Contacts of the helix formed by residues 338 - 351 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331K VAL* 5.1 0.2 - - - -
337K GLY* 1.3 71.8 - - - +
339K ARG* 1.3 72.3 + - - +
340K GLU* 3.0 29.3 + - - +
341K VAL* 3.0 36.6 + - + +
342K THR* 2.8 27.8 + - - -
471K THR* 3.9 33.1 - - + +
473K ASP* 4.2 10.2 + - - +
474K LYS* 5.7 5.8 - - + -
475K LEU* 4.8 5.1 + - - +
1481K EDO 4.6 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 339 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331K VAL* 4.0 26.4 - - + +
337K GLY 3.6 2.4 + - - -
338K GLU* 1.3 80.7 + - - +
340K GLU* 1.3 70.2 + - + +
342K THR* 3.3 1.9 + - - -
343K LEU* 2.9 57.7 + - + +
389K ALA* 6.2 0.4 - - - +
392K GLU* 2.8 43.0 + - - -
393K ILE* 3.5 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338K GLU* 3.0 23.2 + - - +
339K ARG* 1.3 93.0 + - + +
341K VAL* 1.3 67.6 + - - +
343K LEU* 3.5 5.8 + - - +
344K GLY 3.1 17.5 + - - -
359K SER* 3.7 19.7 + - - +
360K ARG* 3.0 49.8 + - - +
475K LEU* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 341 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310K HIS* 3.4 35.4 - - + +
312K ARG* 4.4 2.3 + - - +
338K GLU* 3.0 28.8 + - + +
340K GLU* 1.3 74.9 - - - +
342K THR* 1.3 62.8 + - - +
344K GLY* 3.3 3.1 + - - -
345K PHE* 3.2 34.6 + - + -
360K ARG 4.0 10.0 - - - +
473K ASP* 4.0 23.3 - - - +
474K LYS 5.0 0.4 - - - -
475K LEU* 3.7 31.2 - - + +
1481K EDO 4.1 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 342 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328K SER 3.7 22.0 + - - +
329K GLY* 5.1 1.3 - - - +
331K VAL* 3.9 19.9 + - + +
337K GLY* 3.6 19.1 + - - -
338K GLU 2.8 20.5 + - - -
339K ARG 3.5 4.0 - - - -
341K VAL* 1.3 74.9 - - - +
343K LEU* 1.3 59.8 + - - +
344K GLY 3.2 0.3 + - - -
345K PHE* 3.2 17.3 + - + -
346K VAL* 2.8 44.2 + - + +
393K ILE* 5.2 3.1 - - + -
394K PHE* 4.5 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339K ARG* 2.9 51.4 + - + +
340K GLU* 3.9 8.3 - - - +
341K VAL 3.4 0.2 - - - -
342K THR* 1.3 76.2 - - + +
344K GLY* 1.3 61.7 + - - +
346K VAL* 3.6 9.9 + - + +
347K ASP* 3.2 29.3 + - - +
360K ARG* 3.4 39.9 - - - +
393K ILE* 3.5 41.1 - - + +
394K PHE* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 344 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312K ARG* 6.2 0.2 - - - -
340K GLU 3.1 11.2 + - - -
341K VAL 3.7 4.0 - - - -
342K THR 3.1 0.2 - - - -
343K LEU* 1.3 76.2 - - - +
345K PHE* 1.3 61.2 + - - +
347K ASP* 3.3 8.6 + - - +
348K LEU* 3.1 23.7 + - - +
360K ARG* 3.8 22.4 - - - +
362K ILE* 3.8 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 345 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295K ARG* 4.7 0.4 - - - -
310K HIS* 4.1 9.4 - + - -
311K PHE* 3.7 38.1 - + + -
312K ARG* 3.7 27.2 - - + +
315K ALA* 4.9 2.9 - - + -
328K SER* 3.2 35.2 - - - -
337K GLY* 6.1 0.7 - - - -
341K VAL* 3.2 34.8 + - + -
342K THR* 3.6 28.9 - - + -
344K GLY* 1.3 72.7 - - - +
346K VAL* 1.3 63.3 + - - +
348K LEU* 3.2 10.2 + - + +
349K MET* 2.9 38.9 + - - +
360K ARG 4.9 0.2 + - - -
1481K EDO 3.9 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 346 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328K SER* 4.2 14.6 - - - -
342K THR* 2.8 29.3 + - + +
343K LEU* 3.8 12.6 - - + +
345K PHE* 1.3 79.0 - - + +
347K ASP* 1.3 57.3 + - - +
349K MET* 3.1 9.1 + - - +
350K ARG* 3.0 67.8 + - - +
376K PRO* 4.3 7.4 - - + -
393K ILE 6.0 0.4 - - - +
394K PHE* 3.9 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 347 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343K LEU 3.2 16.5 + - - +
344K GLY* 3.5 10.7 - - - +
345K PHE 3.3 0.2 - - - -
346K VAL* 1.3 78.1 - - - +
348K LEU* 1.3 57.3 + - - +
350K ARG* 4.5 13.3 + - - -
351K ASP* 2.9 58.9 + - - +
354K VAL* 3.5 19.1 - - + +
360K ARG* 4.3 14.7 + - - -
362K ILE* 5.3 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137K ASP* 5.0 0.9 - - - +
312K ARG* 4.0 31.0 - - + +
315K ALA* 6.1 2.2 - - + -
316K LYS* 3.8 38.0 - - + +
319K ARG* 2.7 24.6 + - - -
344K GLY 3.1 14.2 + - - +
345K PHE* 3.2 10.5 + - + +
347K ASP* 1.3 79.7 - - - +
349K MET* 1.3 52.7 + - + +
354K VAL* 3.8 30.1 - - + -
362K ILE* 4.2 21.5 - - + -
366K GLN* 3.9 15.9 - - + -
368K TRP* 2.9 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 349 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311K PHE* 4.7 2.0 - - - -
315K ALA* 3.9 22.9 - - + +
319K ARG* 3.0 22.6 + - + +
326K LEU* 3.6 37.9 - - + +
328K SER* 4.4 10.1 - - - -
345K PHE* 2.9 34.1 + - - +
346K VAL* 3.1 11.8 + - - +
348K LEU* 1.3 78.8 - - - +
350K ARG* 1.3 55.8 + - + +
374K VAL* 2.9 41.6 + - + +
376K PRO* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 350 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155K ILE* 3.8 15.8 - - + +
319K ARG* 3.9 1.5 + - - -
346K VAL* 3.0 36.2 + - - +
347K ASP* 4.5 9.9 + - - -
349K MET* 1.3 79.4 - - + +
351K ASP* 1.3 73.4 + - - +
373K GLY* 3.6 19.3 + - - -
374K VAL 3.6 16.6 - - - +
376K PRO* 3.6 18.2 - - + +
393K ILE 5.3 1.8 + - - -
394K PHE* 2.8 33.1 + - - +
397K ASP* 2.9 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 351 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319K ARG* 2.8 25.8 + - - -
347K ASP* 2.9 43.7 + - - +
350K ARG* 1.3 90.1 + - - +
352K ASP* 1.3 60.6 + - - +
353K TYR 4.2 7.1 - - - +
354K VAL* 3.9 12.6 - - + +
368K TRP* 3.2 8.3 - - - -
----------------------------------------------------------
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