Contacts of the helix formed by residues 66 - 76 (chain E) in PDB entry 1GMO
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 66 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E VAL* 3.2 9.7 - - - +
65E ASN* 1.3 87.1 - - + +
67E ALA* 1.3 65.5 + - - +
68E ASP* 3.0 32.4 + - - +
69E GLN* 3.0 25.9 + - - +
70E CYS 3.8 0.2 + - - -
89E PHE* 4.1 4.3 - - - -
94E LYS* 5.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ILE* 5.6 3.4 - - + -
66E THR* 1.3 70.6 - - - +
68E ASP* 1.3 59.3 + - - +
70E CYS* 2.7 26.9 + - - +
71E ALA* 3.0 11.7 + - - +
87E PHE* 4.1 4.0 - - + -
89E PHE* 3.6 45.1 - - + -
119E TYR* 4.7 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASN 4.7 16.3 + - - +
39E ILE* 4.2 16.9 - - - +
66E THR* 3.0 28.5 + - - +
67E ALA* 1.3 78.4 + - - +
69E GLN* 1.3 55.7 + - - +
71E ALA* 3.0 9.7 + - - +
72E ASP* 2.9 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E VAL* 3.7 24.5 - - + +
65E ASN* 4.8 1.1 - - + +
66E THR* 3.0 23.3 + - - +
68E ASP* 1.3 78.1 - - - +
70E CYS* 1.3 61.4 + - - +
72E ASP* 4.7 3.7 - - - +
73E ARG* 3.5 23.2 + - - +
96E CYS* 4.5 1.3 - - - -
98E TRP* 4.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E VAL* 4.1 2.2 - - - -
67E ALA* 2.7 11.8 + - - +
69E GLN* 1.3 76.1 - - - +
71E ALA* 1.3 65.8 + - - +
73E ARG 3.6 0.2 + - - -
74E CYS* 3.1 11.8 + - - +
87E PHE* 3.5 23.1 - - + -
89E PHE* 3.5 31.9 - - - -
96E CYS* 2.0 51.4 - - + -
98E TRP* 2.9 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E THR* 3.5 14.4 - - - +
39E ILE* 3.8 28.7 - - + +
42E PHE* 3.9 3.1 - - + -
67E ALA 3.0 7.7 + - - +
68E ASP* 3.0 8.9 + - - +
70E CYS* 1.3 73.3 - - - +
72E ASP* 1.3 55.4 + - - +
74E CYS* 2.8 6.4 + - - +
75E THR* 2.7 35.4 + - - -
87E PHE* 3.4 24.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASN* 3.3 24.5 + - - +
38E THR* 2.5 47.7 + - - +
68E ASP* 2.9 24.4 + - - +
69E GLN* 4.7 3.7 - - - +
71E ALA* 1.3 74.4 - - - +
73E ARG* 1.3 57.3 + - - +
75E THR* 3.8 2.1 - - - -
76E ARG* 3.0 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E LYS* 4.7 8.5 - - - +
69E GLN 3.5 18.8 + - - +
70E CYS 4.0 2.5 - - - +
71E ALA 3.2 1.2 - - - -
72E ASP* 1.3 79.4 - - - +
74E CYS* 1.3 57.1 + - - +
76E ARG* 3.5 4.9 - - - +
77E ASN* 3.0 19.1 + - - -
78E LYS* 2.7 34.2 + - + +
79E GLY* 3.0 32.2 + - - -
80E LEU* 3.6 13.4 - - + +
98E TRP* 3.5 39.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E PHE* 3.8 22.2 - - + -
70E CYS 3.1 14.5 + - - +
71E ALA 2.8 8.8 + - - +
73E ARG* 1.3 76.3 - - - +
75E THR* 1.3 61.9 + - - +
77E ASN* 2.8 21.8 + - - +
80E LEU* 4.3 0.9 - - - -
84E CYS* 2.0 66.2 - - - +
86E ALA 4.6 2.2 - - - -
87E PHE* 4.0 10.1 - - + -
98E TRP* 3.8 6.0 - - + +
121E ASN* 4.8 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E THR* 2.8 43.6 + - + -
41E GLU* 5.0 9.2 - - + +
42E PHE* 3.6 13.6 - - + -
71E ALA 2.7 16.6 + - - -
72E ASP* 3.8 4.7 - - - -
74E CYS* 1.3 73.9 - - - +
76E ARG* 1.3 61.8 + - + +
77E ASN* 3.2 4.9 + - - +
121E ASN* 5.1 7.9 - - - +
142F ILE* 4.9 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E THR* 6.3 1.8 - - - -
72E ASP* 3.0 34.6 + - - +
73E ARG* 3.5 2.8 - - - +
75E THR* 1.3 79.3 - - + +
77E ASN* 1.3 55.2 + - - +
78E LYS* 2.4 36.7 + - + +
142F ILE* 5.9 1.3 - - - -
----------------------------------------------------------
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