Contacts of the helix formed by residues 393 - 404 (chain G) in PDB entry 5JLH
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 ASP 393 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377G ASN 4.6 6.8 - - - +
379G ALA* 3.5 21.8 + - - +
381G LYS* 5.9 0.8 - - - +
391G MET* 3.3 27.1 - - - +
392G PRO* 1.3 76.2 - - + +
394G ASN* 1.3 63.7 + - - +
395G THR* 3.6 20.8 + - + +
396G ALA* 4.2 12.4 + - - +
397G ALA 4.8 0.2 + - - -
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Residues in contact with ASN 394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391G MET* 4.4 11.9 + - + -
392G PRO 3.7 4.2 + - - +
393G ASP* 1.3 72.0 - - - +
395G THR* 1.3 64.0 + - - +
396G ALA 3.2 1.3 - - - -
397G ALA 3.6 1.4 + - - -
398G GLN* 2.7 50.5 + - - +
408G VAL* 4.8 13.0 - - + +
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Residues in contact with THR 395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393G ASP* 4.0 21.3 - - + +
394G ASN* 1.3 85.4 + - - +
396G ALA* 1.3 77.4 + - + +
398G GLN* 3.3 6.9 - - - +
399G LYS* 2.9 23.8 + - - +
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Residues in contact with ALA 396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374G GLN* 4.7 6.1 - - - +
377G ASN* 3.8 42.0 - - + +
378G ILE* 4.1 7.0 - - + +
391G MET* 6.0 0.4 - - - -
393G ASP* 4.2 12.4 + - - +
394G ASN 3.2 0.8 - - - -
395G THR* 1.3 83.3 - - + +
397G ALA* 1.3 57.5 + - - +
399G LYS* 2.7 37.3 + - - +
400G LEU* 2.9 6.3 + - - +
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Residues in contact with ALA 397 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378G ILE* 4.4 6.2 - - + +
391G MET* 3.5 37.3 - - + -
394G ASN 3.6 2.1 + - - +
396G ALA* 1.3 79.0 - - - +
398G GLN* 1.3 56.8 + - - +
400G LEU* 3.2 12.2 + - + +
401G CYS* 2.9 34.9 + - - -
408G VAL* 4.8 4.7 - - + -
411G PHE* 4.1 23.3 - - + -
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Residues in contact with GLN 398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394G ASN* 2.7 37.4 + - - +
395G THR* 3.3 9.2 - - - +
397G ALA* 1.3 71.2 - - - +
399G LYS* 1.3 58.9 + - - +
401G CYS* 3.2 13.0 + - - +
402G ARG* 2.9 42.3 + - + +
408G VAL* 3.7 28.5 - - - +
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Residues in contact with LYS 399 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319G LEU 4.8 0.9 - - - +
320G LEU* 2.9 56.6 + - + +
322G GLU* 4.0 24.4 + - - +
374G GLN* 3.2 36.0 - - + +
377G ASN* 5.1 3.1 - - - +
395G THR* 2.9 12.4 + - - +
396G ALA* 2.7 21.6 + - - +
398G GLN* 1.3 72.3 - - - +
400G LEU* 1.3 54.1 + - - +
402G ARG* 3.1 12.9 + - - +
403G LEU* 2.9 30.1 + - + +
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Residues in contact with LEU 400 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371G ALA* 4.5 17.0 - - + +
374G GLN* 5.0 13.8 + - + +
375G PHE* 4.5 28.3 - - + -
378G ILE* 5.9 5.2 - - + -
396G ALA 2.9 6.5 + - - +
397G ALA* 3.3 17.3 - - + +
399G LYS* 1.3 78.2 - - - +
401G CYS* 1.3 58.5 + - - +
403G LEU* 2.9 8.9 + - + +
404G LEU* 2.8 52.8 + - + +
406G LEU* 5.1 4.3 - - + -
411G PHE* 3.8 40.4 - - + -
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Residues in contact with CYS 401 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397G ALA 2.9 22.7 + - - -
398G GLN* 3.4 17.0 - - - +
400G LEU* 1.3 75.0 - - - +
402G ARG* 1.3 57.5 + - - +
404G LEU 2.5 26.8 - - - +
405G GLY 4.3 0.3 - - - -
406G LEU* 3.0 37.7 + - - +
407G GLY 3.8 2.7 - - - -
408G VAL* 3.3 35.9 - - - +
411G PHE* 4.6 10.1 - - - -
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Residues in contact with ARG 402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318G ASP 5.2 1.4 + - - -
320G LEU* 3.4 40.6 - - - +
367G ARG* 5.9 0.7 - - - -
398G GLN* 2.9 34.3 + - - +
399G LYS* 3.3 13.9 - - + +
401G CYS* 1.3 75.7 - - - +
403G LEU* 1.3 62.0 - - - +
404G LEU 3.2 6.3 + - - +
631G ASP* 4.9 2.9 - - - +
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Residues in contact with LEU 403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318G ASP 5.2 2.0 - - - +
319G LEU* 4.5 14.1 - - - +
367G ARG* 3.3 70.1 - - + +
370G SER* 3.7 13.9 - - - +
371G ALA* 3.5 27.1 - - + +
374G GLN* 3.8 13.0 - - + +
399G LYS* 2.9 13.0 + - + +
400G LEU* 2.9 13.1 + - - +
402G ARG* 1.3 75.6 - - - +
404G LEU* 1.3 68.7 + - + +
631G ASP* 4.0 8.8 - - - +
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Residues in contact with LEU 404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368G MET* 5.3 8.7 - - + -
371G ALA* 4.8 14.1 - - + -
375G PHE* 5.2 8.1 - - + -
400G LEU* 2.8 34.4 + - + +
401G CYS 2.5 23.3 - - - +
402G ARG 3.4 7.1 - - - +
403G LEU* 1.3 89.2 - - + +
405G GLY* 1.3 57.1 + - - +
406G LEU* 4.1 15.5 - - + +
626G LEU* 3.8 25.4 - - + -
629G SER* 5.2 0.2 - - - +
630G THR* 4.6 2.1 - - - +
631G ASP* 4.1 12.7 - - - +
634G THR* 3.8 32.1 - - + +
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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