Contacts of the strand formed by residues 71 - 78 (chain E) in PDB entry 2GOO
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 THR 71 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ILE* 4.8 9.4 - - - +
64E GLU 3.2 7.4 - - - -
65E GLU* 3.8 24.2 - - + +
69E GLY 3.6 6.0 + - - +
70E GLU* 1.3 75.5 + - - +
72E THR* 1.3 64.8 + - - +
115E LEU* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LYS* 5.5 5.1 + - - -
62E ILE 3.8 0.3 - - - +
63E ILE* 3.3 7.9 - - - +
64E GLU* 2.9 49.6 + - - +
66E ASP* 6.1 1.3 - - + +
70E GLU* 4.9 9.0 - - + +
71E THR* 1.3 79.7 - - - +
73E LEU* 1.3 66.1 + - - +
74E ALA* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LYS* 5.2 1.7 + - - -
41E SER* 4.6 8.1 + - - +
61E ALA* 4.7 5.2 - - + -
62E ILE 3.3 20.4 - - - +
63E ILE* 4.2 17.7 - - + +
72E THR* 1.3 80.0 - - - +
74E ALA* 1.3 68.4 + - - +
75E SER* 6.3 0.2 - - - -
111E LEU 5.3 2.5 - - - +
112E GLN* 6.1 0.4 - - - -
113E PRO* 4.5 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LYS* 3.8 16.4 - - - +
41E SER* 3.3 17.5 - - - +
43E HIS* 3.6 22.9 - - + +
61E ALA* 3.4 2.3 - - - +
62E ILE* 2.8 42.0 + - + -
64E GLU* 4.4 4.9 - - - +
72E THR* 5.8 0.7 - - - +
73E LEU* 1.3 78.1 - - - +
75E SER* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E TYR* 3.7 7.6 + - - +
40E CYS* 3.4 5.9 - - - -
41E SER* 2.9 46.3 + - - +
43E HIS* 3.5 11.5 - - - +
60E PHE* 3.3 23.6 - - - -
61E ALA* 4.3 5.6 - - - -
73E LEU* 6.3 0.4 - - - -
74E ALA* 1.3 76.6 - - - +
76E GLY* 1.3 59.2 + - - +
108E ASN* 3.6 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E CYS* 3.8 0.6 - - - +
39E TYR 3.3 14.4 + - - -
40E CYS* 3.9 10.3 - - - -
43E HIS* 4.5 4.5 - - - -
53E CYS* 4.0 2.0 - - - -
59E CYS* 3.4 6.1 - - - -
60E PHE* 2.9 41.2 + - - -
75E SER* 1.3 79.0 - - - +
77E CYS* 1.3 60.2 + - - -
108E ASN* 3.4 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ALA* 3.4 11.7 - - + +
53D ASP* 2.9 29.0 + - + -
54D HIS* 6.6 0.4 - - + -
38E CYS* 3.6 14.1 - - - -
43E HIS 5.6 0.6 + - - -
53E CYS* 2.1 63.3 - - + -
54E ILE 3.7 11.2 - - - +
55E THR* 3.8 12.3 - - - -
58E HIS 3.4 5.8 - - - -
60E PHE* 3.5 4.1 - - - -
76E GLY* 1.3 72.9 - - - -
78E MET* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D PRO* 4.2 6.3 - - + -
51D LEU 4.6 2.2 - - - +
53D ASP* 4.0 3.1 - - - +
55E THR* 3.2 8.1 + - - -
58E HIS* 2.8 40.7 + - + +
60E PHE* 4.0 15.5 - - + -
77E CYS* 1.3 75.1 - - - +
79E LYS* 1.3 75.8 + - - +
83E SER* 3.6 15.0 - - - -
86E GLN* 3.7 42.0 - - + +
87E CYS* 3.6 23.3 - - - -
99E ILE* 3.8 25.4 - - + -
101E CYS* 3.9 11.7 - - - -
----------------------------------------------------------
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