Contacts of the helix formed by residues 332 - 348 (chain T) in PDB entry 5L4K
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 SER 332 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328T THR 3.0 9.7 + - - -
329T THR* 2.4 30.6 + - - -
330T ILE 3.8 1.7 + - - -
331T PRO* 1.3 72.4 - - - +
333T THR* 1.3 80.3 + - - +
334T GLU 3.3 0.2 + - - -
335T LEU* 3.6 6.8 + - - +
336T ALA* 3.2 21.1 + - - +
249U PHE* 6.5 1.1 - - - -
303V MET* 4.4 8.5 - - - +
306V THR* 3.7 24.7 - - - -
307V VAL* 3.8 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 333 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363O MET* 3.7 28.7 - - - -
366O LEU* 3.9 17.5 - - + +
330T ILE 4.1 4.7 + - - -
331T PRO 2.6 5.8 + - - -
332T SER* 1.3 88.1 + - - +
334T GLU* 1.3 77.4 + - - +
336T ALA* 3.2 6.8 + - - +
337T LYS* 3.0 26.7 + - - +
307V VAL* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330T ILE 4.6 4.9 - - - +
331T PRO* 2.5 21.4 + - + +
333T THR* 1.3 85.5 + - - +
335T LEU* 1.3 66.2 + - + +
337T LYS* 3.1 42.2 + - - +
338T GLN* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470S ARG* 4.1 15.7 - - + +
473S GLN* 3.2 31.8 + - + +
474S LEU* 5.7 0.9 - - + -
331T PRO* 3.6 29.5 + - + -
332T SER* 3.6 6.0 + - - +
334T GLU* 1.3 79.3 - - + +
336T ALA* 1.3 57.7 + - - +
338T GLN* 3.1 21.9 + - - +
339T VAL* 3.0 31.9 + - - +
249U PHE* 5.7 4.5 - - + -
250U TYR* 4.2 21.5 - - + +
253U THR* 5.9 1.3 - - + -
303V MET* 3.6 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363O MET* 5.3 5.4 - - + -
366O LEU* 5.2 5.8 - - + -
367O VAL* 5.6 3.6 - - + -
332T SER 3.2 12.9 + - - +
333T THR* 3.2 11.6 + - - +
334T GLU 3.2 0.6 - - - -
335T LEU* 1.3 73.8 - - - +
337T LYS* 1.3 65.3 + - - +
339T VAL* 3.4 1.1 + - - -
340T ILE* 3.0 29.4 + - - +
300V LEU* 3.5 25.5 - - + +
303V MET* 3.8 15.2 - - + -
304V LEU* 5.0 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 337 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366O LEU* 3.6 33.3 - - + +
367O VAL* 6.4 0.2 - - - -
370O GLN* 3.4 40.0 + - - +
333T THR* 3.0 17.0 + - - +
334T GLU* 3.2 42.7 + - - +
336T ALA* 1.3 77.7 - - - +
338T GLN* 1.3 63.6 + - + +
340T ILE* 3.1 6.5 + - - +
341T GLU* 2.9 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 338 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473S GLN* 4.0 13.7 + - - +
474S LEU* 5.1 7.7 - - - +
477S HIS* 3.3 51.9 + - + +
334T GLU* 3.1 11.9 + - - +
335T LEU* 3.1 23.2 + - - +
337T LYS* 1.3 79.1 - - + +
339T VAL* 1.3 65.2 + - + +
341T GLU* 2.8 19.5 + - - +
342T TYR* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473S GLN* 5.8 3.1 - - - +
335T LEU 3.0 15.0 + - - +
336T ALA 3.8 5.6 - - - +
338T GLN* 1.3 72.6 - - + +
340T ILE* 1.3 65.7 + - + +
342T TYR* 3.0 30.1 + - + +
343T ALA* 3.1 11.2 + - + +
257U MET* 5.9 2.9 - - - -
296V ILE* 3.3 34.4 - - + +
297V VAL* 5.9 0.4 - - + -
299V CYS* 4.0 9.6 - - + -
300V LEU* 3.7 27.4 - - + +
303V MET* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 340 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367O VAL* 4.1 15.5 - - + -
370O GLN* 4.1 14.4 - - + +
371O ALA* 3.4 49.8 - - + +
375O LEU* 4.5 3.6 - - + -
336T ALA 3.0 18.9 + - - +
