Contacts of the helix formed by residues 67 - 78 (chain D) in PDB entry 1ORZ
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 ASP 67 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 5.2 4.0 - - - +
54D THR* 5.6 1.9 - - - +
55D ALA* 4.3 15.9 - - - +
58D THR* 4.5 11.0 + - - +
66D ALA* 1.3 102.8 - - + +
68D SER* 1.3 60.0 + - - +
69D PHE* 3.0 27.6 + - + -
70D PHE* 3.2 24.0 + - + +
71D SER* 3.6 4.7 + - - -
132D LYS* 4.0 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C PHE* 5.9 2.9 - - - -
65D ALA* 3.0 35.3 + - - +
66D ALA 2.9 6.3 + - - -
67D ASP* 1.3 75.6 - - - +
69D PHE* 1.3 60.5 + - - +
70D PHE 3.2 0.4 - - - -
71D SER* 3.6 8.8 - - - -
72D VAL* 2.7 44.1 + - - +
119D LYS* 4.5 15.7 - - - -
127D VAL* 5.7 5.5 - - - +
128D VAL* 6.2 0.7 - - - -
132D LYS* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ASP* 3.9 24.0 - - + -
68D SER* 1.3 80.1 - - - +
70D PHE* 1.3 59.8 + - - +
72D VAL* 2.7 21.7 - - - +
73D MET* 3.1 8.7 + - - +
119D LYS* 2.9 45.0 + - + +
120D LEU* 3.8 9.0 - - + -
123D GLU* 2.9 33.2 - - - -
128D VAL* 2.7 43.3 - - + -
132D LYS* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 3.0 41.5 - - + -
67D ASP* 3.2 18.9 + - + +
68D SER 3.2 0.2 - - - -
69D PHE* 1.3 81.2 - - - +
71D SER* 1.3 58.7 + - - +
73D MET* 3.3 10.2 + - - +
74D LEU* 2.9 66.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C PHE* 6.2 2.7 - - - -
51D LEU* 4.6 3.6 - - - +
52D ALA* 4.8 6.1 - - - +
55D ALA* 2.9 33.2 - - - +
67D ASP 3.6 6.3 + - - -
68D SER* 3.1 12.6 + - - -
70D PHE* 1.3 76.5 - - - +
72D VAL* 1.3 61.7 + - - +
74D LEU* 2.9 14.0 + - - +
75D LEU* 2.7 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C PHE* 3.6 33.7 - - + -
68D SER* 2.7 23.3 + - - +
69D PHE 2.7 24.7 - - - +
71D SER* 1.3 72.5 - - - +
73D MET* 1.3 64.9 + - + +
75D LEU* 3.1 18.7 + - + +
76D GLY* 3.2 9.2 + - - -
112D VAL* 5.3 2.6 - - - +
115D PHE* 5.0 2.8 - - + +
116D GLY* 4.1 21.0 + - - +
119D LYS* 2.9 43.1 - - + +
120D LEU* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PHE 3.1 8.4 + - - +
70D PHE* 3.6 12.6 - - + +
71D SER 3.1 0.2 - - - -
72D VAL* 1.3 85.2 - - + +
74D LEU* 1.3 55.7 + - + +
76D GLY* 3.1 11.3 + - - -
77D TYR* 2.8 56.9 + - + +
116D GLY* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D VAL* 3.1 39.2 - - + +
51D LEU* 2.9 59.0 - - + -
52D ALA* 4.1 5.4 - - + +
70D PHE* 2.9 35.9 - - + +
71D SER* 2.9 10.2 + - - +
73D MET* 1.3 75.0 - - + +
75D LEU* 1.3 65.4 + - - +
77D TYR* 3.1 30.1 + - + +
78D CYS 3.2 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 6.4 1.8 - - + -
53C MET* 5.7 11.4 - - + +
54C GLY* 5.2 10.3 - - - +
57C PHE* 3.8 43.5 - - + -
48D VAL* 4.9 0.4 - - - -
71D SER 2.7 12.2 + - - +
72D VAL* 3.1 13.4 + - - +
74D LEU* 1.3 77.4 - - - +
76D GLY* 1.3 62.2 + - - +
78D CYS* 3.0 34.5 + - + +
79D TYR* 3.6 2.6 + - - -
82D PHE* 5.6 9.6 - - + -
112D VAL* 4.8 8.6 - - + +
115D PHE* 5.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 3.8 7.9 + - - -
72D VAL 3.2 5.1 + - - -
73D MET* 3.1 9.0 + - - -
75D LEU* 1.3 78.6 - - - +
77D TYR* 1.3 55.6 + - - +
79D TYR* 2.9 30.0 + - - +
112D VAL* 3.0 31.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 4.5 17.9 - + - +
44D PHE* 3.9 35.6 - + + +
48D VAL* 3.6 16.6 - - + -
73D MET* 2.8 62.7 - - + -
74D LEU* 3.1 25.7 + - + +
76D GLY* 1.3 69.6 - - - +
78D CYS* 1.3 55.0 + - - +
79D TYR* 2.8 15.3 + - - +
80D MET* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 5.8 2.5 - - + -
45D ALA* 5.4 6.3 - - - +
48D VAL* 3.2 39.5 - - - -
49D VAL* 5.3 3.1 - - - -
52D ALA* 6.0 1.3 - - - -
74D LEU 3.2 5.1 + - - -
75D LEU* 3.0 28.3 + - + +
77D TYR* 1.3 73.3 - - - +
79D TYR* 1.3 50.3 + - - +
80D MET* 2.8 12.2 - - - +
81D GLU* 2.6 50.6 + - - +
82D PHE* 4.0 7.3 + - + -
----------------------------------------------------------
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