Contacts of the helix formed by residues 368 - 376 (chain A) in PDB entry 6XYY
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 368 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ASP* 3.1 1.6 + - - +
367A GLU* 1.3 78.2 - - - +
369A THR* 1.3 66.0 + - - +
370A TYR 3.3 3.1 - - - -
371A PHE* 3.2 7.5 + - - +
372A LEU* 2.9 23.8 + - - +
432A GLY* 3.9 8.5 + - - -
435A VAL* 3.7 12.7 - - - +
436A GLY* 3.6 25.3 - - - -
440A PHE* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ASP* 3.5 24.2 + - + +
367A GLU 3.6 1.2 - - - -
368A GLY* 1.3 74.7 - - - +
370A TYR* 1.3 71.2 + - - +
372A LEU* 3.1 8.1 + - - +
373A LEU* 2.8 23.9 + - - +
429A GLN* 5.0 5.6 - - - +
432A GLY* 4.6 14.1 + - - -
475A TRP* 4.2 18.6 - - + +
476A MET* 2.8 52.9 + - - +
479A LEU* 4.3 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 4.8 2.9 - - - -
367A GLU 4.5 2.1 + - - +
368A GLY 3.3 0.6 - - - -
369A THR* 1.3 83.0 + - - +
371A PHE* 1.3 92.4 + + + +
373A LEU* 3.4 6.0 + - + +
374A TYR* 3.1 66.0 + + + -
472A TRP* 4.8 5.6 - + - -
476A MET* 4.8 5.8 - - - -
479A LEU* 4.3 15.9 - - + -
480A HIS* 3.4 39.5 - + + +
602A 760 3.1 63.9 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
327A ILE* 3.5 22.6 - - + +
328A LEU* 3.6 30.3 - - + -
330A PHE* 4.7 5.4 - + - -
367A GLU 3.6 20.2 - - - -
368A GLY* 3.2 6.5 + - - +
370A TYR* 1.3 98.1 - + - +
372A LEU* 1.3 66.1 + - - +
374A TYR* 3.3 3.7 + - + -
375A ASP* 3.0 27.5 + - - +
435A VAL* 4.6 1.3 - - + -
440A PHE* 3.5 28.9 - + - -
480A HIS* 4.0 21.3 - + - -
601A PPI 3.6 23.6 - - + -
602A 760 4.0 15.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 4.1 8.2 - - + +
368A GLY 2.9 17.2 + - - +
369A THR* 3.6 2.7 - - - +
371A PHE* 1.3 77.1 - - - +
373A LEU* 1.3 62.5 + - - +
376A PHE* 3.2 34.5 + - + +
380A PHE* 3.5 32.9 - - + -
396A ILE* 4.4 3.1 - - + -
400A ILE* 4.2 13.7 - - + -
428A GLN* 4.1 11.0 - - + +
431A ILE* 3.5 26.2 - - + -
432A GLY* 4.0 23.1 - - - +
435A VAL* 4.6 7.2 - - + -
475A TRP* 4.4 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 4.1 16.2 - - + -
369A THR 2.8 15.5 + - - +
370A TYR* 3.7 4.7 - - - +
372A LEU* 1.3 76.3 - - - +
374A TYR* 1.3 68.6 + - + +
377A ILE* 3.2 30.1 + - + +
380A PHE* 3.9 17.7 - - + +
381A ASP* 3.8 16.8 - - - +
382A LYS* 3.7 38.6 - - + +
472A TRP* 4.0 13.5 - - + -
475A TRP* 3.9 11.6 - - + -
476A MET* 3.6 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 4.0 12.1 - + - +
73A TYR* 3.5 56.9 + + + -
74A PHE* 3.8 20.9 - + - -
80A GLU* 2.9 35.6 + - - +
370A TYR* 3.1 60.6 + + + +
371A PHE* 3.9 5.8 - - + +
372A LEU 3.2 0.4 - - - -
373A LEU* 1.3 89.0 - - + +
375A ASP* 1.3 65.5 + - - +
376A PHE 3.4 0.9 + - - -
377A ILE* 3.8 18.3 + - + +
472A TRP* 4.0 9.5 - + - -
602A 760 4.7 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A TYR* 3.0 38.2 + - - -
326A GLY* 4.1 0.7 - - - -
327A ILE* 3.4 37.4 + - + +
328A LEU 4.4 0.5 + - - -
371A PHE* 3.0 20.9 + - - +
374A TYR* 1.3 81.5 - - - +
376A PHE* 1.3 79.4 + - + +
377A ILE 3.7 0.9 - - - -
378A ASP* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 4.4 9.2 - - + -
372A LEU* 3.2 24.3 + - + +
373A LEU 3.7 3.4 - - - -
375A ASP* 1.3 99.3 - - + +
377A ILE* 1.3 55.8 + - - +
378A ASP* 3.0 9.0 - - - -
379A TYR* 2.9 54.2 + + + +
380A PHE* 3.4 18.0 + - + -
396A ILE* 4.0 17.7 - - + -
399A ASN* 3.4 41.7 - - + -
400A ILE* 3.8 28.0 - - + -
----------------------------------------------------------
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