Contacts of the strand formed by residues 288 - 295 (chain A) in PDB entry 4Y5U
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 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A THR* 1.3 83.8 - - - +
289A PHE* 1.3 64.7 + - - +
290A GLN* 5.3 3.4 - - - +
361A LYS 4.9 0.9 - - - +
362A ASN* 3.6 38.1 - - + +
363A LEU 3.1 10.5 - - - +
364A LEU* 4.5 13.0 - - + +
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Residues in contact with PHE 289 (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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279A PRO* 4.3 11.7 - - + -
280A PRO* 3.7 31.4 - - + -
283A LEU* 3.7 35.2 - - + -
287A THR 3.5 17.5 - - - -
288A LYS* 1.3 75.0 - - - +
290A GLN* 1.3 68.1 + - - +
315A MET* 5.5 0.4 - - + -
340A ILE* 4.2 15.7 - - + -
360A PHE 4.0 0.3 - - - +
361A LYS 4.1 1.8 - - - -
362A ASN* 3.6 2.3 - - - -
363A LEU* 2.8 73.1 + - + +
365A LEU* 3.9 20.6 - - + -
386A VAL* 4.9 8.5 - - + -
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Residues in contact with GLN 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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277A LYS* 4.1 24.1 - - + -
278A GLN 3.8 4.7 - - - +
279A PRO* 3.6 18.4 - - - +
280A PRO* 4.0 4.3 - - - +
288A LYS* 5.3 5.0 - - - +
289A PHE* 1.3 80.4 - - - +
291A ALA* 1.3 61.8 + - - +
360A PHE 3.3 7.5 - - - +
361A LYS* 1.4 57.1 + - - +
362A ASN* 4.0 6.3 + - - +
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Residues in contact with ALA 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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277A LYS* 3.4 17.7 - - - +
279A PRO* 3.8 16.4 - - + -
289A PHE 4.3 0.2 - - - -
290A GLN* 1.3 75.6 - - - +
292A GLY* 1.3 59.0 + - - +
359A LEU* 3.8 1.1 - - - +
360A PHE* 2.9 35.1 + - - +
363A LEU* 4.3 12.3 - - + +
388A PHE* 3.7 29.6 - - + -
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Residues in contact with GLY 292 (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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275A VAL* 3.3 6.9 - - - +
276A GLU* 2.9 24.1 + - - -
277A LYS* 2.9 29.7 + - - +
291A ALA* 1.3 75.5 - - - +
293A VAL* 1.3 65.8 + - - -
358A ALA 3.5 7.9 - - - -
359A LEU* 4.4 11.0 - - - -
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Residues in contact with VAL 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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273A PHE* 4.1 24.7 - - + -
274A LEU 3.1 13.9 - - - +
275A VAL* 4.2 5.8 - - + -
276A GLU* 4.7 1.7 - - - +
292A GLY* 1.3 78.0 - - - +
294A ARG* 1.3 62.5 + - - +
311A VAL* 4.4 4.9 - - + -
347A LEU* 4.6 0.8 - - + +
357A SER* 3.3 4.5 - - - -
358A ALA* 2.8 57.3 + - + +
359A LEU* 4.9 0.2 - - - +
360A PHE* 4.3 6.3 - - + -
388A PHE* 3.5 42.8 - - + -
405A ALA* 4.7 1.6 - - + -
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Residues in contact with ARG 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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220A SER* 5.1 1.2 + - - -
221A LEU* 3.5 35.6 - - + +
222A ALA* 3.9 14.6 - - - +
225A GLN* 2.8 36.0 + - - +
272A CYS 3.4 4.5 - - - +
273A PHE* 3.7 5.8 - - - -
274A LEU* 2.8 32.4 + - + +
276A GLU* 3.5 37.4 + - + +
293A VAL* 1.3 75.5 - - - +
295A PHE* 1.3 63.2 + - - +
296A LEU* 3.8 20.3 - - + +
347A LEU* 5.2 0.2 - - - -
354A ASN 3.9 3.0 + - - -
355A CYS* 3.7 24.6 - - - +
356A CYS 3.5 15.7 - - - +
357A SER* 4.3 2.9 - - - -
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Residues in contact with PHE 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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225A GLN* 4.4 2.1 - - - +
269A VAL* 3.7 38.1 - - + -
272A CYS* 3.7 17.7 - - + -
273A PHE* 4.2 4.9 - + + -
294A ARG* 1.3 73.6 - - - +
296A LEU* 1.3 65.6 + - - +
297A LEU* 3.3 18.1 + - + -
298A GLY* 3.2 37.2 + - - -
301A PHE* 4.9 4.0 - + + -
302A LEU* 4.1 20.2 - - + -
347A LEU* 4.0 20.1 - - + +
356A CYS* 2.8 30.3 + - - +
392A PHE* 4.0 20.6 - + - -
403A LEU* 3.9 17.5 - - + -
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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