Contacts of the helix formed by residues 29 - 45 (chain 2) in PDB entry 5IY6
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 GLY 29 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282 PRO* 1.3 67.5 - - - +
302 VAL* 1.3 54.8 + - - +
312 LEU 3.3 0.2 - - - -
322 ASP* 3.0 27.7 - - - +
332 ARG* 3.4 12.0 + - - +
253 GLN* 2.1 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292 GLY* 1.3 71.4 - - - -
312 LEU* 1.3 68.6 + - + +
332 ARG* 3.0 10.0 + - + +
342 LEU* 2.9 62.5 + - + +
233 GLY 4.4 5.2 - - - +
243 LYS 1.9 34.1 - - - +
253 GLN* 2.0 54.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282 PRO* 3.1 9.1 + - + +
302 VAL* 1.3 72.6 - - + +
322 ASP* 1.3 65.1 + - - +
332 ARG 3.3 0.2 + - - -
352 TYR* 3.0 34.7 + - + +
622 LEU* 3.6 30.2 - - + +
243 LYS 4.6 0.2 - - - +
253 GLN 2.2 35.7 + - - +
333 THR* 2.2 79.6 - - + +
363 LYS* 4.2 3.1 - - + -
2213 PRO* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282 PRO 4.2 2.5 + - - +
292 GLY* 3.0 19.2 + - - +
312 LEU* 1.3 78.0 - - - +
332 ARG* 1.3 93.8 + - - +
352 TYR* 3.9 1.5 - - - +
362 GLY* 2.9 22.3 + - - -
622 LEU* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292 GLY 3.4 13.9 + - - +
302 VAL* 3.0 10.5 + - - +
322 ASP* 1.3 95.8 + - - +
342 LEU* 1.4 70.5 + - + +
362 GLY* 3.0 10.4 + - - -
372 HIS* 3.1 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302 VAL* 2.9 41.0 + - + +
332 ARG* 1.4 81.0 - - + +
352 TYR* 1.3 83.4 + - + +
372 HIS* 3.1 6.0 + - + +
382 PRO* 2.8 29.5 - - - +
2193 GLN* 6.0 1.6 - - - +
2213 PRO* 5.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312 LEU* 3.0 20.5 + - + +
322 ASP* 4.6 0.9 - - - +
342 LEU* 1.3 93.9 - - + +
362 GLY* 1.3 62.4 + - - +
382 PRO* 3.3 12.6 - - + +
392 ALA* 3.0 19.6 + - - +
582 ARG* 4.6 15.9 - - + -
592 MET* 5.1 14.1 - - + +
612 PHE* 5.3 3.8 - + - -
622 LEU* 2.9 59.5 - - + -
2213 PRO* 1.6 59.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 36 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322 ASP 2.9 19.3 + - - -
332 ARG* 3.0 3.7 + - - -
352 TYR* 1.3 75.1 - - - +
372 HIS* 1.3 65.6 + - - +
392 ALA* 2.8 10.4 + - - +
402 THR* 2.8 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 37 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332 ARG 3.1 9.2 + - - +
342 LEU* 3.1 9.3 + - + +
362 GLY* 1.3 75.3 - - - +
382 PRO* 1.3 75.8 - - + +
402 THR* 2.9 27.7 + - + +
412 CYS* 2.9 15.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 38 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342 LEU 2.8 26.5 - - - +
352 TYR* 3.7 10.8 - - + +
362 GLY 3.2 0.2 - - - -
372 HIS* 1.3 90.8 - - + +
392 ALA* 1.3 58.8 + - - +
412 CYS* 2.9 26.2 - - - -
422 LEU* 3.1 4.9 + - - +
552 TRP* 3.9 32.8 - - + +
582 ARG* 5.6 7.4 - - + -
592 MET* 3.6 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352 TYR 3.0 12.7 + - - +
362 GLY* 2.8 15.6 + - - +
382 PRO* 1.3 77.0 - - - +
402 THR* 1.3 62.8 + - - +
422 LEU* 3.5 1.9 + - - +
432 ALA* 3.1 22.7 + - - +
592 MET* 3.5 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 40 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362 GLY 2.8 14.5 + - - -
372 HIS* 3.2 23.0 + - + +
392 ALA* 1.3 75.3 - - - +
412 CYS* 1.4 67.8 + - - +
432 ALA* 3.0 8.7 + - + +
442 VAL* 2.9 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 41 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372 HIS* 2.9 13.5 + - + +
382 PRO* 2.9 27.1 + - + -
402 THR* 1.4 76.5 - - - +
422 LEU* 1.3 67.1 + - - +
442 VAL* 2.7 31.6 - - + +
452 PHE* 3.3 6.4 + - - +
512 LEU* 5.0 4.3 - - + +
552 TRP* 3.2 52.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382 PRO 3.1 8.7 + - - +
392 ALA 4.0 3.8 - - - +
412 CYS* 1.3 83.6 - - - +
432 ALA* 1.3 64.1 + - - +
452 PHE 3.6 3.0 + - - +
462 ARG* 3.3 22.9 + - - +
512 LEU* 4.0 8.7 - - + -
522 ALA* 3.5 28.1 - - + +
552 TRP* 2.9 33.0 - - + -
562 VAL* 3.5 35.4 - - + +
592 MET* 3.1 30.5 - - + -
882 GLY* 5.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392 ALA 3.1 13.7 + - - +
402 THR* 3.0 14.1 + - + +
422 LEU* 1.3 77.6 - - - +
442 VAL* 1.3 64.2 + - - +
462 ARG* 3.2 22.4 + - - +
842 GLU* 5.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402 THR* 2.9 13.9 + - + +
412 CYS* 2.7 34.1 - - + +
432 ALA* 1.3 77.9 - - - +
452 PHE* 1.4 94.8 + - + +
462 ARG 3.1 4.2 + - - -
472 GLU* 4.8 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412 CYS 3.3 3.6 + - - -
422 LEU* 3.7 4.6 - - - +
442 VAL* 1.4 120.5 - - + +
462 ARG* 1.3 59.4 + - - +
472 GLU* 3.6 2.7 - - - +
482 LEU 5.3 1.4 + - - -
492 PRO* 5.4 8.8 - - + +
512 LEU* 3.0 45.7 + - + +
522 ALA* 5.2 1.7 + - - +
----------------------------------------------------------
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