Contacts of the strand formed by residues 390 - 396 (chain B) in PDB entry 4IF8
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 TYR 390 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B PHE* 3.6 24.2 - + - -
272B PHE* 3.9 25.8 - + + -
273B ILE 3.8 12.1 - - - +
274B LEU* 4.0 14.6 - - + -
275B PRO* 4.3 2.7 - - - -
280B LEU* 5.1 2.0 - - - -
309B PRO* 3.7 18.1 + - + +
311B LEU* 3.5 24.6 - - + +
360B MET* 4.5 0.9 - - - +
386B ILE* 3.4 20.9 - - + -
388B LYS 3.4 14.1 - - - +
389B PRO* 1.3 73.6 - - - +
391B LEU* 1.3 75.3 + - - +
392B LEU* 4.5 5.6 - - + -
407B LYS* 3.5 3.5 - - - +
408B ILE* 2.7 68.4 + - + +
411B PRO* 4.4 0.2 - - - +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 6.3 0.7 - - + -
60B LEU* 4.2 23.1 - - + -
271B ILE 3.7 0.3 - - - +
272B PHE* 3.7 3.8 - - - -
273B ILE* 2.9 53.9 + - + +
280B LEU* 4.4 10.3 - - + -
283B LEU* 3.8 35.4 - - + -
284B GLU* 4.8 8.1 - - + +
287B LEU* 4.4 16.6 - - + -
295B TRP* 5.5 0.7 - - + -
390B TYR* 1.3 78.3 - - - +
392B LEU* 1.3 61.4 + - - +
405B LEU* 5.7 4.5 - - + -
406B GLY 3.2 4.7 - - - +
407B LYS* 3.8 33.7 - - + -
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Residues in contact with LEU 392 (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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73B PHE* 4.3 18.1 - - + -
270B ALA* 4.3 1.3 - - + -
271B ILE 3.5 9.9 - - - +
272B PHE* 3.7 35.4 - - + -
273B ILE* 4.9 0.2 - - - -
311B LEU* 3.8 27.4 - - + -
358B LEU* 4.9 4.3 - - + -
360B MET* 4.5 8.3 - - + -
390B TYR* 4.2 9.4 + - + -
391B LEU* 1.3 74.4 - - - +
393B LEU* 1.3 65.1 + - - +
394B ILE* 4.0 28.9 - - + -
404B PHE 4.0 0.5 - - - +
405B LEU* 3.4 7.5 - - - +
406B GLY* 2.7 42.6 + - - +
408B ILE* 4.7 6.1 - - + -
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Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B MET* 4.2 16.2 - - + -
57B PHE* 4.1 21.5 - - + -
269B THR 3.4 2.9 - - - +
270B ALA* 3.6 0.3 - - - -
271B ILE* 2.7 56.3 + - + +
273B ILE* 4.3 6.3 - - + -
292B PHE* 4.5 10.5 - - + -
295B TRP* 4.6 12.3 - - + -
392B LEU* 1.3 75.0 - - - +
394B ILE* 1.3 66.4 + - - +
395B TYR* 3.8 23.2 + - + -
402B VAL* 3.8 22.0 - - + -
404B PHE 3.5 2.5 - - - +
405B LEU* 3.9 21.8 - - + -
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Residues in contact with ILE 394 (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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210B PHE* 4.0 18.8 - - + -
264B TYR* 3.7 22.0 - - + +
268B ILE* 3.7 25.1 - - + -
269B THR 3.3 3.1 - - - +
270B ALA* 3.8 21.5 - - + -
358B LEU* 3.7 20.6 - - + -
360B MET* 5.5 0.7 - - - -
392B LEU* 4.0 25.4 - - + -
393B LEU* 1.3 71.3 - - - +
395B TYR* 1.3 57.5 + - - +
402B VAL* 3.7 2.3 - - - -
403B LEU* 2.9 35.3 + - + -
404B PHE* 2.9 30.8 + - + +
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Residues in contact with TYR 395 (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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49B ALA* 4.6 8.2 - - + +
53B MET* 4.2 19.1 - - + -
268B ILE* 3.3 5.1 - - - -
269B THR* 2.8 38.1 + - - -
271B ILE* 4.1 13.9 - - + -
292B PHE* 3.9 24.5 - + - -
296B LYS* 4.1 5.4 + - - -
393B LEU* 3.8 12.5 + - + -
394B ILE* 1.3 74.1 - - - +
396B SER* 1.4 72.5 + - - +
397B GLU* 3.3 32.8 + - - -
400B PRO* 3.8 18.4 - - - +
401B SER 3.4 26.7 - - - -
402B VAL* 4.1 11.9 - - + -
403B LEU* 5.0 0.2 - - - -
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Residues in contact with SER 396 (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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123B LEU* 3.9 16.4 - - - +
267B ASN 3.5 5.8 - - - -
268B ILE* 3.8 20.4 - - - +
395B TYR* 1.4 85.8 - - - +
397B GLU* 1.3 58.8 - - - +
399B ILE 2.5 26.6 + - - -
400B PRO* 3.5 13.2 - - - +
401B SER* 3.0 26.6 + - - -
403B LEU* 4.0 8.3 - - - +
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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