Contacts of the helix formed by residues 368 - 381 (chain J) in PDB entry 5G04
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 HIS 368 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210J LYS* 4.0 7.3 + - - -
212J TYR* 3.3 42.9 - + - -
213J ASN* 4.0 4.8 - - - -
366J GLY 4.1 1.4 + - - -
367J CYS* 1.3 73.4 - - - +
369J LEU* 1.3 81.0 + - + +
370J PRO 3.5 0.4 - - - -
371J MET* 3.4 6.4 + - - +
372J LEU* 3.0 34.1 + - + +
394J ALA* 3.9 24.1 - - + +
397J ILE* 3.7 22.1 - - + +
398J ALA* 4.6 7.2 - - + +
401J ASP* 2.6 35.9 + - + -
404J VAL* 5.0 8.5 - - + -
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Residues in contact with LEU 369 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 4.6 26.9 - - + -
2G LEU 4.9 2.9 - - - +
3G ARG* 4.3 25.1 - - + +
212J TYR* 4.3 16.2 - - + -
243J TYR* 6.0 0.7 - - + -
338J ILE* 4.3 7.4 - - + -
367J CYS* 3.4 11.4 - - - -
368J HIS* 1.3 101.7 - - + +
370J PRO* 1.3 70.1 - - + +
372J LEU* 3.2 16.0 + - + +
373J TYR* 2.7 59.6 + - + +
403J PHE* 5.8 1.8 - - + -
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Residues in contact with PRO 370 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338J ILE* 4.5 12.3 - - + -
357J TYR* 3.9 9.9 - - + +
360J ALA* 4.1 11.7 - - + +
361J ALA* 3.5 39.3 - - + +
364J MET* 4.5 10.1 - - + +
367J CYS* 3.3 25.6 - - - +
369J LEU* 1.3 93.6 - - + +
371J MET* 1.3 61.5 - - + +
373J TYR* 3.2 9.5 + - + +
374J ILE* 3.0 29.0 + - - +
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Residues in contact with MET 371 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758F MET* 4.8 13.2 - - + -
361J ALA* 4.6 11.9 - - + +
364J MET 4.5 9.9 - - - +
365J LYS* 5.3 1.6 - - - -
366J GLY 5.0 4.3 - - - +
367J CYS 3.1 27.4 - - - +
368J HIS 3.4 5.8 + - - +
369J LEU 3.3 0.4 - - - -
370J PRO* 1.3 80.5 - - + +
372J LEU* 1.3 66.8 + - - +
374J ILE* 3.4 14.7 + - + +
375J GLY* 3.0 18.0 + - - -
390J PHE* 3.7 21.8 - - + +
393J GLN* 3.9 32.8 - - - +
394J ALA* 4.2 13.5 - - + -
397J ILE* 3.7 22.4 - - + -
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Residues in contact with LEU 372 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368J HIS* 3.0 24.5 + - + +
369J LEU* 3.3 26.9 - - + +
370J PRO 3.2 0.2 - - - -
371J MET* 1.3 76.1 - - - +
373J TYR* 1.3 67.4 + - + +
375J GLY* 3.0 4.7 + - - -
376J LEU* 2.9 49.4 + - + +
391J PHE* 3.4 16.1 - - + -
394J ALA* 4.1 12.9 - - + +
403J PHE* 4.2 33.9 - - + +
404J VAL* 4.8 7.0 - - + +
407J GLU* 4.3 9.2 - - + -
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Residues in contact with TYR 373 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G LEU 3.5 3.3 + - - -
3G ARG* 2.8 38.6 - - - +
4G ARG* 3.0 52.4 + - + -
338J ILE* 4.9 7.2 - - + -
342J HIS* 3.8 11.4 - - - -
357J TYR* 3.7 30.7 - + + -
369J LEU* 2.7 55.3 + - + +
370J PRO* 3.8 6.3 - - + +
372J LEU* 1.3 78.3 - - + +
374J ILE* 1.3 65.1 + - - +
376J LEU* 3.1 12.4 + - + +
377J GLU* 2.9 29.2 + - - +
403J PHE* 5.4 1.5 - + - -
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Residues in contact with ILE 374 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758F MET* 4.4 4.5 - - - -
354J MET* 3.3 21.1 - - + +
357J TYR* 3.7 20.4 - - + +
358J PHE* 3.5 35.0 - - + -
361J ALA* 3.9 15.5 - - + -
370J PRO 3.0 19.7 + - - +
