Contacts of the strand formed by residues 389 - 395 (chain B) in PDB entry 4FDI
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 THR 389 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B HIS* 4.3 5.9 + - - +
104B ALA* 3.4 17.2 + - + +
385B TYR* 3.3 5.5 - - - -
386B ARG 2.9 36.9 + - - -
387B GLY 3.2 0.8 - - - -
388B ASP* 1.3 97.1 + - - +
390B LEU* 1.3 60.9 + - - +
391B MET* 3.1 17.1 + - - +
403B TRP* 3.4 43.4 - - + +
432B LEU* 5.6 0.5 - - - +
605B GOL 4.6 0.4 - - - +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B PHE* 4.1 11.7 - - + -
384B TYR 3.9 2.2 - - - +
385B TYR* 3.6 31.8 - - + +
388B ASP 4.2 0.6 + - - -
389B THR* 1.3 69.7 - - - +
391B MET* 1.3 63.0 + - - +
392B ALA 3.3 30.7 - - - +
393B ALA* 4.5 5.2 - - + -
402B PHE* 4.0 17.0 - - + +
403B TRP* 3.6 4.7 - - - -
472B VAL* 4.0 18.6 - - + -
475B HIS* 3.8 29.2 - - + -
476B GLN* 4.2 11.2 - - - +
605B GOL 2.7 34.3 + - - +
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Residues in contact with MET 391 (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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104B ALA* 4.0 14.8 - - - -
313B THR* 3.2 31.4 - - + +
384B TYR 2.8 10.2 + - - +
386B ARG* 3.6 31.4 - - + +
389B THR* 3.6 20.2 - - - +
390B LEU* 1.3 74.1 - - - +
392B ALA* 1.3 56.8 + - + +
401B HIS* 3.4 1.9 - - - -
402B PHE 2.7 31.6 + - - -
403B TRP* 3.1 46.7 + - + +
404B THR 4.1 9.2 - - - -
405B TRP* 4.1 11.0 - - + +
432B LEU* 4.1 12.3 - - + -
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Residues in contact with ALA 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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313B THR 4.6 2.2 - - - +
383B PHE* 3.7 0.3 - - - -
384B TYR* 2.8 45.0 + - + -
390B LEU* 3.3 14.2 - - - +
391B MET* 1.3 82.8 - - + +
393B ALA* 1.3 61.4 + - - +
399B LYS* 3.9 19.7 - - - -
400B ALA 3.0 13.9 - - - +
401B HIS* 4.1 12.1 - - + +
402B PHE* 4.3 0.9 - - - -
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Residues in contact with ALA 393 (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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381B PRO* 5.8 1.1 - - + -
382B ILE 3.2 6.7 - - - +
383B PHE* 3.9 14.6 - - + -
384B TYR* 4.1 1.8 - - - -
390B LEU* 4.5 0.4 - - + -
392B ALA* 1.3 77.0 - - - +
394B THR* 1.3 62.2 + - - +
398B HIS 4.0 0.7 - - - +
399B LYS* 3.4 0.6 - - - -
400B ALA* 2.8 31.2 + - - -
402B PHE* 4.2 2.7 - - + -
468B ILE* 3.8 15.8 - - + +
471B VAL* 5.8 1.3 - - + -
472B VAL* 3.7 30.7 - - + -
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Residues in contact with THR 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 4.8 1.1 - - - +
339B LEU* 4.2 17.7 - - + +
380B ARG 4.0 1.6 - - - +
381B PRO* 3.4 7.8 - - - +
382B ILE* 2.8 39.0 + - - -
384B TYR* 2.8 27.9 + - - +
393B ALA* 1.3 72.3 - - - +
395B LEU* 1.3 63.8 + - - +
396B GLY 4.0 15.0 - - - +
398B HIS 3.3 10.8 - - - +
399B LYS* 3.2 20.6 - - - +
444B LEU* 4.0 18.6 - - + +
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Residues in contact with LEU 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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339B LEU* 4.6 0.7 - - - -
379B ASP* 3.9 23.1 - - - +
380B ARG* 3.5 29.6 - - - +
381B PRO* 3.8 8.1 - - + -
393B ALA 4.2 0.8 + - - -
394B THR* 1.3 73.0 - - - +
396B GLY* 1.3 66.9 + - - +
398B HIS* 2.9 18.7 + - - +
467B ARG* 2.8 70.0 + - + +
468B ILE* 3.9 12.4 - - + +
471B VAL* 3.7 28.7 - - + -
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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