Contacts of the helix formed by residues 341 - 362 (chain C) in PDB entry 2I0J
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 341 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C GLU* 2.0 19.0 + - - +
340C ALA* 1.3 78.2 - - - +
342C MET* 1.3 59.7 + - - +
343C MET* 3.8 6.6 + - - +
344C GLY* 3.0 22.6 + - - -
345C LEU* 2.8 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C GLU* 3.3 23.3 + - - +
340C ALA 4.4 0.2 - - - -
341C SER* 1.3 70.0 + - - +
343C MET* 1.3 64.4 + - - +
345C LEU* 3.2 14.1 + - - +
346C LEU* 2.9 34.2 + - + +
408C LEU* 5.6 0.9 - - - -
410C LEU* 3.4 37.0 - - + -
414C GLN* 3.0 39.7 - - + +
415C GLY* 5.1 0.4 - - - -
417C SER* 4.2 5.8 - - - +
418C VAL* 3.6 13.9 - - + +
421C MET* 4.1 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C I0G 4.3 20.9 - - + -
341C SER* 3.8 5.5 + - - +
342C MET* 1.3 77.3 - - - +
344C GLY* 1.3 57.3 + - - +
346C LEU* 4.3 3.8 - - - -
347C THR* 2.6 48.0 + - - +
418C VAL* 4.3 14.7 - - + +
421C MET* 3.1 32.1 - - + -
524C HIS* 3.8 22.0 - - + +
525C LEU* 4.2 20.9 - - + -
528C MET* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C ALA 5.0 0.2 - - - -
341C SER* 3.0 27.4 + - - -
343C MET* 1.3 75.9 - - - +
345C LEU* 1.3 56.6 + - - +
347C THR* 3.8 3.7 - - - -
348C ASN* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C SER* 3.5 18.9 + - - +
330C GLU 3.4 25.7 + - - +
331C TYR* 3.7 26.0 - - + -
340C ALA* 3.5 27.1 + - + +
341C SER 2.8 9.8 + - - +
342C MET* 3.6 13.7 - - - +
344C GLY* 1.3 72.8 - - - +
346C LEU* 1.3 65.1 + - + +
348C ASN* 3.9 4.9 - - + +
349C LEU* 3.1 23.9 + - - +
352C ARG* 5.7 0.2 + - - -
408C LEU* 4.0 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C I0G 4.0 28.6 - - + -
342C MET* 2.9 39.0 + - + +
343C MET* 3.7 4.7 - - - +
345C LEU* 1.3 71.6 - - + +
347C THR* 1.3 60.6 + - - +
349C LEU* 3.2 7.7 + - + +
350C ALA* 2.9 29.4 + - - +
404C PHE* 3.6 52.9 - - + -
408C LEU* 3.8 18.8 - - + -
410C LEU* 4.8 3.4 - - + -
421C MET* 4.3 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C I0G 5.2 5.0 - - - +
343C MET* 2.6 40.2 + - - +
344C GLY* 3.8 3.8 - - - -
346C LEU* 1.3 72.0 - - - +
348C ASN* 1.3 65.0 + - - +
350C ALA* 3.1 9.0 + - + +
351C ASP* 3.0 38.1 + - - +
525C LEU* 5.0 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C GLU* 3.4 28.4 - - + +
344C GLY 2.9 19.3 + - - +
345C LEU* 3.9 6.3 - - + +
347C THR* 1.3 78.3 - - - +
349C LEU* 1.3 62.2 + - - +
351C ASP* 3.4 10.0 + - - +
352C ARG* 3.3 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C I0G 4.1 14.1 - - + -
327C LEU* 4.3 20.0 - - + +
328C TYR 3.9 27.8 - - - +
329C SER* 4.5 3.8 - - - +
345C LEU 3.1 14.8 + - - +
346C LEU* 3.3 9.0 - - + +
348C ASN* 1.3 77.0 - - - +
350C ALA* 1.3 62.9 + - - +
351C ASP 3.3 0.2 + - - -
352C ARG* 3.3 12.5 + - - +
353C GLU* 3.1 35.4 + - - +
404C PHE* 3.7 41.3 - - + +
405C ALA* 4.5 4.5 - - + -
408C LEU* 4.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C I0G 3.9 25.8 - - + -
346C LEU 2.9 13.3 + - - +
347C THR* 3.5 10.3 - - + +
349C LEU* 1.3 76.4 - - - +
351C ASP* 1.3 60.5 + - - +
353C GLU* 3.4 3.3 + - - +
354C LEU* 3.0 30.1 + - - +
383C TRP* 5.0 5.2 - - + -
387C LEU* 3.7 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C THR* 3.0 30.4 + - - +
348C ASN* 3.6 14.2 + - - +
349C LEU 3.2 0.2 - - - -
350C ALA* 1.3 78.4 - - - +
352C ARG* 1.3 66.7 + - + +
354C LEU* 3.3 28.7 - - - +
355C VAL* 3.7 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C LEU* 3.5 24.5 - - + +
