Contacts of the helix formed by residues 393 - 406 (chain A) in PDB entry 1UOU
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 ARG 393 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASP* 3.8 5.8 - - - +
391A LEU* 3.7 23.1 - - + +
392A VAL* 1.3 74.1 - - - +
394A ALA* 1.3 66.0 + - - +
395A LEU 3.5 0.2 - - - -
396A PRO* 3.7 24.8 - - + +
397A LEU* 3.8 8.0 - - - +
457A GLU 4.4 9.3 + - - -
458A ALA* 2.8 31.9 + - - +
460A VAL* 3.5 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 4.0 27.1 - - + +
273A MET 4.8 4.5 - - - +
274A ASP* 3.1 28.4 + - - +
275A LYS 4.1 10.3 - - - +
276A PRO* 4.4 10.1 - - - -
392A VAL 3.7 0.4 + - - -
393A ARG* 1.3 72.3 - - - +
395A LEU* 1.3 59.9 + - - +
397A LEU* 3.3 6.8 - - - +
398A ALA* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 5.4 0.9 - - - -
150A HIS* 3.5 41.7 - - + +
240A ALA 6.2 0.9 - - - +
393A ARG* 4.9 0.2 - - - +
394A ALA* 1.3 76.6 - - - +
396A PRO* 1.3 75.1 - - + +
398A ALA* 3.3 3.5 + - - +
399A LEU* 3.0 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ARG* 3.7 34.1 - - + +
395A LEU* 1.3 95.8 - - + +
397A LEU* 1.3 55.4 + - - +
399A LEU* 3.8 9.3 - - + +
400A VAL* 3.1 35.6 + - - +
454A ALA* 3.6 22.7 - - + +
455A LEU* 4.9 0.9 - - - -
457A GLU* 4.9 4.9 - - + +
458A ALA* 4.0 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 5.0 1.6 - - + -
276A PRO* 4.0 26.5 - - + -
281A VAL* 4.3 17.5 - - + -
392A VAL* 4.6 10.5 - - + -
393A ARG 3.8 7.2 + - - +
394A ALA 3.3 9.6 + - - +
395A LEU 3.1 0.4 - - - -
396A PRO* 1.3 78.7 - - - +
398A ALA* 1.3 64.7 + - - +
400A VAL* 3.4 2.3 + - - +
401A LEU* 3.0 39.6 + - + +
421A ALA* 4.7 7.4 - - + -
423A LEU* 4.8 7.9 - - + -
437A TRP* 5.3 0.4 - - + -
438A LEU* 3.7 24.0 - - + -
455A LEU* 3.6 24.5 - - + -
458A ALA* 4.7 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 3.6 28.4 - - + +
150A HIS* 3.5 35.9 - - + +
281A VAL* 5.6 1.8 - - + -
394A ALA 3.0 9.0 + - - +
395A LEU* 3.8 5.2 - - - +
397A LEU* 1.3 72.5 - - - +
399A LEU* 1.3 65.9 + - - +
401A LEU* 4.1 6.6 - - - +
402A HIS* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A HIS* 4.6 15.5 - - + +
395A LEU* 3.0 46.3 + - + +
396A PRO* 3.8 8.1 - - + +
398A ALA* 1.3 77.6 - - - +
400A VAL* 1.3 63.3 + - + +
402A HIS* 3.4 6.3 + - + +
403A GLU* 3.2 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A PRO 3.1 16.4 + - - +
397A LEU 4.1 0.2 - - - +
398A ALA 3.4 0.2 - - - -
399A LEU* 1.3 76.3 - - + +
401A LEU* 1.3 57.1 + - + +
403A GLU* 3.0 30.3 - - - +
404A LEU* 3.1 22.2 + - + +
451A GLN* 3.9 27.4 - - + +
454A ALA* 3.7 28.9 - - + -
455A LEU* 3.6 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 3.5 36.8 - - + +
397A LEU* 3.0 31.6 + - + +
398A ALA* 4.1 4.3 - - - +
400A VAL* 1.3 74.2 - - - +
402A HIS* 1.3 56.2 + - - +
404A LEU* 3.6 19.3 - - + +
405A GLY* 2.7 32.2 + - - -
419A VAL* 4.4 5.3 - - + +
420A GLY* 4.1 27.6 - - - +
421A ALA* 4.1 15.9 - - + +
440A VAL* 4.7 7.9 - - + -
455A LEU* 5.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLY* 6.3 2.9 - - - -
149A GLY 3.5 25.0 + - - -
150A HIS* 4.6 10.6 - - + -
203A ASP* 5.1 9.4 - - - -
398A ALA 3.0 18.6 + - - +
399A LEU* 3.6 7.6 - - + +
401A LEU* 1.3 72.9 - - - +
403A GLU* 1.3 65.7 + - - +
405A GLY* 3.9 1.5 - - - -
406A ALA* 3.1 28.0 + - + +
415A LEU* 6.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A LEU 3.2 9.1 + - - +
400A VAL* 3.0 20.2 + - - +
402A HIS* 1.3 80.8 - - - +
404A LEU* 1.3 61.1 + - + +
406A ALA* 3.2 21.8 + - - +
416A ARG* 4.7 1.2 + - - -
451A GLN* 3.2 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A VAL* 3.1 23.1 + - + +
401A LEU* 3.4 10.3 + - + +
403A GLU* 1.3 76.2 - - + +
405A GLY* 1.3 58.6 + - - +
406A ALA 3.2 0.2 - - - -
416A ARG* 3.1 27.9 + - - +
419A VAL* 3.9 19.5 - - + +
440A VAL* 4.0 19.1 - - + -
442A ARG* 4.3 15.3 - - + -
443A ASP* 5.4 1.0 + - - +
444A GLY* 6.5 0.7 - - - -
445A PRO 5.8 2.7 - - - +
447A LEU* 3.7 25.1 - - + -
451A GLN* 3.4 34.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A HIS* 6.5 0.9 - - - -
401A LEU 2.7 23.4 + - - -
402A HIS* 3.9 2.7 - - - -
403A GLU 3.2 0.2 - - - -
404A LEU* 1.3 72.4 - - - +
406A ALA* 1.3 62.3 + - - +
415A LEU* 3.7 25.0 - - - +
416A ARG* 3.8 20.7 + - - +
419A VAL* 4.1 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A HIS* 3.1 17.7 + - + +
403A GLU* 3.3 16.6 - - - +
404A LEU 3.2 1.0 - - - -
405A GLY* 1.3 82.0 - - - +
415A LEU* 5.3 3.6 - - - -
416A ARG* 3.4 33.4 + - - -
----------------------------------------------------------
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