Contacts of the helix formed by residues 390 - 397 (chain B) in PDB entry 1U0E
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 PHE 390 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLN* 3.9 23.1 - - + +
356A MET* 3.7 31.1 - - + +
357A GLU 5.0 0.9 - - - +
338B LEU* 3.8 22.4 - - + -
379B TRP* 3.5 35.9 - + - -
381B GLU* 3.9 25.1 - - + -
386B GLY* 2.9 27.0 + - - -
389B ALA* 1.3 83.6 - - + +
391B TYR* 1.3 90.6 + + - +
392B GLN* 3.1 3.1 - - - -
393B LEU* 3.0 17.6 + - - +
394B ILE* 3.5 12.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLY 5.1 0.4 - - - -
514A VAL* 5.2 2.0 - - + -
338B LEU* 3.5 26.7 - - + +
340B TYR* 2.8 33.5 + - - -
381B GLU 5.4 0.3 + - - -
383B GLY* 4.7 3.5 - - - -
386B GLY* 3.1 29.5 + - - -
387B GLN* 3.4 38.6 + - + +
389B ALA 3.8 0.2 - - - -
390B PHE* 1.3 98.2 - + - +
392B GLN* 1.3 66.1 + - - +
394B ILE* 3.6 12.3 - - + -
395B HIS* 2.8 38.4 + - + -
405B PHE* 3.5 10.1 - + - -
431B GLN* 3.1 28.3 - - + +
435B LEU* 5.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A MET 4.1 0.2 - - - +
357A GLU* 3.4 48.9 + - + +
360A GLY 2.9 24.5 + - - +
361A LYS* 3.5 16.9 - - - +
511A GLN* 3.2 14.3 - - - +
512A TRP 4.9 0.4 - - - +
513A GLY* 2.7 31.5 + - - -
514A VAL* 4.4 14.5 - - + +
389B ALA 5.3 0.2 - - - -
390B PHE* 4.2 0.4 - - - +
391B TYR* 1.3 75.9 - - - +
393B LEU* 1.3 58.5 + - - +
395B HIS* 3.4 1.2 + - - +
396B GLN* 2.9 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A MET* 3.6 37.9 + - + +
360A GLY* 3.7 28.7 - - - -
375A GLY 3.6 24.2 - - - +
376A PRO 3.6 17.0 - - - +
377A ILE* 4.2 7.0 - - + -
390B PHE 3.0 10.6 + - - +
392B GLN* 1.3 77.3 - - - +
394B ILE* 1.3 62.2 + - - +
397B GLY* 2.8 30.3 + - - -
399B LYS* 4.3 16.1 - - + +
401B ILE* 3.7 25.8 - - + -
471B ARG* 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ALA* 5.3 0.2 - - + -
338B LEU* 4.4 3.4 - - + -
379B TRP* 4.3 9.2 - - + -
390B PHE* 3.8 37.0 - - + +
391B TYR* 3.1 26.6 + - + +
393B LEU* 1.3 78.5 - - + +
395B HIS* 1.3 51.2 - - + +
399B LYS 4.8 3.9 - - - +
401B ILE* 4.2 28.7 - - + +
403B CYS* 4.1 31.0 - - - -
405B PHE* 6.1 0.2 - - + -
435B LEU* 3.7 23.8 - - + -
471B ARG* 2.8 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A TYR* 5.7 0.2 - - - -
513A GLY 3.7 25.6 - - - +
514A VAL* 5.5 1.3 - - - -
517A GLY 5.2 4.1 + - - -
391B TYR* 2.8 38.2 + + + +
392B GLN 4.0 1.1 - - - +
394B ILE* 1.3 77.8 - - + +
396B GLN* 1.3 61.9 + - + +
431B GLN* 2.8 30.2 + - - -
434B ALA* 3.8 24.0 + - + +
435B LEU* 3.5 34.7 - - + +
467B PHE* 3.8 25.6 - + + +
468B GLU 4.9 6.1 + - - -
469B GLY 5.2 0.5 + - - -
471B ARG* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLY 3.6 3.8 - - - -
361A LYS* 3.2 25.4 - - - +
362A TYR* 3.2 29.3 + - + -
512A TRP* 3.7 3.8 + - - +
513A GLY* 3.1 33.4 + - - +
392B GLN* 2.9 23.5 + - - +
395B HIS* 1.3 83.9 - - + +
397B GLY* 1.3 63.6 + - - +
464B HIS 3.1 23.1 + - - +
466B VAL 2.9 27.2 + - - +
467B PHE* 4.0 15.7 - - + -
471B ARG* 4.3 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLY* 3.8 19.5 + - - -
361A LYS 3.9 2.9 - - - -
362A TYR* 4.2 5.7 - - - +
369A ARG* 4.9 4.9 + - - -
374A THR* 4.6 0.7 - - - -
393B LEU* 2.8 22.8 + - - -
395B HIS 3.9 0.8 - - - -
396B GLN* 1.3 82.7 - - - +
398B THR* 1.3 65.4 + - - +
399B LYS 3.5 2.9 - - - -
471B ARG* 3.4 16.3 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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