Contacts of the helix formed by residues 357 - 365 (chain B) in PDB entry 1YA8
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 TRP 357 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.4 10.8 - - + -
356B GLY* 1.3 73.7 - - - +
358B LEU* 1.3 85.2 + - + +
359B ILE 3.5 2.0 - - - -
360B PRO* 3.0 13.4 - - - +
361B MET* 3.0 61.0 + - + +
457B SER* 3.3 35.7 - - - -
459B MET* 3.3 36.2 + - + +
460B LYS* 3.8 30.1 - - + -
461B PRO* 3.8 19.5 - - + -
464B VAL* 4.0 6.0 - - + +
467B ASP* 2.9 21.2 + - - +
4004B SMB 5.4 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.7 3.6 - - + -
100B LEU* 3.3 39.5 - - + -
101B PHE* 3.2 38.6 - - + -
357B TRP* 1.3 86.7 - - + +
359B ILE* 1.3 66.1 + - + +
361B MET* 3.4 6.3 - - + +
363B LEU* 2.9 36.5 + - + +
467B ASP* 2.9 22.8 + - - +
468B HIS* 3.4 27.8 - - + +
4002B SMB 5.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B GLU 3.4 20.2 - - - +
355B PHE* 3.6 21.1 - - + -
358B LEU* 1.3 73.2 - - + +
360B PRO* 1.3 73.7 - - + +
363B LEU* 3.1 9.4 + - - +
364B MET* 3.0 37.5 + - + +
425B MET* 4.7 3.4 - - + -
426B PHE* 3.6 27.4 - - + -
467B ASP* 5.1 0.6 + - - -
468B HIS* 3.5 35.9 - - + +
4002B SMB 4.2 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PHE* 3.2 53.8 - - + +
356B GLY 4.0 5.4 - - - +
357B TRP 3.0 20.9 - - - +
359B ILE* 1.3 88.3 - - + +
361B MET* 1.3 54.8 + - - +
364B MET* 3.1 3.8 + - + -
365B SER 2.8 25.1 + - - -
366B TYR* 2.8 32.2 + - + -
368B LEU* 4.8 8.1 - - + -
418B LEU* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 5.0 6.3 - - + -
100B LEU* 4.1 13.9 - - + -
357B TRP* 3.0 68.4 + - + +
358B LEU* 4.1 6.1 - - + +
360B PRO* 1.3 80.2 - - - +
363B LEU* 1.3 81.6 + - + +
365B SER* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ALA 6.0 0.7 - - - +
96B LEU* 3.3 36.1 - - + -
97B LEU* 4.3 21.3 - - + +
100B LEU* 4.3 2.5 - - + -
304B LEU* 4.6 7.6 - - - +
305B SER* 5.4 1.0 - - - -
358B LEU* 2.9 37.1 + - + +
359B ILE* 3.1 6.9 + - - +
361B MET* 1.3 91.8 - - + +
364B MET* 1.3 59.6 + - + +
365B SER* 3.3 4.3 + - - -
4002B SMB 4.1 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU 3.7 19.7 - - - +
305B SER* 3.9 4.5 + - - +
306B LEU* 3.4 54.8 + - + +
355B PHE* 5.0 3.8 - - - -
359B ILE* 3.0 34.9 + - + +
360B PRO* 3.7 4.7 - - + +
363B LEU* 1.3 76.8 - - + +
365B SER* 1.3 74.9 + - - +
366B TYR* 3.4 6.7 + - + +
388B LEU* 3.4 44.9 - - + -
4002B SMB 5.6 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B SER* 4.2 10.9 + - - -
308B LEU* 5.9 0.5 - - - +
360B PRO 2.8 3.6 + - - -
361B MET* 3.0 13.4 + - - +
363B LEU 4.1 4.5 + - - -
364B MET* 1.3 83.7 - - - +
366B TYR* 1.3 67.5 + - - +
367B PRO* 3.4 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU* 3.8 22.7 - - + -
355B PHE* 4.1 27.8 - + - -
360B PRO* 2.8 27.3 + - + +
361B MET* 5.1 0.2 - - - +
364B MET* 3.2 7.2 - - + -
365B SER* 1.3 79.9 - - - +
367B PRO* 1.3 63.7 - - + +
368B LEU* 2.8 47.0 + - + +
381B LEU* 3.5 21.4 - - + +
385B SER* 2.5 29.9 + - - -
388B LEU* 4.6 6.7 - - + -
417B PHE* 3.4 24.5 - + - -
421B ILE* 3.3 18.7 - - + +
----------------------------------------------------------
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