371J MET* 3.6 15.5 - - - +
373J TYR* 1.3 73.3 - - - +
375J GLY* 1.3 62.4 + - - +
377J GLU* 3.3 3.1 + - - +
378J TYR* 3.0 26.2 + - + -
390J PHE* 3.6 33.9 - - + -
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Residues in contact with GLY 375 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371J MET 3.0 14.0 + - - -
372J LEU 3.0 5.1 + - - -
374J ILE* 1.3 76.7 - - - +
376J LEU* 1.3 61.5 + - - +
377J GLU 3.2 0.2 + - - -
378J TYR 3.2 1.7 + - - -
379J GLY* 3.1 17.7 + - - -
387J ALA* 3.3 17.4 - - - +
390J PHE* 3.9 14.3 - - - +
391J PHE* 3.2 20.1 - - - -
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Residues in contact with LEU 376 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ARG* 3.7 50.5 - - + +
5G LYS 5.5 2.7 - - - +
6G PRO* 6.3 1.1 - - + -
7G THR* 5.2 10.3 - - + +
372J LEU* 2.9 32.9 + - + +
373J TYR* 3.1 15.0 + - + +
375J GLY* 1.3 74.4 - - - +
377J GLU* 1.3 62.0 + - + +
379J GLY* 3.4 2.6 + - - +
380J LEU* 3.2 29.9 + - + +
391J PHE* 3.3 4.3 - - - -
407J GLU* 3.3 44.6 - - + +
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Residues in contact with GLU 377 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ARG* 4.2 8.5 + - - +
345J ALA* 3.2 30.3 - - - +
350J HIS* 3.2 42.3 - - + +
353J ALA* 3.6 14.9 - - - +
354J MET* 3.4 32.1 - - + -
357J TYR* 3.7 11.5 - - + -
373J TYR 2.9 18.0 + - - +
374J ILE 3.5 0.9 - - - +
376J LEU* 1.3 75.9 - - + +
378J TYR* 1.3 66.3 + - - +
380J LEU* 3.4 8.6 + - - +
381J THR* 3.1 25.2 + - - +
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Residues in contact with TYR 378 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757F LEU* 3.3 32.0 - - + +
354J MET* 4.0 23.2 - - + +
358J PHE* 4.3 3.1 - + - -
374J ILE* 3.0 27.6 + - + +
375J GLY 3.2 4.5 + - - +
377J GLU* 1.3 77.4 - - - +
379J GLY* 1.3 61.9 + - - +
381J THR* 3.0 23.1 + - - -
382J ASN 3.1 0.2 + - - -
383J ASN* 3.1 31.8 + - + +
386J LEU* 3.9 29.4 - - + -
387J ALA* 3.9 16.2 - - + +
390J PHE* 3.5 36.3 - + - -
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Residues in contact with GLY 379 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375J GLY 3.1 13.4 + - - -
376J LEU* 3.4 4.4 + - - -
377J GLU 3.2 0.4 - - - -
378J TYR* 1.3 75.6 - - - +
380J LEU* 1.3 60.0 + - - +
382J ASN* 2.9 23.9 + - - -
383J ASN 4.8 2.7 - - - -
384J SER* 5.6 1.8 - - - -
387J ALA* 3.7 11.6 - - - +
391J PHE* 6.0 0.9 - - - -
411J VAL* 6.1 2.5 - - - -
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Residues in contact with LEU 380 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ARG* 4.2 24.9 - - - +
7G THR* 5.0 16.8 - - + -
345J ALA 6.1 0.7 - - - +
350J HIS* 3.9 34.0 - - + +
376J LEU* 3.2 17.2 + - + +
377J GLU* 3.8 9.0 - - - +
378J TYR 3.3 0.4 - - - -
379J GLY* 1.3 77.7 - - - +
381J THR* 1.3 62.2 + - - +
382J ASN* 3.4 2.6 + - - +
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Residues in contact with THR 381 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350J HIS* 3.4 36.8 - - + +
377J GLU 3.1 11.1 + - - +
378J TYR* 3.0 28.6 + - - -
379J GLY 3.2 0.2 - - - -
380J LEU* 1.3 76.3 - - - +
382J ASN* 1.3 68.0 + - - +
383J ASN* 3.4 10.7 + - - +
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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