Contacts of the helix formed by residues 393 - 409 (chain G) in PDB entry 5X8Q
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 CYS 393 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317G TRP* 3.9 11.7 - - + -
388G PHE 5.2 1.2 + - - -
391G LEU* 3.1 17.7 - - + +
392G GLY* 1.4 85.1 - - - +
394G SER* 1.3 64.7 + - - +
395G GLU* 3.3 20.6 - - - +
396G LEU* 3.2 14.8 + - + -
397G ILE* 3.2 25.9 + - + +
479G HIS* 3.6 31.4 - - - -
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Residues in contact with SER 394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385G MET* 5.3 0.7 - - - +
388G PHE 6.0 0.9 - - - -
389G ARG* 6.4 2.7 - - - +
392G GLY* 3.7 2.3 - - - -
393G CYS* 1.3 75.6 - - - +
395G GLU* 1.3 65.2 + - - +
397G ILE* 3.3 7.1 + - - +
398G SER* 2.9 32.5 + - - -
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Residues in contact with GLU 395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392G GLY 4.5 2.4 - - - +
393G CYS* 3.4 17.8 - - - +
394G SER* 1.3 94.7 + - - +
396G LEU* 1.3 74.0 + - - +
398G SER* 3.8 5.9 - - - -
399G SER* 2.9 31.5 + - - -
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Residues in contact with LEU 396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G TRP* 4.7 1.3 - - + -
393G CYS* 3.2 16.7 + - + +
395G GLU* 1.3 88.8 - - + +
397G ILE* 1.3 60.9 + - + +
399G SER* 3.0 5.2 + - - -
400G ILE* 2.8 55.4 + - + +
472G LEU* 4.5 11.0 - - + +
475G LEU* 4.1 35.2 - - + -
476G CYS* 4.5 6.7 - - - -
479G HIS* 3.5 35.9 - - + +
9000G 82R 4.6 14.1 - - + -
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Residues in contact with ILE 397 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G TRP* 6.0 0.2 - - + -
385G MET* 4.1 17.5 - - + +
388G PHE* 4.0 28.5 - - + +
391G LEU* 3.8 20.2 - - + -
393G CYS* 3.2 18.5 + - + +
394G SER* 3.3 8.5 + - - +
396G LEU* 1.3 76.6 - - + +
398G SER* 1.3 57.3 + - - +
400G ILE* 3.3 4.9 + - - +
401G PHE* 2.9 55.7 + - + -
9000G 82R 3.6 38.6 - - + -
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Residues in contact with SER 398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385G MET* 3.7 26.2 - - - +
394G SER 2.9 18.0 + - - -
395G GLU* 3.8 7.9 - - - -
397G ILE* 1.3 76.7 - - - +
399G SER* 1.3 58.7 + - - +
401G PHE* 3.3 3.1 + - - +
402G ASP* 2.9 40.1 + - - +
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Residues in contact with SER 399 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395G GLU 2.9 19.1 + - - -
396G LEU* 3.0 8.5 + - - -
398G SER* 1.3 75.1 - - - +
400G ILE* 1.3 61.4 + - - +
402G ASP* 3.3 11.1 + - - +
403G PHE* 2.9 29.6 + - - +
471G LYS* 5.0 5.7 + - - -
472G LEU* 3.7 25.4 - - - +
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Residues in contact with ILE 400 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362G LEU* 4.3 12.8 - - + -
365G MET* 3.4 38.6 - - + -
396G LEU* 2.8 46.7 + - + +
397G ILE* 3.6 6.5 - - + +
399G SER* 1.3 74.3 - - - +
401G PHE* 1.3 57.9 + - + +
403G PHE* 3.4 3.9 + - + +
404G SER* 2.9 27.4 + - - +
472G LEU* 4.2 16.8 - - + -
476G CYS* 3.9 11.7 - - - -
9000G 82R 3.7 35.0 - - + -
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Residues in contact with PHE 401 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G MET* 5.2 6.5 - - + -
369G TYR* 3.7 28.0 + + - +
374G ARG* 3.5 26.9 - - + -
375G THR* 4.4 1.8 - - - -
376G VAL* 3.6 30.3 - - + -
383G GLY 4.3 2.0 - - - -
384G GLY 3.9 4.9 - - - -
385G MET* 3.7 41.1 - - + -
388G PHE* 4.3 7.0 - + - -
397G ILE* 2.9 42.2 + - + +
398G SER* 3.5 6.1 - - - +
399G SER 3.3 0.2 - - - -
400G ILE* 1.3 80.3 - - + +
