Contacts of the strand formed by residues 78 - 86 (chain E) in PDB entry 3QAZ
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 VAL 78 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ILE* 5.3 4.7 - - + -
37E ALA* 3.8 18.2 - - + -
38E TRP 3.7 13.5 - - - +
39E PRO* 3.6 29.2 - - + -
44E TRP* 5.3 1.6 - - + -
72E LEU* 3.8 25.6 - - + -
76E ASP* 5.1 2.0 - - + -
77E ILE* 1.3 73.6 - - - +
79E THR* 1.3 63.0 + - - +
80E LEU* 3.5 4.1 + - + +
98E PHE* 3.2 41.1 + - + +
100E PRO* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E HIS 3.4 5.2 - - - +
38E TRP* 2.8 49.4 + - + +
40E ASP* 6.0 1.4 - - - +
77E ILE* 3.8 4.5 + - - +
78E VAL* 1.3 70.8 - - - +
80E LEU* 1.3 63.9 + - - +
81E ARG* 4.2 27.3 - - + +
95E ILE* 6.2 0.7 - - + -
96E GLN 4.0 4.9 - - - +
97E ASP* 2.8 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E PHE* 3.9 15.3 - - + -
10E CYS* 3.9 30.1 - - + -
18E ILE* 5.2 4.7 - - + -
35E VAL* 4.9 5.6 - - + -
36E HIS 3.8 2.0 - - - +
37E ALA* 3.5 31.2 - - + +
62E LEU* 4.1 11.9 - - + -
78E VAL* 4.0 7.0 - - + +
79E THR* 1.3 74.1 - - - +
81E ARG* 1.3 65.7 + - - +
95E ILE* 3.5 1.2 - - - +
96E GLN* 3.0 43.8 + - + +
98E PHE* 3.6 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E VAL* 3.2 10.0 - - - +
36E HIS* 3.0 37.1 + - + +
38E TRP* 6.6 0.4 - - - -
79E THR* 4.2 20.3 - - + +
80E LEU* 1.3 80.3 - - - +
82E VAL* 1.3 65.1 + - - +
83E LEU* 4.1 14.6 - - + -
92E VAL* 4.1 18.4 - - - +
94E ALA 3.2 5.8 - - - +
95E ILE* 3.3 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E PHE* 3.2 42.4 - - + -
22E TRP* 3.8 23.3 - - + +
33E CYS* 5.3 1.3 - - + -
34E GLN 3.2 13.5 - - - +
35E VAL* 4.2 1.6 - - + -
50E LEU* 3.4 25.1 - - + -
81E ARG* 1.3 73.7 - - - +
83E LEU* 1.3 60.6 + - - +
84E CYS 4.1 0.2 - - - -
93E MET* 2.5 38.0 + - + +
94E ALA* 3.1 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E GLN* 2.6 44.5 + - + +
36E HIS* 4.4 30.7 - - + +
81E ARG* 4.2 11.9 - - + -
82E VAL* 1.3 83.3 - - - +
84E CYS* 1.3 60.9 + - - +
90E TRP* 3.2 40.6 - - + -
91E ARG 3.2 3.8 - - - +
92E VAL* 3.4 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E TRP* 3.7 9.6 - - - -
31E THR* 5.4 1.8 - - - -
32E SER 3.2 3.1 - - - +
33E CYS* 2.0 48.7 - - - -
82E VAL* 5.5 0.4 - - - -
83E LEU* 1.3 73.9 - - - +
85E ARG* 1.3 68.5 + - - +
86E GLU* 3.1 2.7 + - + +
90E TRP* 3.5 2.2 - - - -
91E ARG* 2.9 32.3 + - + +
93E MET* 3.5 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E THR* 4.1 15.8 + - - -
32E SER* 2.4 42.8 + - - +
84E CYS* 1.3 70.6 - - - +
86E GLU* 1.3 59.3 + - - +
87E GLY 4.2 12.6 + - - +
88E VAL 5.1 8.1 + - - -
89E ARG 3.7 17.8 + - - +
90E TRP* 3.3 36.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E CYS* 3.1 11.1 + - + +
85E ARG* 1.3 74.4 - - - +
87E GLY* 1.3 63.2 + - - +
89E ARG* 3.8 34.1 + - - +
91E ARG* 3.7 32.6 + - + +
----------------------------------------------------------
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