Contacts of the strand formed by residues 290 - 297 (chain B) in PDB entry 4X41
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 PHE 290 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B PHE* 4.0 6.3 - + - -
221B LEU* 4.7 5.4 - - + -
275B ILE* 3.4 20.9 - - + -
276B LYS* 3.7 48.7 - - + +
288B LEU 3.2 18.2 - - - -
289B SER* 1.3 75.2 - - - +
291B THR* 1.3 76.7 + - - +
292B SER* 3.6 13.9 - - - +
358B ILE* 4.7 16.6 - - + -
359B SER* 3.4 1.1 - - - -
360B MET* 3.0 72.4 + - + +
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Residues in contact with THR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B PHE* 1.3 85.2 + - - +
292B SER* 1.3 71.1 + - - +
357B THR* 5.3 9.4 - - - +
358B ILE 3.3 12.8 - - - +
359B SER* 3.2 14.3 - - - -
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Residues in contact with SER 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU 5.0 0.9 - - - -
275B ILE* 2.5 45.1 + - - -
276B LYS* 5.2 1.0 - - - +
290B PHE* 3.6 7.0 - - - +
291B THR* 1.3 80.4 + - - +
293B ALA* 1.3 62.3 + - - +
294B PHE* 4.2 0.9 - - - -
356B GLY 4.1 0.2 - - - +
357B THR* 3.2 4.8 - - - -
358B ILE* 2.7 46.1 + - - +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B CYS* 4.9 1.9 - - - -
274B LEU 4.7 5.9 - - - +
292B SER* 1.3 75.4 - - - +
294B PHE* 1.3 62.3 + - - +
295B CYS* 5.6 1.3 - - - -
356B GLY 3.2 8.5 - - - +
357B THR* 4.1 13.7 - - + +
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B VAL* 4.0 13.9 - - + -
273B CYS* 3.6 26.2 - - + -
274B LEU 4.5 4.5 - - - +
275B ILE* 3.8 15.5 - - + -
292B SER 4.2 4.0 - - - -
293B ALA* 1.3 77.1 - - - +
295B CYS* 1.3 69.9 + - - +
296B LEU* 3.7 31.0 - - + -
307B LEU* 4.4 9.9 - - + -
354B ILE 4.5 1.8 - - - -
355B TYR* 3.6 1.9 - - - +
356B GLY* 2.6 65.3 + - - +
357B THR 4.2 1.3 - - - -
358B ILE* 3.8 27.4 - - + -
374B VAL* 5.0 2.2 - - + -
376B LEU* 3.7 22.7 - - + -
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Residues in contact with CYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B ASN* 4.1 10.4 + - - -
273B CYS* 4.0 11.3 - - - +
293B ALA* 5.6 1.3 - - - -
294B PHE* 1.3 80.3 - - - +
296B LEU* 1.3 65.5 + - - +
297B GLN* 3.7 2.4 + - - +
353B GLU* 3.7 17.8 - - - +
354B ILE 3.6 5.2 - - - -
355B TYR* 3.5 28.7 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B VAL* 3.9 11.2 - - + +
224B VAL* 4.1 6.5 - - - -
225B ALA* 3.8 18.2 - - + +
270B THR* 3.7 25.8 - - + +
271B ASN* 3.2 21.5 - - - +
273B CYS* 3.6 27.6 - - + -
294B PHE* 3.7 28.0 - - + -
295B CYS* 1.3 71.2 - - - +
297B GLN* 1.3 60.5 - - - +
298B ILE 3.7 1.9 + - - -
307B LEU* 4.3 9.9 - - + -
352B GLU 3.7 0.2 - - - +
353B GLU* 3.8 2.8 - - - -
354B ILE* 3.0 48.0 + - + +
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B THR* 3.3 15.2 - - - -
271B ASN* 2.6 31.0 + - - +
295B CYS 3.7 2.4 + - - -
296B LEU* 1.3 70.7 - - - +
298B ILE* 1.3 73.5 + - - +
299B GLN* 3.6 16.8 + - + +
350B ARG* 5.6 5.9 - - - +
351B GLY* 4.6 14.1 - - - +
352B GLU 3.6 7.9 - - - +
353B GLU* 3.6 20.3 + - - +
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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