Contacts of the strand formed by residues 412 - 418 (chain B) in PDB entry 3IJE
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 412 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361B ASP 5.9 2.0 - - - +
363B PRO* 4.2 33.5 - - + +
364B GLU* 5.7 2.8 + - - +
408B GLN* 3.4 33.6 - - + +
410B LYS* 3.4 13.9 + - + +
411B GLU* 1.3 78.9 - - - +
413B SER* 1.3 56.1 + - - +
429B VAL* 2.6 49.8 + - + +
431B PHE* 5.1 4.3 - - + -
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Residues in contact with SER 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ASP* 3.9 14.8 - - - +
363B PRO* 5.6 0.2 - - - -
411B GLU* 3.0 19.3 + - - -
412B LYS* 1.3 75.0 - - - +
414B PHE* 1.3 63.7 + - - +
426B ILE* 4.7 10.8 - - - -
427B VAL 3.6 6.3 - - - -
428B GLN* 3.6 17.0 - - - +
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Residues in contact with PHE 414 (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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90B LEU* 5.5 0.2 - - + -
100B PHE* 5.4 2.2 - + - -
359B VAL* 4.2 11.7 - - + -
360B ARG 3.2 8.7 - - - +
361B ASP* 3.2 26.9 - - - +
362B LEU* 4.3 1.1 - - - -
363B PRO* 3.7 17.0 - - + -
366B LEU* 3.9 15.3 - - + -
368B LEU* 4.2 20.0 - - + -
401B ALA* 5.6 2.7 - - + -
413B SER* 1.3 71.8 - - - +
415B THR* 1.3 68.9 + - - +
416B ILE* 3.7 26.2 - - + -
426B ILE* 3.6 4.6 - - - +
427B VAL* 2.7 73.8 + - + -
429B VAL* 3.4 17.5 - - + -
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Residues in contact with THR 415 (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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358B GLU 3.7 0.7 - - - +
359B VAL* 3.4 5.9 - - - +
360B ARG* 3.0 56.7 + - + +
361B ASP* 4.3 5.8 - - - +
414B PHE* 1.3 80.1 - - - +
416B ILE* 1.3 65.6 + - - +
417B LYS* 4.2 10.6 + - - +
424B SER* 4.0 15.3 - - - -
425B LEU 3.4 8.5 + - - -
426B ILE* 4.6 12.3 - - - -
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Residues in contact with ILE 416 (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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100B PHE* 4.0 14.6 - - + -
102B ILE* 4.0 8.1 - - + +
357B LEU* 4.0 24.2 - - + -
358B GLU 3.2 11.4 - - - +
359B VAL* 4.8 4.5 - - + -
368B LEU* 3.9 22.0 - - + -
370B PHE* 4.6 6.5 - - + -
399B ILE* 3.4 33.9 - - + -
414B PHE* 3.7 22.0 - - + -
415B THR* 1.3 71.7 - - - +
417B LYS* 1.3 62.5 + - - +
425B LEU* 2.8 43.9 + - + +
427B VAL* 4.4 4.3 - - + -
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Residues in contact with LYS 417 (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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102B ILE* 5.5 0.2 - - - -
303B ASN* 3.4 15.1 - - - +
357B LEU* 3.3 7.2 - - - -
358B GLU* 2.5 53.8 + - + +
360B ARG* 3.1 39.9 - - + +
415B THR* 4.2 9.2 - - - +
416B ILE* 1.3 74.7 - - - +
418B PRO* 1.3 88.9 + - + +
420B GLY 3.9 0.6 - - - +
421B PHE 2.8 29.7 + - - -
422B LYS 4.4 3.4 - - - +
423B ASP 3.5 11.0 - - - +
424B SER* 3.5 16.6 - - - +
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Residues in contact with PRO 418 (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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83B VAL* 4.0 11.4 - - + -
104B VAL* 3.6 23.1 - - + -
355B VAL* 4.2 9.9 - - + -
356B GLU 3.3 9.9 - - - +
357B LEU* 3.4 12.3 - - + -
417B LYS* 1.3 106.9 + - + +
419B VAL* 1.3 66.9 - - - +
421B PHE* 3.2 39.7 + - + +
423B ASP 3.6 13.9 - - - +
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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