Contacts of the helix formed by residues 401 - 416 (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 ASP 401 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212J TYR 2.7 23.1 - - - +
213J ASN 2.8 18.1 - - - +
214J LYS* 3.6 1.2 + - - -
215J PRO* 4.0 1.9 - - - +
368J HIS* 2.6 31.9 + - + +
398J ALA 4.5 7.0 - - - +
399J PRO 3.2 5.1 + - - -
400J GLU* 1.3 76.3 - - - +
402J PRO* 1.4 76.4 - - - +
403J PHE* 3.9 18.1 - - - +
404J VAL* 3.3 15.9 - - + +
405J MET* 3.1 26.5 + - - +
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Residues in contact with PRO 402 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215J PRO* 3.3 41.1 - - + -
400J GLU 4.0 1.8 - - - +
401J ASP* 1.4 87.6 - - - +
403J PHE* 1.3 57.5 + - + +
405J MET* 3.9 6.9 - - - +
406J HIS* 2.9 31.9 + - - +
428J ALA* 4.0 17.1 - - + +
431J LYS* 4.2 15.0 - - + -
432J ILE* 4.0 18.6 - - + +
444J TRP* 3.7 24.9 - - + -
447J LEU* 6.1 0.2 - - + -
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Residues in contact with PHE 403 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ARG* 3.2 36.8 - - + -
4G ARG 3.1 25.6 - - - -
6G PRO* 3.7 19.2 - - + +
212J TYR 6.1 0.2 - - - -
215J PRO* 6.3 2.0 - - + -
243J TYR 5.6 0.7 - - - -
245J CYS* 4.6 2.9 - - - -
368J HIS* 5.3 0.4 - - - +
369J LEU* 5.8 0.9 - - + -
372J LEU* 4.2 22.9 - - + +
373J TYR* 5.4 1.8 - + - -
401J ASP* 3.1 16.5 - - - +
402J PRO* 1.3 83.0 - - + +
404J VAL* 1.3 62.9 + - - +
406J HIS* 3.6 4.1 + - - +
407J GLU* 3.1 23.0 + - - +
443J LYS* 3.5 29.6 - - + -
444J TRP* 3.6 32.3 - + - -
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Residues in contact with VAL 404 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368J HIS* 5.0 9.4 - - + -
372J LEU* 4.8 10.8 - - + -
391J PHE* 3.9 11.4 - - + +
394J ALA* 3.8 30.7 - - + +
395J LEU* 3.7 32.1 - - + +
398J ALA 4.6 3.8 - - - +
399J PRO 4.5 2.9 - - - +
401J ASP* 3.3 29.9 + - + +
403J PHE* 1.3 77.8 - - - +
405J MET* 1.3 66.7 + - + +
407J GLU* 3.2 5.5 + - - +
408J VAL* 3.0 34.8 + - + +
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Residues in contact with MET 405 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395J LEU* 4.4 4.3 - - + -
399J PRO 3.5 15.0 - - - +
400J GLU* 4.1 0.4 - - - -
401J ASP 3.1 38.2 + - - +
402J PRO* 3.9 4.0 - - - +
404J VAL* 1.3 78.0 - - + +
406J HIS* 1.3 64.1 + - - +
408J VAL* 3.4 2.6 + - - +
409J GLY 3.1 17.7 + - - -
424J TRP* 3.7 39.0 - - + +
427J ASP* 3.2 46.0 - - - +
428J ALA* 4.0 8.7 - - + -
431J LYS* 3.4 28.0 - - + -
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Residues in contact with HIS 406 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G PRO* 3.1 30.6 - - + +
7G THR 3.1 12.1 + - - -
402J PRO 2.9 18.4 + - - +
403J PHE 3.6 6.1 - - - +
405J MET* 1.3 75.8 - - - +
407J GLU* 1.3 65.5 + - - +
409J GLY 3.1 2.3 + - - -
410J VAL* 3.1 22.7 + - + +
425J PHE* 3.4 30.1 - + - -
428J ALA* 4.1 6.4 - - + +
444J TRP* 4.3 9.4 - + + -
446J PRO* 4.5 0.6 - - - +
447J LEU* 3.6 32.1 - - - +
450J ASN* 2.8 33.7 + - + -
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Residues in contact with GLU 407 (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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6G PRO* 5.0 1.7 - - - +
7G THR* 2.9 40.3 + - - +
372J LEU* 4.3 4.0 - - + -
376J LEU* 3.3 27.2 - - + +
391J PHE* 3.1 41.0 - - + -
403J PHE 3.1 17.3 + - - +
404J VAL 3.2 4.0 + - - +
406J HIS* 1.3 76.1 - - - +
408J VAL* 1.3 65.5 + - - +
410J VAL* 3.1 18.7 + - - +
411J VAL* 3.2 17.6 + - - +
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Residues in contact with VAL 408 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388J GLU* 4.2 18.4 - - - +
391J PHE* 3.9 26.9 - - + +
392J SER* 5.2 0.9 - - - +
395J LEU* 3.9 21.5 - - + -
404J VAL* 3.0 16.1 + - + +
405J MET 3.7 6.5 - - - +
