Contacts of the helix formed by residues 73 - 82 (chain D) in PDB entry 5JCZ
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 TYR 73 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1711C TRP* 4.8 6.7 - + - -
1755C LYS* 6.4 2.9 - - + -
1757C LYS* 3.1 38.3 + - - -
1784C TYR* 5.6 2.7 - - - -
1791C GLU* 4.2 37.5 - - + -
1792C GLU 4.1 16.7 + - - -
72D ARG* 1.3 79.1 - - - +
74D ARG* 1.3 66.0 + - - +
75D ALA* 3.1 6.5 - - + +
76D ILE* 3.1 36.1 + - + +
77D THR* 3.2 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ARG 3.4 3.6 + - - -
73D TYR* 1.3 72.5 - - - +
75D ALA* 1.3 56.6 + - - +
77D THR* 3.3 7.7 + - - -
78D SER* 2.9 28.5 + - - -
111D ASP* 4.3 20.4 + - - +
112D HIS* 3.5 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1711C TRP* 3.6 18.8 - - + -
1788C ASN* 4.8 8.7 - - + +
1791C GLU* 3.8 22.4 - - + +
73D TYR* 3.1 3.9 - - + +
74D ARG* 1.3 80.0 - - - +
76D ILE* 1.3 57.6 + - - +
78D SER* 3.3 9.1 + - - -
79D ALA* 3.0 22.7 + - - +
82D ARG* 4.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1711C TRP* 3.6 43.3 - - + -
1715C MET* 4.4 19.6 - - - +
1753C GLN* 4.6 12.3 - - + +
46D VAL* 4.7 11.2 - - + -
72D ARG* 3.8 21.1 - - + -
73D TYR* 3.1 36.9 + - + +
75D ALA* 1.3 74.4 - - - +
77D THR* 1.3 60.5 + - - +
79D ALA* 3.2 3.6 + - - +
80D TYR* 2.9 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ARG* 3.0 40.9 + - - +
73D TYR 3.2 5.1 + - - -
74D ARG* 3.3 10.8 + - - -
76D ILE* 1.3 76.9 - - - +
78D SER* 1.3 63.7 + - - +
80D TYR* 3.2 6.0 + - - +
81D TYR* 3.1 55.4 + - + -
108D GLU* 3.9 9.0 + - - +
112D HIS* 3.8 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ARG* 2.9 16.1 + - - -
75D ALA* 3.4 14.1 - - - -
76D ILE 3.2 0.2 - - - -
77D THR* 1.3 76.1 - - - +
79D ALA* 1.3 56.6 + - - +
81D TYR* 3.4 2.8 + - - +
82D ARG* 2.9 53.3 + - - +
112D HIS* 3.8 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1633C ILE 5.4 2.4 - - - +
1711C TRP* 4.1 20.2 - - + -
1715C MET* 4.6 8.7 - - + -
13D LYS* 3.2 15.9 + - - -
65D TRP* 3.7 7.9 - - + -
75D ALA 3.0 13.6 + - - +
76D ILE 3.2 7.4 + - - +
78D SER* 1.3 76.3 - - - +
80D TYR* 1.3 62.8 + - - +
82D ARG* 3.5 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1715C MET* 5.1 1.1 - - - +
13D LYS* 3.1 23.4 + - - -
15D VAL* 3.3 33.2 - - + +
16D LEU 2.7 27.5 + - - -
17D ILE* 4.2 9.6 - - + -
46D VAL* 4.0 18.4 - - + -
65D TRP* 3.2 47.6 + + + -
66D ASP* 3.4 11.3 - - - -
67D THR* 3.4 32.3 + - + -
72D ARG* 5.5 5.6 - - - +
76D ILE* 2.9 14.1 + - + +
77D THR* 3.4 13.5 - - - +
78D SER 3.2 0.2 - - - -
79D ALA* 1.3 78.0 - - - +
81D TYR* 1.3 74.8 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D VAL* 4.2 12.6 - - + -
17D ILE* 3.3 35.7 - - + +
72D ARG* 5.5 0.2 - - - -
77D THR* 3.1 35.7 + - + +
78D SER 4.1 1.1 - - - +
80D TYR* 1.3 87.9 - + - +
82D ARG* 1.3 65.6 + - - +
83D GLY 3.3 0.9 + - - -
84D ALA* 3.1 22.9 + - - +
105D TRP 4.3 0.3 + - - -
108D GLU* 2.4 43.8 + - + +
109D LEU* 3.4 38.1 + - + -
112D HIS* 3.6 35.2 - - + +
113D ALA* 4.1 12.7 - - + +
114D ASP 5.3 0.7 + - - -
117D ILE* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1634C GLN* 5.6 15.2 - - - +
13D LYS* 2.6 29.3 + - - +
75D ALA 4.5 2.2 + - - -
78D SER* 2.9 45.8 + - - +
79D ALA* 3.6 30.3 - - - +
80D TYR 3.4 1.6 - - - -
81D TYR* 1.3 74.9 - - - +
83D GLY* 1.3 61.2 + - - +
84D ALA 3.1 0.9 + - - -
112D HIS 5.3 3.6 - - - -
----------------------------------------------------------
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