Contacts of the helix formed by residues 386 - 395 (chain H) in PDB entry 1UW9
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 HIS 386 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332H VAL* 3.5 44.8 - - + +
381H GLY 3.6 12.5 + - - -
382H ILE* 3.3 11.0 - - + -
383H HIS* 2.9 58.9 + + - +
385H TRP* 1.3 78.0 - - + +
387H MET* 1.3 62.9 + - - +
388H PRO* 3.4 1.3 - - - -
389H ALA* 3.2 10.2 + - - +
390H LEU* 3.0 35.1 + - + +
465H ILE 4.3 8.0 + - - -
466H LYS* 5.0 6.5 - - + -
467H PHE* 4.5 6.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 387 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H LEU* 4.5 1.1 - - + -
383H HIS 3.7 1.6 + - - -
384H VAL* 3.0 18.8 + - - +
386H HIS* 1.3 77.1 - - - +
388H PRO* 1.3 68.2 - - + +
390H LEU* 3.2 5.3 + - - +
391H VAL* 3.0 29.9 + - + +
400H LEU* 3.7 28.7 - - - -
402H PHE* 3.4 32.5 - - + -
420H ASN* 3.4 31.6 - - - +
423H ALA* 3.7 29.4 - - + +
424H LEU* 3.7 15.9 - - + +
427H CYS* 3.9 7.2 - - - -
445H ILE* 4.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 388 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384H VAL 4.0 1.8 - - - +
385H TRP 3.4 17.5 - - - +
386H HIS 3.5 0.9 - - - -
387H MET* 1.3 95.1 - - + +
389H ALA* 1.3 56.9 + - - +
391H VAL* 3.5 1.2 + - - +
392H GLU* 3.0 29.5 + - - +
427H CYS* 3.6 22.2 - - + -
437H LEU* 3.7 21.5 - - + +
441H GLY* 3.6 42.8 - - - +
445H ILE* 3.8 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 389 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332H VAL* 4.4 23.3 - - + -
339H ARG* 6.2 0.2 - - - +
385H TRP 5.8 0.4 - - - +
386H HIS* 3.2 11.5 + - - +
388H PRO* 1.3 79.8 - - - +
390H LEU* 1.3 57.5 + - - +
392H GLU* 3.3 7.7 + - - +
393H ILE* 2.8 41.2 + - + +
437H LEU 5.6 0.9 - - - -
438H ALA* 6.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330H THR* 3.8 28.5 - - - +
332H VAL* 4.2 8.1 - - + -
378H ALA* 4.2 12.6 - - + -
382H ILE* 3.7 24.9 - - + -
386H HIS* 3.0 33.6 + - + +
387H MET* 3.2 7.6 + - - +
389H ALA* 1.3 72.9 - - - +
391H VAL* 1.3 61.1 + - - +
393H ILE* 4.6 1.1 - - + -
394H PHE* 2.9 52.9 + - + +
400H LEU* 4.1 19.9 - - + +
402H PHE* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 391 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387H MET* 3.0 25.3 + - + +
388H PRO 3.9 3.4 - - - +
390H LEU* 1.3 75.7 - - - +
392H GLU* 1.3 58.5 + - - +
395H GLY* 2.8 35.8 + - - +
396H ASP* 5.1 1.6 - - - +
400H LEU* 4.5 4.5 - - + -
424H LEU* 3.7 30.1 - - + +
427H CYS* 4.2 15.0 - - + -
428H THR* 4.7 9.4 - - - +
431H ARG* 4.0 24.4 + - - +
437H LEU* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 392 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339H ARG* 2.8 43.8 + - - -
388H PRO 3.0 18.2 + - - +
389H ALA* 3.6 7.8 - - - +
390H LEU 3.2 0.2 - - - -
391H VAL* 1.3 78.8 - - - +
393H ILE* 1.3 65.0 + - - +
395H GLY* 4.4 1.9 + - - -
431H ARG* 6.6 0.2 - - - +
436H ASP* 5.8 0.4 - - - +
437H LEU* 4.3 14.3 - - + +
438H ALA* 4.5 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 393 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330H THR 4.3 6.3 - - - +
331H VAL* 3.9 37.0 - - + -
332H VAL* 4.8 4.9 - - + -
339H ARG* 3.4 32.8 - - + +
342H THR* 5.2 2.2 - - + -
343H LEU* 3.4 34.4 - - + +
346H VAL* 5.9 0.9 - - - +
350H ARG* 5.3 2.3 + - - -
389H ALA* 2.8 36.0 + - + +
390H LEU* 3.3 4.7 + - + +
392H GLU* 1.3 78.7 - - - +
394H PHE* 1.3 88.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 394 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H SER* 3.3 19.7 - - - -
329H GLY 3.3 23.3 - - - -
330H THR* 4.2 8.3 - - - -
342H THR* 4.4 8.1 - - + -
346H VAL* 3.9 27.1 - - + -
350H ARG* 2.8 33.0 + - - +
376H PRO* 4.5 6.5 - - + -
378H ALA* 3.7 20.9 - - + -
390H LEU* 2.9 39.1 + - + +
393H ILE* 1.3 97.7 - - + +
395H GLY* 1.3 63.8 + - - +
397H ASP 4.4 0.2 + - - -
398H ALA* 3.7 27.6 - - + -
400H LEU* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 395 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H GLY* 4.9 3.3 + - - -
391H VAL* 2.8 31.2 + - - +
392H GLU 4.4 1.8 + - - -
393H ILE 3.7 1.0 - - - -
394H PHE* 1.3 82.7 - - - +
396H ASP* 1.3 66.8 + - - +
397H ASP 3.6 0.2 + - - -
398H ALA* 4.4 3.6 - - - +
400H LEU* 5.9 1.2 - - - +
431H ARG* 4.4 9.6 - - - -
----------------------------------------------------------
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