Contacts of the helix formed by residues 367 - 377 (chain A) in PDB entry 2YTZ
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 PRO 367 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A TYR* 3.9 0.9 - - - +
350A TYR* 4.2 7.9 - - + +
365A SER 4.0 5.6 - - - +
366A ALA* 1.3 89.4 - - + +
368A TYR* 1.3 67.8 + - - +
369A GLU* 3.8 15.5 - - + +
370A VAL* 3.1 22.8 + - + +
371A PHE* 3.0 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 2.8 47.3 + - + +
257A GLY 4.0 2.2 - - - -
258A LYS* 3.5 48.7 - - + +
259A PHE 5.9 0.2 - - - +
322A TYR* 3.3 34.5 + + + +
327A ILE* 4.3 4.7 - - + -
367A PRO* 1.3 70.5 - - - +
369A GLU* 1.3 87.5 + - + +
371A PHE* 2.9 14.8 + - + +
372A ILE* 3.0 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 3.1 29.9 - - - +
367A PRO* 3.8 11.2 - - + +
368A TYR* 1.3 92.9 + - + +
370A VAL* 1.3 64.4 + - + +
372A ILE* 3.2 7.3 + - - +
373A GLU* 3.0 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 4.6 1.1 - - + -
348A GLN* 4.5 4.0 - - - +
350A TYR* 3.2 46.4 - - + +
366A ALA* 3.9 7.9 - - + -
367A PRO* 3.1 24.1 + - + +
369A GLU* 1.3 78.9 - - + +
371A PHE* 1.3 59.1 + - - +
373A GLU* 3.2 17.0 + - - +
374A THR* 2.8 44.0 + - - +
377A ARG* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A TYR* 3.5 52.5 - + + -
324A THR* 4.3 20.2 - - - -
327A ILE* 3.8 20.0 - - + -
341A ILE* 4.0 19.7 - - + -
345A LEU* 4.0 23.3 - - + -
362A ILE* 4.2 12.1 - - + -
364A THR* 4.3 4.3 - - + -
366A ALA* 4.7 2.6 - - + +
367A PRO 3.0 11.9 + - - +
368A TYR* 2.9 11.5 + - - +
370A VAL* 1.3 80.4 - - - +
372A ILE* 1.3 67.6 + - + +
374A THR* 3.4 5.0 + - - -
375A ILE* 3.2 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 3.6 35.2 - - + -
368A TYR* 3.0 58.5 + - + +
369A GLU* 3.7 6.5 - - - +
371A PHE* 1.3 76.6 - - + +
373A GLU* 1.3 66.8 + - + +
375A ILE* 3.3 14.5 - - + +
376A LYS* 3.1 44.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A GLU* 3.0 25.9 + - + +
370A VAL* 3.6 18.7 - - - +
372A ILE* 1.3 77.4 - - + +
374A THR* 1.3 63.3 + - - +
376A LYS* 3.2 11.4 + - - +
377A ARG* 3.2 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LYS* 3.5 12.7 + - - +
341A ILE* 4.5 6.3 - - + +
344A ALA* 3.7 24.0 - - + +
345A LEU* 4.0 18.8 - - + +
348A GLN* 3.0 31.1 + - - +
370A VAL* 2.8 27.2 + - - +
371A PHE* 3.8 4.3 - - - -
373A GLU* 1.3 75.4 - - - +
375A ILE* 1.3 64.8 + - - +
376A LYS 3.3 0.5 + - - -
377A ARG* 3.4 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A THR* 5.4 6.7 - - + -
327A ILE* 3.7 29.8 - - + -
328A GLY* 5.5 4.0 - - - +
336A LYS* 3.7 32.3 + - - +
341A ILE* 3.8 39.0 - - + -
371A PHE* 3.2 24.5 + - + +
372A ILE* 3.3 27.6 - - + +
374A THR* 1.3 75.2 - - - +
376A LYS* 1.3 64.9 + - + +
377A ARG 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ILE* 3.1 41.7 + - + +
373A GLU* 3.2 8.9 + - + +
374A THR 3.1 0.6 - - - -
375A ILE* 1.3 83.8 - - + +
377A ARG* 1.3 61.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LYS* 4.1 24.9 - - - -
348A GLN* 3.2 38.2 + - - +
370A VAL* 5.7 0.6 - - - +
373A GLU* 3.2 40.5 + - - +
374A THR* 3.4 19.7 + - - +
375A ILE 3.4 1.6 - - - -
376A LYS* 1.3 82.2 - - + +
----------------------------------------------------------
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