Contacts of the helix formed by residues 349 - 366 (chain C) in PDB entry 2XLR
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 349 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C PRO* 1.3 79.6 - - - +
350C LYS* 1.3 66.1 + - - +
351C GLU* 3.6 11.9 + - - +
352C GLU* 3.1 37.0 + - - +
353C MET* 3.1 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 4.9 5.5 + - - +
310C GLU 3.5 20.6 - - - +
311C ASP* 3.2 26.0 + - - +
349C SER* 1.3 74.0 - - - +
351C GLU* 1.3 63.6 + - - +
353C MET* 3.3 24.1 + - + +
354C LYS* 3.0 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C SER* 3.6 10.6 + - - +
350C LYS* 1.3 80.7 - - - +
352C GLU* 1.3 63.9 + - + +
354C LYS* 3.3 7.3 + - - +
355C ALA* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C TYR* 5.2 1.1 - - - -
348C PRO* 3.8 17.8 - - + +
349C SER* 3.1 36.5 + - - +
351C GLU* 1.3 78.4 - - + +
353C MET* 1.3 61.9 + - - +
355C ALA* 3.2 7.4 + - - +
356C ASP* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C TYR* 3.6 45.3 - - + -
308C VAL* 4.9 4.0 - - - -
310C GLU* 3.6 40.4 - - + +
313C PRO* 4.4 15.0 - - + -
347C LEU* 4.4 14.6 - - + -
348C PRO* 4.0 19.7 - - + +
349C SER 3.1 11.3 + - - +
350C LYS* 3.3 25.1 + - + +
352C GLU* 1.3 73.9 - - - +
354C LYS* 1.3 57.8 + - - +
356C ASP* 3.4 2.6 + - - +
357C SER* 3.0 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY 5.2 4.0 - - - +
35A GLU* 3.0 39.7 + - + +
301C LEU* 6.3 0.6 - - - +
302C ASN* 3.0 22.8 + - - +
310C GLU* 2.9 38.6 + - - +
311C ASP* 5.0 1.3 + - - -
350C LYS* 3.0 40.6 + - + +
351C GLU* 3.7 7.0 - - - +
353C MET* 1.3 78.5 - - - +
355C ALA* 1.3 56.2 + - - +
357C SER* 3.5 3.3 + - - +
358C MET* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C GLU 3.1 13.2 + - - +
352C GLU* 3.2 10.3 + - - +
354C LYS* 1.3 72.9 - - - +
356C ASP* 1.3 66.0 - - - +
358C MET* 3.4 15.2 + - + +
359C ALA* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C TRP* 5.5 0.3 - - - -
304C TYR* 3.7 28.8 + - + +
305C LYS* 4.4 20.5 + - - +
352C GLU 2.9 12.4 + - - +
353C MET 3.5 8.5 - - - +
355C ALA* 1.3 75.2 - - - +
357C SER* 1.3 61.6 + - - +
359C ALA* 3.2 8.3 + - - +
360C TRP* 3.2 45.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C TRP* 3.3 26.5 + - - +
301C LEU* 4.3 11.1 - - - +
302C ASN 5.1 3.4 - - - -
303C LEU 3.5 14.2 + - - -
304C TYR* 4.0 4.2 - - - -
305C LYS 4.9 0.3 + - - -
310C GLU* 2.7 33.3 + - - -
353C MET 3.0 8.2 + - - -
354C LYS* 4.0 4.3 - - - -
356C ASP* 1.3 76.2 + - - +
358C MET* 1.3 62.1 + - - +
360C TRP 3.4 0.5 + - - -
361C ARG* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS 3.8 12.8 - - - +
33A GLY* 4.1 25.6 - - - +
34A ALA* 4.7 6.5 - - - -
301C LEU* 5.2 0.2 - - - -
354C LYS 3.0 18.1 + - - +
355C ALA* 3.7 13.9 - - + +
356C ASP 3.3 0.2 - - - -
357C SER* 1.3 76.4 - - - +
359C ALA* 1.3 55.3 + - - +
361C ARG* 3.1 6.7 + - - +
362C GLU* 2.7 58.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C ALA 3.2 12.0 + - - +
356C ASP* 3.2 11.2 + - - +
358C MET* 1.3 75.8 - - - +
360C TRP* 1.3 64.9 + - + +
362C GLU* 3.2 17.3 + - - +
363C LYS* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C TRP* 3.4 44.8 - + + +
305C LYS* 5.4 6.4 - - + +
356C ASP* 3.2 46.7 + - - -
357C SER 3.8 1.3 - - - +
358C MET 3.3 0.2 - - - -
359C ALA* 1.3 78.1 - - + +
361C ARG* 1.3 57.0 + - - +
363C LYS* 3.4 4.4 + - + +
364C GLU* 3.0 16.3 + - - +
376C TYR* 2.8 56.1 + + - -
379C ASP* 4.2 10.8 - - + -
380C TYR* 3.6 43.1 - + + -
383C ASN* 4.5 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLN 3.8 7.9 + - - -
31A GLU* 2.9 41.9 + - - +
32A LYS 4.0 15.3 - - - -
33A GLY* 4.0 2.2 - - - +
294C THR* 5.4 0.2 + - - -
297C ARG* 3.3 27.7 - - - +
299C TRP* 2.7 34.1 + - + -
301C LEU* 3.6 34.7 - - + +
357C SER 3.0 17.7 + - - +
358C MET* 3.1 4.7 + - - +
360C TRP* 1.3 73.8 - - - +
362C GLU* 1.3 66.9 + - - +
364C GLU* 2.7 29.2 + - - +
365C LEU* 3.1 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 4.2 13.9 - - + +
358C MET* 2.7 46.4 + - - +
359C ALA* 3.5 19.3 + - - +
361C ARG* 1.3 75.4 - - - +
363C LYS* 1.3 63.3 + - - +
365C LEU* 3.4 17.4 + - + +
366C THR* 3.6 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ALA 3.1 15.2 + - - +
360C TRP* 3.8 7.4 - - + +
362C GLU* 1.3 75.6 - - - +
364C GLU* 1.3 59.6 + - - +
366C THR* 2.9 44.6 - - + +
367C LEU* 3.5 10.4 - - + +
376C TYR* 3.7 23.6 - - + -
379C ASP* 5.9 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ARG* 3.0 37.0 + - - +
298C LEU* 3.6 14.4 + - + +
299C TRP* 3.1 26.7 + - + +
360C TRP 3.0 15.4 + - - +
361C ARG* 2.7 39.8 + - - +
363C LYS* 1.3 77.0 - - - +
365C LEU* 1.3 60.8 + - - +
367C LEU* 3.3 31.6 + - + +
376C TYR* 3.6 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 3.7 46.0 - - + +
32A LYS* 4.0 21.5 - - + -
297C ARG* 4.0 13.2 - - - +
361C ARG* 3.1 19.2 + - + +
362C GLU* 3.7 12.3 - - + +
363C LYS 3.2 0.6 - - - -
364C GLU* 1.3 76.1 - - - +
366C THR* 1.3 58.1 + - - +
367C LEU 3.3 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLU 3.6 7.4 + - - -
363C LYS* 2.9 34.5 + - + +
365C LEU* 1.3 77.3 - - - +
367C LEU* 1.3 73.0 + - + +
368C VAL* 3.5 13.4 + - - +
372C GLU* 4.8 8.1 - - - +
----------------------------------------------------------
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