Contacts of the strand formed by residues 79 - 87 (chain E) in PDB entry 1RTA
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 MET 79 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E VAL* 4.0 10.5 - - + -
49E GLU* 3.9 28.0 - - + +
53E ASP* 5.2 4.5 - - - +
54E VAL* 3.6 30.3 - - + -
57E VAL* 4.2 8.3 - - + -
75E SER* 3.4 21.1 - - - +
77E SER* 5.4 5.8 - - - -
78E THR* 1.3 76.7 - - - +
80E SER* 1.3 67.0 + - - +
81E ILE* 3.5 6.8 + - + +
103E ASN* 3.3 3.9 - - - -
104E LYS 2.6 31.0 + - - +
106E ILE* 3.4 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E SER 2.6 29.1 + - - -
19E ALA* 5.1 0.4 - - - -
47E VAL* 3.8 3.5 - - - +
48E HIS* 3.0 36.4 + - - +
49E GLU* 4.0 5.2 + - - -
79E MET* 1.3 71.2 - - - +
81E ILE* 1.3 63.9 - - - +
101E GLN* 3.8 10.5 - - - -
102E ALA 2.9 11.2 - - - -
103E ASN* 3.2 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E THR* 4.2 6.7 - - - +
46E PHE 3.1 6.7 - - - +
47E VAL* 3.5 31.0 - - + -
48E HIS* 4.0 0.2 - - - -
79E MET 3.7 12.8 - - - +
80E SER* 1.3 77.8 - - - +
82E THR* 1.3 64.7 + - - +
83E ASP* 3.8 14.8 - - - +
100E THR 3.6 0.9 - - - +
101E GLN* 3.3 5.6 - - - +
102E ALA* 2.7 45.8 + - + +
104E LYS* 3.6 36.6 - - + -
106E ILE* 4.0 14.1 - - + -
123E SER* 3.7 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ALA* 3.3 14.4 - - - +
25E TYR* 3.4 29.4 - - + -
26E CYS* 3.8 11.9 - - - -
44E ASN 4.2 0.2 - - - +
45E THR* 3.3 2.1 - - - -
46E PHE* 2.8 35.1 + - + +
48E HIS* 3.0 24.5 + - - -
81E ILE* 1.3 74.8 - - - +
83E ASP* 1.3 64.3 + - - +
84E CYS* 3.8 3.4 - - - -
99E THR* 3.6 16.4 - - + -
100E THR 3.0 4.9 - - - +
101E GLN* 3.2 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E VAL* 5.3 0.7 - - + -
44E ASN 3.5 7.2 - - - +
45E THR* 3.2 27.3 + - + -
81E ILE* 3.8 17.6 - - - +
82E THR* 1.3 73.3 - - - +
84E CYS* 1.3 61.0 + - - +
85E ARG* 2.9 44.2 + - - +
98E LYS 2.9 14.6 - - - +
99E THR* 3.6 2.6 - - - -
100E THR* 2.7 27.6 + - - +
102E ALA* 6.3 1.6 - - - -
104E LYS* 4.9 6.5 + - - -
123E SER* 4.4 9.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
26E CYS* 2.0 51.8 - - + -
30E MET* 4.0 15.5 - - - -
43E VAL* 3.0 26.7 - - - +
44E ASN 2.8 14.4 + - - +
46E PHE* 3.6 25.6 - - - -
82E THR* 3.8 5.6 - - - -
83E ASP* 1.3 73.3 - - - +
85E ARG* 1.3 61.1 + - - +
86E GLU 4.0 0.2 + - - -
97E TYR* 4.1 6.9 - - + -
98E LYS 3.3 5.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
302C T 5.6 1.6 + - - -
42E PRO 3.9 1.3 - - - +
43E VAL* 4.0 22.6 - - + +
83E ASP* 2.9 43.5 + - - +
84E CYS* 1.3 75.1 - - - +
86E GLU* 1.4 66.2 + - - +
87E THR* 3.3 0.5 + - - -
97E TYR* 3.1 3.7 - - - -
98E LYS* 2.8 42.2 + - + +
100E THR* 4.1 17.6 + - - +
104E LYS* 5.4 5.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
40E CYS* 3.9 23.2 - - - +
41E LYS 3.3 25.1 - - - +
42E PRO* 2.8 24.0 + - + +
85E ARG* 1.4 69.7 - - - +
87E THR* 1.3 60.8 + - - +
88E GLY 3.9 1.0 + - - -
90E SER* 3.2 30.6 + - - +
92E TYR 5.5 0.5 + - - -
96E ALA 3.6 0.4 - - - -
97E TYR* 3.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E ARG 3.3 3.7 + - - -
86E GLU* 1.3 72.0 - - - +
88E GLY* 1.4 68.1 + - - +
89E SER* 3.1 6.5 + - - -
90E SER* 3.0 22.1 + - - +
96E ALA* 3.0 41.1 + - + +
97E TYR* 3.9 6.5 - - - +
98E LYS* 4.9 7.4 - - - -
----------------------------------------------------------
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