Contacts of the helix formed by residues 395 - 408 (chain G) in PDB entry 4U0Z
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 GLN 395 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390G THR 4.1 7.9 + - - -
391G ILE* 4.3 1.7 - - + +
392G ARG* 3.0 56.1 + - + +
394G GLU* 1.4 77.3 - - + +
396G ARG* 1.4 61.8 + - - +
397G SER 3.4 0.7 - - - -
398G ASP* 3.1 17.5 + - - +
399G TYR* 3.0 22.4 + - - +
417G PHE* 3.3 22.9 - - + -
421G CYS* 3.2 26.5 - - - +
424G THR* 5.3 5.5 + - - -
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Residues in contact with ARG 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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232G ALA 5.6 0.4 - - - -
233G ILE* 3.4 42.5 + - + +
234G GLU 5.9 0.4 - - - -
392G ARG 3.6 3.0 + - - -
393G LYS 3.3 17.2 + - - +
394G GLU 3.3 2.4 - - - +
395G GLN* 1.4 72.6 - - - +
397G SER* 1.3 63.5 + - - +
399G TYR* 3.1 5.3 + - - +
400G TYR* 3.0 60.5 + - + -
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Residues in contact with SER 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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394G GLU 4.0 11.6 + - - -
396G ARG* 1.3 77.0 - - - +
398G ASP* 1.4 65.1 + - - +
400G TYR* 3.7 4.9 + - - +
401G HIS* 3.2 22.0 + - - +
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Residues in contact with ASP 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 GLU 5.0 1.1 - - - +
395G GLN* 3.1 20.5 + - - +
397G SER* 1.4 77.5 + - - +
399G TYR* 1.4 55.1 + - - +
401G HIS* 3.1 8.9 + - - +
402G VAL* 2.9 40.6 + - + +
417G PHE* 3.8 18.4 - - + -
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Residues in contact with TYR 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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233G ILE* 4.0 21.1 - - + -
356G HIS* 2.7 43.0 + + - -
370G GLY 4.5 0.2 + - - -
374G ARG* 3.3 28.1 + - - +
391G ILE* 3.8 14.4 - - + -
395G GLN 3.0 12.8 + - - +
396G ARG* 3.1 8.7 + - - +
398G ASP* 1.4 75.0 - - - +
400G TYR* 1.3 72.5 + + - +
402G VAL* 3.4 6.4 - - - +
403G LEU* 3.2 34.8 + - + +
414G PHE* 3.7 16.2 - + - -
417G PHE* 3.7 29.5 - + + -
501G APC 3.3 25.7 + - - -
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Residues in contact with TYR 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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233G ILE* 4.2 8.4 + - + -
234G GLU* 5.4 2.4 - - - -
316G VAL* 5.9 0.7 - - + -
396G ARG* 3.0 54.7 + - + +
397G SER* 4.1 5.2 - - - +
399G TYR* 1.3 91.4 - + - +
401G HIS* 1.3 64.5 + - - +
403G LEU* 3.9 6.4 - - - +
404G GLU* 3.1 37.6 + - - +
501G APC 3.2 65.1 + + - +
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Residues in contact with HIS 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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161G TYR* 5.9 3.4 - + - -
397G SER 3.2 14.7 + - - +
398G ASP* 3.1 12.8 + - - +
400G TYR* 1.3 79.3 - - - +
402G VAL* 1.4 67.6 + - + +
404G GLU* 3.3 15.9 + - + +
405G ALA* 3.1 33.2 + - + +
413G PRO* 6.5 0.2 - - + -
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Residues in contact with VAL 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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398G ASP* 2.9 23.7 + - + +
399G TYR* 3.4 16.6 - - - +
401G HIS* 1.4 84.2 - - + +
403G LEU* 1.4 61.5 + - - +
405G ALA* 3.5 8.5 + - - +
406G ALA* 3.3 20.8 + - - +
410G ASP 4.9 0.5 - - - +
413G PRO* 3.9 26.2 - - + +
414G PHE* 3.7 38.5 + - + +
417G PHE* 3.9 19.3 - - + -
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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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356G HIS* 4.8 1.3 - - - +
357G TYR* 3.9 23.7 - - + -
360G VAL* 4.2 12.3 - - + -
399G TYR* 3.2 39.1 + - + +
400G TYR 3.9 4.5 - - - +
401G HIS 3.3 0.2 - - - -
402G VAL* 1.4 72.2 - - - +
404G GLU* 1.4 64.3 + - - +
406G ALA* 3.4 7.1 + - - +
407G ASN* 3.3 26.7 + - - +
414G PHE* 3.8 31.0 - - + -
501G APC 3.7 55.0 - - + +
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Residues in contact with GLU 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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317G GLY* 5.1 6.9 - - - -
318G HIS* 4.9 19.9 + - + -
400G TYR* 3.1 24.8 + - - +
401G HIS* 3.4 19.9 - - + +
403G LEU* 1.4 75.2 - - - +
405G ALA* 1.4 56.9 + - - +
407G ASN* 3.0 28.6 + - - +
408G GLU* 3.0 23.8 + - - +
501G APC 3.4 20.9 + - - +
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Residues in contact with ALA 405 (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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161G TYR* 4.2 18.0 - - + +
401G HIS* 3.1 20.9 + - + +
402G VAL* 3.5 13.7 - - - +
403G LEU 3.4 0.4 - - - -
404G GLU* 1.4 74.1 - - - +
406G ALA* 1.4 57.6 + - - +
408G GLU* 3.7 16.1 - - - +
409G GLY 3.5 4.5 + - - -
410G ASP* 3.0 30.5 + - - +
413G PRO* 4.4 15.5 - - + -
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Residues in contact with ALA 406 (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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357G TYR* 3.3 40.4 + - + -
402G VAL 3.3 12.4 + - - +
403G LEU* 3.6 4.9 - - - +
404G GLU 3.2 0.8 - - - -
405G ALA* 1.4 72.8 - - - +
407G ASN* 1.4 66.1 + - - +
408G GLU 3.2 1.1 - - - -
409G GLY* 3.1 15.2 + - - -
410G ASP 3.3 11.7 - - - +
411G VAL* 3.7 21.5 - - + +
414G PHE* 5.0 3.8 - - + -
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Residues in contact with ASN 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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319G HIS* 3.8 20.3 - - + +
357G TYR* 2.8 30.5 + - - -
361G TYR* 3.6 15.8 - - + -
403G LEU 3.4 10.7 + - - -
404G GLU* 3.0 10.5 + - - +
406G ALA* 1.4 77.1 - - - +
408G GLU* 1.3 61.9 + - + +
409G GLY* 3.3 1.7 + - - -
501G APC 2.8 39.0 + - - -
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Residues in contact with GLU 408 (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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137G PRO* 6.5 1.8 - - - -
161G TYR* 4.9 10.5 - - - +
165G ARG* 5.3 14.3 - - + +
404G GLU* 3.0 27.2 + - + +
405G ALA* 3.7 13.7 - - - +
406G ALA 3.2 0.2 - - - -
407G ASN* 1.3 77.6 - - + +
409G GLY* 1.4 53.9 + - - +
410G ASP 4.0 0.7 - - - -
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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