Contacts of the helix formed by residues 69 - 78 (chain C) in PDB entry 3REZ
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 LEU 69 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C THR 3.9 0.2 - - - +
41C SER* 3.8 32.3 - - - -
42C VAL 4.5 0.7 - - - +
63C TRP* 3.8 25.1 - - + -
64C ARG 3.5 24.9 - - - +
65C CYS* 3.8 24.7 - - - -
66C ASP* 3.0 11.0 + - - +
68C SER* 1.3 75.1 - - - +
70C THR* 1.3 63.0 - - - +
71C TYR 3.3 2.7 - - - -
72C LEU* 3.3 18.8 + - + +
73C ARG* 3.1 23.0 + - - +
88C LEU* 5.2 0.9 - - + -
101C LEU* 3.8 24.9 - - + -
109C LEU* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA* 5.1 11.9 - - - +
67C CYS* 2.7 33.3 + - + +
68C SER 3.4 0.5 - - - -
69C LEU* 1.3 76.0 - - - +
71C TYR* 1.3 61.5 + - - +
73C ARG* 3.5 7.2 + - - +
74C LEU* 2.9 33.8 + - - +
106C GLU* 4.1 28.0 - - + +
109C LEU* 3.9 24.5 - - + -
110C ARG* 5.2 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG* 3.9 3.4 - - - -
103A TYR* 3.5 39.9 - + + +
42C VAL* 4.2 11.0 - - + +
43C PRO 3.4 14.4 - - - -
44C PRO* 3.8 18.6 - - + -
45C GLY* 3.3 26.7 - - - -
46C ALA* 3.4 18.8 + - + -
47C PHE* 2.9 43.1 + + - +
48C ASP* 3.6 8.7 + - - -
68C SER 4.8 4.8 + - - +
69C LEU 3.3 0.2 - - - -
70C THR* 1.3 78.8 + - - +
72C LEU* 1.3 65.6 + - - +
74C LEU* 3.2 11.7 + - - +
75C TRP* 2.9 32.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 3.9 20.6 - - + +
47C PHE* 4.0 23.8 - - + -
58C LEU* 3.8 23.6 - - + -
63C TRP* 3.8 29.8 - - + -
68C SER 5.4 0.4 + - - -
69C LEU* 3.3 24.4 + - + +
71C TYR* 1.3 83.8 - - - +
73C ARG* 1.3 57.2 + - - +
75C TRP* 3.3 3.4 + - + +
76C LEU* 2.9 42.1 + - + +
88C LEU* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU 3.1 17.5 + - - +
70C THR* 3.7 6.3 - - - +
72C LEU* 1.3 73.8 - - - +
74C LEU* 1.3 63.5 + - - +
76C LEU* 3.3 4.3 + - - +
77C GLU* 3.0 58.6 + - + +
101C LEU* 3.2 42.0 + - + +
102C PRO* 3.1 20.1 + - - +
104C LEU 3.0 22.8 + - - -
105C ALA* 4.9 2.6 - - - +
106C GLU* 4.7 21.9 + - - +
109C LEU* 3.7 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 5.0 4.9 - - - +
102A PRO 4.0 7.1 - - - +
103A TYR* 3.4 42.6 - - - +
104A LEU 3.9 14.4 - - - +
105A ALA* 4.0 12.8 - - + +
70C THR* 2.9 17.8 + - - +
71C TYR* 3.3 11.7 - - - +
73C ARG* 1.3 80.4 - - - +
75C TRP* 1.3 61.3 + - - +
77C GLU* 3.4 6.2 + - + +
78C ASP* 3.2 24.6 + - - +
106C GLU* 4.6 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 3.5 42.8 + + + -
47C PHE* 3.8 35.0 + + + +
53C LEU* 3.6 37.2 - - + +
54C ARG 4.1 11.7 - - - -
55C THR* 5.3 0.2 - - - -
56C ALA* 4.3 21.8 - - + -
71C TYR* 2.9 21.2 + - + +
72C LEU* 3.6 10.8 - - + +
74C LEU* 1.3 76.6 - - - +
76C LEU* 1.3 93.9 + - + +
77C GLU 3.5 0.5 + - - -
78C ASP 3.7 2.4 + - - -
82C ARG* 2.8 71.4 + - + +
85C TYR* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ALA 5.4 1.6 - - - +
58C LEU* 3.9 18.8 - - + -
72C LEU* 2.9 27.7 + - + +
73C ARG* 3.8 5.4 - - - +
75C TRP* 1.3 109.4 - - + +
77C GLU* 1.3 53.7 + - + +
78C ASP 3.5 0.2 - - - -
82C ARG* 3.4 17.8 - - + +
85C TYR* 4.1 7.4 - - + +
86C ARG* 2.8 57.8 + - + +
88C LEU* 3.7 35.9 - - + -
101C LEU* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ARG* 3.0 48.0 + - + +
74C LEU* 4.0 6.3 - - + +
75C TRP 3.3 0.2 - - - -
76C LEU* 1.3 76.6 - - + +
78C ASP* 1.3 63.8 + - - +
79C ARG* 3.4 3.2 + - - -
86C ARG* 3.3 44.8 + - - +
102C PRO* 3.3 29.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 2.8 34.2 - - - +
86A ARG* 3.0 27.8 + - - -
102A PRO* 3.7 7.9 - - - +
103A TYR* 3.7 20.4 - - + -
74C LEU 3.2 14.9 + - - +
75C TRP 3.8 5.6 - - - +
76C LEU 3.5 2.2 - - - -
77C GLU* 1.3 78.6 - - - +
79C ARG* 1.3 92.1 + - - +
80C PRO* 4.7 1.2 - - - +
82C ARG* 3.9 2.0 - - - +
----------------------------------------------------------
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