337T LYS* 3.3 11.2 - - - +
339T VAL* 1.3 74.9 - - + +
341T GLU* 1.3 64.7 + - - +
343T ALA* 3.0 9.3 + - - +
344T ARG* 3.0 21.7 + - + +
191U ILE* 3.9 17.3 - - + -
300V LEU* 3.5 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 341 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477S HIS* 6.6 0.2 - - + -
337T LYS 2.9 11.5 + - - +
338T GLN* 2.8 23.1 + - - +
340T ILE* 1.3 69.4 - - - +
342T TYR* 1.3 71.1 + - + +
344T ARG* 2.8 40.0 + - - +
345T GLN* 3.1 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 342 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473S GLN* 4.5 2.0 + - - -
477S HIS* 3.2 42.8 + + - +
480S ILE* 3.4 36.7 - - + +
481S SER* 4.4 7.6 - - - -
484S LEU* 6.3 0.7 - - - -
338T GLN* 3.0 32.1 + - + -
339T VAL* 3.5 21.5 - - + +
341T GLU* 1.3 79.1 - - + +
343T ALA* 1.3 65.2 + - - +
345T GLN* 2.9 26.0 + - - +
346T LEU* 3.0 20.3 + - + +
257U MET* 3.8 19.0 - - + +
260U VAL* 5.5 3.8 - - + -
296V ILE* 4.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375O LEU* 4.0 6.1 - - + -
339T VAL 3.1 6.7 + - - +
340T ILE* 3.0 11.5 + - - +
342T TYR* 1.3 79.3 - - - +
344T ARG* 1.3 62.9 + - - +
346T LEU* 3.0 9.0 + - - +
347T GLU* 2.9 24.8 + - - +
187U LEU* 3.8 25.9 - - + +
191U ILE* 3.7 29.2 - - + -
296V ILE* 5.1 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370O GLN* 3.9 30.1 + - - +
373O ASP* 5.0 0.8 + - - -
374O ILE* 3.5 42.9 - - + +
375O LEU* 3.7 23.8 - - + -
340T ILE* 3.0 19.1 + - + +
341T GLU* 2.8 39.2 + - - +
343T ALA* 1.3 71.4 - - - +
345T GLN* 1.3 57.0 + - - +
348T MET* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 345 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481S SER* 4.7 15.4 + - - +
484S LEU* 3.0 44.8 - - + +
485S ASP* 4.5 4.3 + - - -
487S HIS* 5.7 0.5 - - - -
488S ASN* 3.7 27.0 + - - +
341T GLU* 3.2 40.3 + - - +
342T TYR* 2.9 18.0 + - - +
344T ARG* 1.3 76.8 - - + +
346T LEU* 1.3 61.4 + - - +
347T GLU 3.5 0.3 + - - -
348T MET* 4.3 7.9 + - - +
267U ARG* 4.8 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484S LEU* 3.6 16.2 - - + -
342T TYR* 3.0 21.0 + - + +
343T ALA* 3.0 4.4 + - - +
345T GLN* 1.3 76.3 - - - +
347T GLU* 1.3 61.4 + - - +
348T MET 4.9 1.3 - - - +
187U LEU* 4.0 21.0 - - + +
264U SER* 5.9 0.4 - - - -
267U ARG* 3.0 46.1 + - - +
292V MET* 3.8 23.6 - - + -
296V ILE* 3.2 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 347 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374O ILE* 5.6 2.9 - - + -
375O LEU* 3.4 30.5 - - + +
343T ALA 2.9 14.3 + - - +
344T ARG 4.1 0.4 - - - +
346T LEU* 1.3 80.4 - - - +
348T MET* 1.3 71.4 + - - +
349T ILE* 4.5 4.7 - - - +
185U GLY* 4.7 11.6 + - - -
186U THR 5.4 0.3 + - - -
187U LEU* 4.0 22.7 + - + +
188U SER* 3.5 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 348 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374O ILE* 5.5 10.4 - - + +
488S ASN* 4.6 7.6 - - - +
492S LYS* 6.1 3.6 - - - +
344T ARG 2.9 18.8 + - - +
345T GLN* 4.3 9.5 + - - +
346T LEU 4.9 1.2 - - - -
347T GLU* 1.3 86.5 + - - +
349T ILE* 1.3 67.9 + - - +
350T VAL* 3.5 30.4 + - + +
----------------------------------------------------------
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