Contacts of the helix formed by residues 394 - 404 (chain B) in PDB entry 5KJH
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 394 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385B LEU* 3.9 9.2 - - - -
390B ILE 5.5 1.3 - - - +
391B GLU 5.7 3.6 - - - -
393B CYS* 1.3 79.7 - - - +
395B LYS* 1.3 63.7 + - - +
396B SER* 3.8 8.2 + - - -
397B ASN* 3.2 33.3 + - - +
398B LEU* 3.0 22.5 + - - +
400B ARG* 4.7 0.9 + - - -
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Residues in contact with LYS 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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305A PRO* 3.6 18.8 - - - +
378B ALA* 4.8 4.8 + - - +
381B LEU* 3.8 22.7 - - + -
382B GLU* 2.8 42.9 + - + +
385B LEU* 3.7 14.7 - - + +
394B THR* 1.3 72.6 - - - +
396B SER* 1.3 51.0 + - - +
398B LEU* 3.0 8.8 + - - +
399B ILE* 2.8 45.1 + - + +
462B ILE* 5.9 2.4 - - - +
463B LEU* 3.9 18.4 - - + -
466B ASP* 2.8 37.8 + - - +
467B LYS* 5.6 0.8 - - - +
468B ASN* 5.5 3.4 - - - +
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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
----------------------------------------------------------
394B THR* 3.3 6.8 - - - -
395B LYS* 1.3 76.1 - - - +
397B ASN* 1.3 57.1 + - - +
399B ILE* 3.4 5.0 + - - +
400B ARG* 2.9 54.6 + - - +
424B TYR* 3.6 26.1 + - - -
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Residues in contact with ASN 397 (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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391B GLU 5.1 6.5 + - - -
393B CYS* 4.9 7.3 - - - +
394B THR* 3.2 35.6 + - - +
396B SER* 1.3 77.6 - - - +
398B LEU* 1.4 58.3 + - - +
400B ARG* 2.9 25.9 + - - +
401B PHE* 3.0 24.9 + - - +
427B ASP 3.2 13.6 + - - +
435B ARG* 3.1 23.0 + - - +
437B ALA* 3.9 10.4 - - + +
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LEU* 4.5 5.4 - - + -
385B LEU* 3.9 22.9 - - + -
393B CYS* 4.8 3.1 - - - -
394B THR 3.0 21.3 + - - +
395B LYS* 3.0 8.5 + - - +
397B ASN* 1.4 74.0 - - - +
399B ILE* 1.4 57.9 + - - +
401B PHE* 3.7 6.3 + - - +
402B MET* 3.2 21.0 + - - +
437B ALA* 3.5 38.1 - - + +
440B PHE* 3.7 37.0 - - + -
441B THR* 3.7 10.1 + - - +
459B LEU* 3.9 7.2 - - + -
463B LEU* 3.4 23.9 - - + +
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Residues in contact with ILE 399 (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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395B LYS* 2.8 38.1 + - + +
396B SER* 3.7 4.7 - - - +
398B LEU* 1.4 72.6 - - - +
400B ARG* 1.4 61.0 + - - +
402B MET* 3.3 10.4 + - + +
403B ALA* 3.0 27.5 + - - +
420B LEU* 3.8 19.5 - - + -
424B TYR* 3.5 39.9 - - + +
463B LEU* 4.0 18.4 - - + -
466B ASP* 4.3 9.0 - - - +
468B ASN* 5.2 0.4 - - + +
469B VAL* 3.5 31.4 - - + -
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Residues in contact with ARG 400 (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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394B THR* 4.7 0.8 + - - -
396B SER* 2.9 37.4 + - - +
397B ASN* 2.9 30.3 + - - +
399B ILE* 1.4 76.5 - - - +
401B PHE* 1.4 58.7 + - - +
403B ALA* 3.3 8.0 + - - +
404B SER* 2.9 30.5 + - - +
421B LEU* 4.4 1.1 - - - +
424B TYR* 2.8 50.7 + - + -
425B SER* 3.4 28.2 + - - +
426B ASP* 3.6 20.2 - - - +
427B ASP 3.3 14.6 + - - -
435B ARG* 3.5 15.3 - - - +
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Residues in contact with PHE 401 (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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397B ASN 3.0 16.9 + - - +
398B LEU* 3.8 5.8 - - - +
399B ILE 3.3 0.2 - - - -
400B ARG* 1.4 73.1 - - - +
402B MET* 1.3 66.8 + - - +
404B SER* 3.2 27.5 + - - +
405B GLN* 3.4 36.6 - - + +
435B ARG* 4.1 18.3 - - + +
437B ALA* 3.8 15.5 - - + -
438B SER* 3.6 40.8 - - - -
441B THR* 3.7 32.3 - - + -
442B GLU* 5.4 2.9 - - - -
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Residues in contact with MET 402 (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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398B LEU 3.2 17.2 + - - +
399B ILE* 3.3 14.1 + - + +
401B PHE* 1.3 77.6 - - - +
403B ALA* 1.4 61.9 + - - +
405B GLN* 3.1 12.8 + - - +
417B LYS* 4.2 1.7 - - - -
420B LEU* 3.9 27.8 - - + -
460B ARG* 2.9 63.6 + - + +
463B LEU* 3.9 32.8 - - + -
464B MET* 4.1 23.6 - - - +
469B VAL* 4.5 6.1 - - + -
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Residues in contact with ALA 403 (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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399B ILE 3.0 16.8 + - - +
400B ARG* 3.3 8.0 + - - +
402B MET* 1.4 76.0 - - - +
404B SER* 1.4 55.7 + - - +
405B GLN 3.3 3.2 + - - -
417B LYS* 3.4 33.9 - - + +
420B LEU* 3.9 25.4 - - + -
421B LEU* 3.9 30.2 - - + +
424B TYR* 6.5 0.4 - - + -
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Residues in contact with SER 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ARG* 2.9 18.5 + - - +
401B PHE* 3.2 15.6 + - - +
403B ALA* 1.4 73.0 - - - +
405B GLN* 1.4 64.3 + - - +
421B LEU* 4.0 14.8 - - - +
426B ASP* 4.0 9.0 + - - -
435B ARG* 5.1 5.2 + - - -
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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