407J GLU* 1.3 75.0 - - - +
409J GLY* 1.3 56.4 + - - +
411J VAL* 3.3 6.6 + - - +
412J ALA* 2.8 29.7 + - + +
424J TRP* 3.3 33.9 - - + +
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Residues in contact with GLY 409 (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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405J MET 3.1 10.9 + - - -
406J HIS 3.1 5.5 + - - -
408J VAL* 1.3 76.2 - - - +
410J VAL* 1.3 56.6 + - - +
412J ALA* 3.2 8.0 + - - +
413J PHE* 2.8 28.1 + - - +
421J ALA* 3.5 6.7 - - - +
424J TRP* 3.7 21.7 - - - +
425J PHE* 3.5 15.7 - - - -
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Residues in contact with VAL 410 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G THR* 3.4 30.1 - - - +
8G ARG 6.1 0.2 - - - -
9G LEU* 3.8 12.1 - - + -
406J HIS* 3.1 19.1 + - + +
407J GLU* 3.1 14.3 + - - +
409J GLY* 1.3 75.8 - - - +
411J VAL* 1.3 58.3 + - + +
413J PHE* 3.2 7.2 + - - +
414J GLN* 3.1 43.9 + - + +
425J PHE* 3.9 8.1 - - + -
450J ASN* 3.8 26.0 - - - +
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Residues in contact with VAL 411 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379J GLY* 6.1 2.5 - - - -
384J SER* 4.5 13.7 - - - +
387J ALA* 5.0 5.6 - - + -
388J GLU* 3.8 30.7 - - + +
391J PHE* 3.5 33.7 - - + -
407J GLU* 3.2 11.7 + - - +
408J VAL* 3.6 7.2 - - - +
410J VAL* 1.3 75.6 - - + +
412J ALA* 1.3 66.8 + - - +
414J GLN* 2.9 21.6 + - + +
415J ASN* 3.1 24.0 + - - +
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Residues in contact with ALA 412 (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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388J GLU* 5.3 0.8 + - - -
408J VAL* 2.8 15.6 + - + +
409J GLY* 3.4 10.8 - - - +
411J VAL* 1.3 74.8 - - - +
413J PHE* 1.3 62.7 + - - +
415J ASN* 3.0 16.9 + - - +
416J GLY 3.0 17.2 + - - -
417J GLU* 3.4 12.6 + - + +
420J THR* 3.8 24.0 - - - +
421J ALA* 3.9 13.2 - - - +
424J TRP* 4.6 4.5 - - + +
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Residues in contact with PHE 413 (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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9G LEU* 3.4 42.6 - - + -
10G GLU 6.0 1.1 - - - -
15G ASP* 6.0 1.1 - - - -
409J GLY 2.8 13.9 + - - +
410J VAL 3.3 11.0 - - - +
411J VAL 3.0 0.4 - - - -
412J ALA* 1.3 78.2 - - - +
414J GLN* 1.3 60.1 + - - +
416J GLY* 3.1 18.4 + - - +
417J GLU 5.1 0.7 - - - +
418J TRP* 3.7 36.4 - + - +
421J ALA* 4.1 8.5 - - + -
425J PHE* 4.9 0.2 - - + -
453J HIS* 4.4 14.6 - + + -
454J VAL* 3.5 40.6 - - + -
457J LYS* 4.2 15.5 - - + -
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Residues in contact with GLN 414 (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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9G LEU* 3.4 26.8 - - - +
384J SER* 6.1 4.0 - - - -
410J VAL* 3.1 24.1 + - + +
411J VAL* 2.9 13.9 + - + +
413J PHE* 1.3 81.5 - - - +
415J ASN* 1.3 63.0 + - - +
416J GLY* 3.1 0.9 + - - -
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Residues in contact with ASN 415 (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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384J SER* 4.7 12.6 + - - -
388J GLU* 5.5 4.9 + - - +
411J VAL* 3.1 22.7 + - - +
412J ALA* 3.0 12.7 + - - +
414J GLN* 1.3 79.7 - - - +
416J GLY* 1.3 61.5 + - - +
417J GLU* 3.3 29.4 + - + +
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Residues in contact with GLY 416 (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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412J ALA 3.0 4.0 + - - -
413J PHE 3.1 14.5 + - - -
414J GLN 3.1 1.5 - - - -
415J ASN* 1.3 79.5 - - - +
417J GLU* 1.3 59.8 + - - +
418J TRP* 3.1 46.1 + - - -
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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