Contacts of the helix formed by residues 338 - 351 (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 GLU 338 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331H VAL* 5.1 0.2 - - - -
336H GLU* 4.9 0.2 - - - +
337H GLY* 1.3 72.2 - - - +
339H ARG* 1.3 79.0 + - - +
340H GLU* 3.0 29.1 + - - +
341H VAL* 3.0 37.6 + - + +
342H THR* 2.9 24.0 + - - -
471H THR* 3.9 32.8 - - + +
473H ASP* 4.2 9.8 + - - +
474H LYS* 5.7 5.8 - - + -
475H LEU* 4.8 5.7 + - - +
1482H EDO 4.9 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 339 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331H VAL* 4.0 27.9 - - + +
337H GLY 3.6 2.0 + - - -
338H GLU* 1.3 80.4 - - - +
340H GLU* 1.3 70.5 + - - +
342H THR* 3.3 1.4 + - - -
343H LEU* 2.9 57.3 + - + +
389H ALA* 6.2 0.2 - - - +
392H GLU* 2.8 42.4 + - - -
393H ILE* 3.4 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H GLU* 3.0 24.2 + - - +
339H ARG* 1.3 92.6 + - + +
341H VAL* 1.3 65.6 + - - +
343H LEU* 3.5 5.0 + - - +
344H GLY 3.1 18.5 + - - -
359H SER* 3.7 20.1 + - - +
360H ARG* 3.1 47.2 + - - +
475H LEU* 4.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 341 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310H HIS* 3.4 36.1 - - + +
312H ARG* 4.4 2.5 + - - +
338H GLU* 3.0 27.4 + - + +
340H GLU* 1.3 73.9 - - - +
342H THR* 1.3 63.6 + - - +
344H GLY* 3.3 3.6 + - - -
345H PHE* 3.2 33.7 + - + -
360H ARG 4.0 9.5 - - - +
473H ASP* 4.0 23.6 - - - +
474H LYS 5.0 0.4 - - - -
475H LEU* 3.7 32.5 - - + +
1482H EDO 4.0 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 342 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H SER 3.7 21.2 + - - +
329H GLY* 5.1 1.5 - - - +
331H VAL* 4.0 20.2 + - + +
337H GLY* 3.6 18.5 + - - -
338H GLU 2.9 21.5 + - - -
339H ARG 3.5 4.5 - - - -
341H VAL* 1.3 73.8 - - - +
343H LEU* 1.3 60.1 + - - +
345H PHE* 3.2 20.0 + - + -
346H VAL* 2.9 43.7 + - + +
393H ILE* 5.2 2.9 - - + -
394H PHE* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339H ARG* 2.9 52.3 + - + +
340H GLU* 3.9 7.9 - - - +
342H THR* 1.3 76.0 - - + +
344H GLY* 1.3 61.8 + - - +
346H VAL* 3.8 10.1 - - + +
347H ASP* 3.2 29.3 + - - +
360H ARG* 3.4 40.4 - - - +
393H ILE* 3.4 42.0 - - + +
394H PHE* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 344 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ARG* 6.2 0.4 - - - -
340H GLU 3.1 11.0 + - - -
341H VAL 3.6 3.8 - - - -
342H THR 3.2 0.4 - - - -
343H LEU* 1.3 77.5 - - - +
345H PHE* 1.3 61.4 + - - +
347H ASP* 3.3 8.1 + - - +
348H LEU* 3.2 22.8 + - - +
360H ARG* 3.8 22.6 - - - +
362H ILE* 3.8 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 345 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295H ARG* 4.6 0.4 - - - -
310H HIS* 4.1 10.1 - + - -
311H PHE* 3.7 37.2 - + + -
312H ARG* 3.7 27.5 - - + +
315H ALA* 4.9 3.6 - - + -
328H SER* 3.3 33.9 - - - -
337H GLY* 6.0 0.2 - - - -
341H VAL* 3.2 28.1 + - + -
342H THR* 3.7 28.7 - - + -
344H GLY* 1.3 73.4 - - - +
346H VAL* 1.3 64.4 + - + +
348H LEU* 3.1 10.7 + - + +
349H MET* 2.8 39.0 + - - +
360H ARG 4.9 0.2 + - - -
1482H EDO 3.8 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 346 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H SER* 4.1 15.3 - - - -
342H THR* 2.9 29.1 + - + +
343H LEU* 3.8 13.0 - - + +
345H PHE* 1.3 79.2 - - + +
347H ASP* 1.3 58.3 + - - +
349H MET* 3.1 9.1 + - - +
350H ARG* 3.0 67.8 + - - +
376H PRO* 4.4 7.0 - - + -
393H ILE 5.9 0.4 - - - +
394H PHE* 3.9 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 347 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343H LEU 3.2 14.7 + - - +
344H GLY* 3.5 10.6 - - - +
345H PHE 3.3 0.2 - - - -
346H VAL* 1.3 77.8 - - - +
348H LEU* 1.3 57.2 + - - +
350H ARG* 4.5 12.7 + - - -
351H ASP* 2.9 59.1 + - - +
354H VAL* 3.5 19.3 - - + +
360H ARG* 4.2 15.0 + - - -
362H ILE* 5.3 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H ASP* 5.0 1.1 - - - +
312H ARG* 4.1 29.4 - - + +
315H ALA* 6.1 1.8 - - + -
316H LYS* 3.8 39.7 - - + +
319H ARG* 2.8 24.1 + - - -
344H GLY 3.2 13.6 + - - +
345H PHE* 3.1 11.0 + - + +
347H ASP* 1.3 78.2 - - - +
349H MET* 1.3 53.4 + - + +
354H VAL* 3.8 30.5 - - + -
362H ILE* 4.2 21.1 - - + -
366H GLN* 3.9 16.8 - - + -
368H TRP* 2.9 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 349 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311H PHE* 4.7 2.0 - - - -
315H ALA* 3.9 23.1 - - + +
319H ARG* 3.1 21.3 + - - +
326H LEU* 3.6 38.8 - - + +
328H SER* 4.4 11.7 - - - -
345H PHE* 2.8 33.7 + - - +
346H VAL* 3.1 10.5 + - - +
348H LEU* 1.3 78.3 - - - +
350H ARG* 1.3 56.6 + - + +
374H VAL* 2.8 37.2 + - + +
376H PRO* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 350 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H ILE* 3.8 15.3 - - + +
319H ARG* 3.9 1.4 + - - -
346H VAL* 3.0 35.9 + - - +
347H ASP* 4.5 9.5 + - - -
349H MET* 1.3 78.9 - - + +
351H ASP* 1.3 73.3 + - - +
373H GLY* 3.6 19.7 + - - -
374H VAL 3.5 16.8 - - - +
376H PRO* 3.6 18.5 - - + +
393H ILE 5.3 1.6 + - - -
394H PHE* 2.8 32.1 + - - +
397H ASP* 2.9 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 351 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H ARG* 2.9 26.0 + - - -
347H ASP* 2.9 47.5 + - - +
350H ARG* 1.3 87.8 + - - +
352H ASP* 1.3 60.5 + - - +
353H TYR 4.2 7.5 - - - +
354H VAL* 3.9 13.2 - - + +
368H TRP* 3.2 7.8 - - - -
----------------------------------------------------------
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