TYR* 5.7 7.2 - - + -
247A PHE* 4.1 18.2 - - + -
292A ILE 3.6 0.4 + - - +
293A ILE* 1.3 73.9 - - - +
295A GLU* 1.3 76.4 + - - +
318A PRO* 4.5 10.0 - - - +
344A LYS* 2.5 28.6 + - + +
345A CYS* 3.8 9.2 - - - +
346A VAL* 5.1 2.0 - - + +
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Residues in contact with GLU 295 (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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293A ILE 3.8 0.4 - - - -
294A LEU* 1.3 88.4 - - - +
296A GLY* 1.3 58.7 + - - +
318A PRO* 4.0 10.9 - - + +
342A PRO 2.8 17.5 - - - +
344A LYS* 2.9 27.2 + - + +
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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