402G ASP* 1.3 56.2 + - - +
404G SER* 3.3 6.1 + - - -
405G HIS* 2.8 34.8 + - - +
9000G 82R 5.8 1.3 - - + -
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Residues in contact with ASP 402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374G ARG* 5.5 4.3 + - - -
398G SER* 2.9 30.3 + - - +
399G SER* 3.3 12.2 + - - +
401G PHE* 1.3 72.0 - - - +
403G PHE* 1.3 61.5 + - - +
405G HIS* 3.1 7.8 + - - +
406G SER* 2.8 36.0 + - - +
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Residues in contact with PHE 403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362G LEU* 3.2 42.6 - - + -
363G VAL* 4.3 8.7 - - + -
365G MET* 6.4 0.4 - - - -
399G SER 2.9 17.7 + - - +
400G ILE* 3.5 7.0 - - + +
402G ASP* 1.3 76.7 - - - +
404G SER* 1.3 62.6 + - - +
406G SER* 3.3 6.2 + - - -
407G LEU* 2.8 52.4 + - + +
467G PRO* 3.6 36.0 - - + +
468G PRO 4.0 9.2 - - - -
469G ALA* 3.5 32.1 - - + -
472G LEU* 3.6 19.3 - - + -
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Residues in contact with SER 404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362G LEU 4.7 0.2 + - - -
365G MET* 3.7 29.7 - - - +
366G CYS* 3.8 19.5 + - - +
369G TYR* 3.9 28.9 - - - +
400G ILE 2.9 19.2 + - - -
401G PHE* 3.7 5.6 - - - -
403G PHE* 1.3 81.1 - - - +
405G HIS* 1.3 58.0 + - - +
407G LEU* 3.9 1.0 - - - +
408G SER* 2.9 30.1 + - - -
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Residues in contact with HIS 405 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369G TYR* 2.8 29.0 + - - +
371G ALA* 3.3 32.6 - - + +
374G ARG* 3.3 38.8 + - - +
401G PHE 2.8 20.9 + - - +
402G ASP* 3.1 8.5 + - - +
404G SER* 1.3 74.2 - - - +
406G SER* 1.3 59.9 + - - +
408G SER* 3.4 3.8 + - - -
409G ALA* 3.2 22.2 + - + +
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Residues in contact with SER 406 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402G ASP* 2.8 21.4 + - - +
403G PHE* 3.7 4.6 - - - -
405G HIS* 1.3 71.2 - - - +
407G LEU* 1.3 64.0 + - - +
409G ALA* 3.3 19.5 + - - +
410G LEU* 3.5 13.3 - - - +
467G PRO* 3.8 25.7 - - - +
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Residues in contact with LEU 407 (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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363G VAL* 3.9 34.5 - - + +
366G CYS* 3.9 24.2 - - + -
403G PHE* 2.8 50.6 + - + +
404G SER* 4.5 0.2 - - - -
406G SER* 1.3 72.0 - - - +
408G SER* 1.3 63.0 + - - +
410G LEU* 3.1 26.1 + - + +
411G HIS 3.8 2.9 + - - -
412G PHE* 4.3 14.9 + - + +
417G ILE* 5.6 1.3 - - + -
420G TYR* 6.0 1.1 - - + -
466G LEU* 3.6 31.0 - - + -
467G PRO* 4.1 8.7 - - + +
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Residues in contact with SER 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G ARG* 5.9 0.5 + - - -
366G CYS* 4.6 11.3 - - - +
369G TYR* 4.3 10.7 + - - -
371G ALA* 3.4 28.8 + - - +
404G SER 2.9 20.1 + - - -
405G HIS* 3.5 6.5 - - - -
407G LEU* 1.3 77.0 - - - +
409G ALA* 1.3 60.9 - - - +
410G LEU 3.1 1.0 + - - -
411G HIS* 3.2 27.8 + - - +
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Residues in contact with ALA 409 (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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405G HIS* 3.2 15.6 + - + +
406G SER* 3.5 14.4 - - - +
407G LEU 3.2 1.0 - - - -
408G SER* 1.3 75.4 - - - +
410G LEU* 1.3 66.4 + - + +
411G HIS* 3.0 24.1 + - - -
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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
------------------------------------------------------------
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