Contacts of the helix formed by residues 395 - 409 (chain A) in PDB entry 4U04
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ILE* 4.5 0.4 - - - -
390A THR 4.4 1.4 - - - +
391A ILE* 3.9 2.8 - - + -
392A ARG* 2.9 45.1 + - + +
394A GLU* 1.4 77.8 - - + +
396A ARG* 1.4 54.6 + - - +
397A SER 3.3 2.7 - - - -
398A ASP* 3.2 16.6 + - + +
399A TYR* 2.8 36.2 + - - +
417A PHE* 3.3 35.6 - - + -
420A LYS* 6.2 1.2 - - - +
421A CYS* 3.6 20.2 - - - -
424A THR* 5.6 0.9 + - - -
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Residues in contact with ARG 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ALA 4.9 2.4 + - - -
233A ILE* 2.9 47.9 + - + +
234A GLU 4.7 2.0 - - - -
235A GLY* 4.7 8.1 - - - +
392A ARG 3.8 1.4 + - - -
393A LYS* 3.2 18.4 + - - +
394A GLU 3.3 1.8 - - - +
395A GLN* 1.4 75.6 - - - +
397A SER* 1.3 57.6 + - - +
399A TYR* 3.4 1.7 + - - +
400A TYR* 3.0 55.3 + - + -
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Residues in contact with SER 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A GLU 4.4 9.2 + - - -
396A ARG* 1.3 76.0 - - - +
398A ASP* 1.3 68.7 + - - +
400A TYR* 3.4 6.3 + - - +
401A HIS* 3.0 29.4 + - - +
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Residues in contact with ASP 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLU 5.1 1.3 - - - +
395A GLN* 3.2 22.0 + - - +
397A SER* 1.3 88.0 + - - +
399A TYR* 1.3 60.9 + - - +
401A HIS* 3.3 7.9 + - - +
402A VAL* 3.1 28.6 + - - +
417A PHE* 3.7 20.0 - - + -
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Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ILE* 3.8 19.1 - - + -
356A HIS* 2.5 43.4 + + - -
360A VAL* 4.6 4.0 - - - +
370A GLY* 4.6 1.4 + - - -
373A SER* 4.5 2.1 + - - -
374A ARG* 3.3 28.9 + - - +
391A ILE* 4.0 11.7 - - + -
395A GLN 2.8 21.9 + - - +
396A ARG 3.5 2.7 - - - +
398A ASP* 1.3 72.9 - - - +
400A TYR* 1.3 83.4 + + - +
402A VAL* 3.4 5.5 - - - +
403A LEU* 3.4 48.1 + - + +
414A PHE* 3.8 10.8 - + - -
417A PHE* 3.8 29.8 - + + -
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Residues in contact with TYR 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE 3.8 4.7 + - - -
234A GLU* 3.2 25.5 + - - -
396A ARG* 3.0 56.6 + - + +
397A SER* 3.4 4.9 + - - +
399A TYR* 1.3 93.1 - + - +
401A HIS* 1.3 59.4 + - - +
403A LEU* 3.5 18.9 + - + +
404A GLU* 3.1 42.6 + - - +
501A TAR 5.5 8.1 + - - -
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Residues in contact with HIS 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A TYR* 6.0 2.5 - + - -
397A SER 3.0 17.4 + - - +
398A ASP* 3.3 9.8 + - - +
400A TYR* 1.3 76.2 - - - +
402A VAL* 1.3 67.4 + - + +
404A GLU* 3.5 17.0 + - - +
405A ALA* 3.1 30.3 + - + +
413A PRO* 6.3 1.3 - - + -
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Residues in contact with VAL 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ASP 3.1 18.9 + - - +
399A TYR* 3.4 11.9 - - - +
401A HIS* 1.3 81.6 - - - +
403A LEU* 1.3 59.7 + - - +
405A ALA* 3.4 7.8 + - - +
406A ALA* 3.0 26.9 + - - +
410A ASP 4.8 0.5 - - - +
413A PRO* 3.5 30.3 - - + +
414A PHE* 3.5 34.0 + - + +
417A PHE* 3.8 25.1 - - + -
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A HIS* 5.1 0.2 - - - +
357A TYR* 3.8 23.7 - - + -
360A VAL* 4.4 25.8 - - + -
399A TYR* 3.4 43.9 + - + +
400A TYR* 3.9 25.1 - - + +
401A HIS 3.4 0.2 - - - -
402A VAL* 1.3 71.9 - - - +
404A GLU* 1.3 59.8 + - - +
406A ALA* 3.2 6.2 + - - +
407A ASN* 3.0 39.0 + - - +
414A PHE* 3.3 29.6 - - + -
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Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A TYR* 3.1 32.5 + - - +
401A HIS* 3.6 17.7 - - - +
403A LEU* 1.3 76.1 - - - +
405A ALA* 1.3 55.8 - - - +
407A ASN* 3.3 13.8 + - - +
408A GLU* 2.9 40.2 + - - +
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Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A TYR* 3.9 27.0 + - + +
401A HIS* 3.1 21.3 + - + +
402A VAL* 3.6 11.7 - - - +
403A LEU 3.3 0.2 - - - -
404A GLU* 1.3 76.2 - - - +
406A ALA* 1.3 57.4 + - - +
408A GLU* 3.5 13.1 + - - +
409A GLY 3.2 9.4 + - - -
410A ASP* 3.0 28.6 + - - +
413A PRO* 4.5 8.3 - - + -
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A TYR* 3.3 40.4 + - + -
402A VAL 3.0 14.4 + - - +
403A LEU* 3.2 5.1 + - - +
405A ALA* 1.3 72.3 - - - +
407A ASN* 1.3 64.7 + - - +
409A GLY* 3.4 12.3 + - - -
410A ASP 3.3 16.9 + - - +
411A VAL* 4.0 19.4 - - + +
414A PHE* 4.6 4.7 - - + -
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Residues in contact with ASN 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A HIS* 4.1 33.0 + - + +
357A TYR* 2.8 34.0 + - - -
361A TYR* 4.2 11.6 - - + +
403A LEU* 3.0 24.8 + - - +
404A GLU* 3.5 12.8 - - - +
406A ALA* 1.3 75.6 - - - +
408A GLU* 1.4 61.4 + - + +
409A GLY* 3.5 1.2 + - - -
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Residues in contact with GLU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A TYR* 5.3 7.0 - - - +
404A GLU* 2.9 30.1 + - - +
405A ALA* 3.7 9.9 - - - +
406A ALA 3.3 0.4 - - - -
407A ASN* 1.4 76.9 - - + +
409A GLY* 1.3 55.3 + - - +
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Residues in contact with GLY 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A THR* 6.1 4.0 - - - -
405A ALA 3.2 1.8 + - - -
406A ALA 3.4 7.3 + - - -
407A ASN 3.3 4.2 - - - -
408A GLU* 1.3 79.3 - - - +
410A ASP* 1.4 61.4 + - - +
411A VAL* 4.2 2.3 + - - +
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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