328C TYR 2.9 30.5 + - - +
329C SER* 3.9 2.2 - - - +
330C GLU* 3.2 50.1 + - - +
348C ASN* 3.3 21.2 + - - +
349C LEU* 3.9 16.0 - - - +
351C ASP* 1.3 80.7 - - + +
353C GLU* 1.3 61.6 + - - +
355C VAL* 3.7 12.9 + - - +
356C HIS* 3.2 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C I0G 2.4 42.1 + - - -
325C PRO 5.3 5.5 - - - +
326C ILE* 6.0 0.3 - - - -
327C LEU* 3.8 27.7 + - + -
349C LEU* 3.1 26.4 + - - +
350C ALA 3.7 4.5 - - - +
351C ASP 3.2 0.2 - - - -
352C ARG* 1.3 74.1 - - - +
354C LEU* 1.3 55.6 + - - +
355C VAL 3.1 0.4 - - - -
356C HIS* 3.0 9.4 + - + +
357C MET* 2.8 35.7 + - - +
387C LEU* 3.9 16.2 - - + +
394C ARG* 3.9 13.7 + - - -
404C PHE 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C ALA 3.0 15.2 + - - +
351C ASP* 3.3 22.6 + - - +
353C GLU* 1.3 76.3 - - - +
355C VAL* 1.3 65.2 + - + +
357C MET* 3.1 31.3 + - + +
358C ILE* 3.2 17.8 + - + +
383C TRP* 3.9 42.4 - - + -
387C LEU* 5.0 1.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C ASP 4.0 12.8 - - - +
352C ARG* 3.8 10.5 - - - +
353C GLU 3.1 0.6 - - - -
354C LEU* 1.3 77.0 - - + +
356C HIS* 1.3 71.8 + - + +
358C ILE* 3.0 26.8 + - - +
359C ASN* 3.5 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C PRO* 4.0 22.2 - - + +
325C PRO* 3.6 28.5 - - + +
327C LEU* 3.7 26.1 - - + +
352C ARG 3.2 23.8 - - - -
353C GLU* 3.0 9.1 + - + +
355C VAL* 1.3 85.1 - - + +
357C MET* 1.3 61.5 + - - +
359C ASN* 3.7 15.6 + - - +
360C TRP* 3.3 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C PRO* 5.4 3.1 - - - -
353C GLU 2.8 10.5 + - - +
354C LEU* 3.2 26.7 - - + +
355C VAL 3.0 0.4 - - - -
356C HIS* 1.3 78.8 - - - +
358C ILE* 1.3 58.3 + - + +
360C TRP* 3.0 24.1 - - + +
361C ALA* 2.8 25.3 + - - +
379C LEU* 4.4 13.9 - - + -
383C TRP* 3.4 43.1 - - - +
386C ILE* 4.1 22.7 - - + -
387C LEU* 3.4 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LEU* 3.5 17.9 - - + +
355C VAL* 3.0 11.4 + - - +
357C MET* 1.3 73.6 - - + +
359C ASN* 1.3 71.9 + - - +
360C TRP 2.9 2.4 + - - -
361C ALA* 3.0 8.7 + - - +
362C LYS* 3.0 40.0 + - + +
379C LEU* 4.0 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C VAL* 3.5 24.3 + - - +
356C HIS* 4.1 17.5 + - - +
357C MET 3.5 0.2 - - - -
358C ILE* 1.3 80.1 - - - +
360C TRP* 1.3 59.3 + - - +
362C LYS* 3.6 16.0 + - - +
363C ARG* 2.9 30.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
319C LEU* 4.9 4.4 + - - +
322C ALA* 3.2 43.9 - - + +
323C GLU* 3.9 5.4 + - - -
324C PRO* 3.9 17.9 - - + -
356C HIS 3.3 12.5 + - - +
357C MET* 3.0 26.0 + - + +
358C ILE 2.9 0.6 - - - -
359C ASN* 1.3 75.6 - - - +
361C ALA* 1.3 75.9 + - + +
363C ARG* 2.6 29.6 + - - +
364C VAL* 3.3 23.8 + - + +
386C ILE* 3.5 30.5 - - + -
446C VAL* 5.2 0.8 - - - +
449C LYS* 3.6 50.2 - - + +
450C SER* 3.8 16.9 + - - -
453C LEU* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C MET 2.8 15.4 + - - +
358C ILE 3.5 7.4 - - - +
360C TRP* 1.3 83.8 - - + +
362C LYS* 1.3 57.9 + - - +
364C VAL* 2.8 30.0 + - - +
367C PHE* 3.2 33.9 - - + +
379C LEU* 3.8 26.0 - - + -
453C LEU* 4.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ILE* 3.0 31.5 + - + +
359C ASN* 3.6 18.4 - - - +
361C ALA* 1.3 77.4 - - - +
363C ARG* 1.3 60.6 + - + +
364C VAL 3.4 2.0 - - - +
367C PHE* 4.1 5.2 - - + -
368C VAL* 3.2 37.8 - - + +
372C LEU* 6.2 1.8 - - - +
375C GLN* 4.3 16.5 + - - +
----------------------------------------------------------
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