Contacts of the helix formed by residues 62 - 74 (chain E) in PDB entry 1G3I
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 GLY 62 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ILE* 4.9 0.7 - - - -
61E VAL* 1.3 80.6 - - - +
63E LYS* 1.3 65.6 + - - +
64E THR 2.9 4.1 + - - -
65E GLU* 3.0 5.2 + - - -
66E ILE* 2.9 40.8 + - - +
454E ATP 3.1 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E MET* 3.6 43.8 - - + +
57E GLY* 3.2 38.4 + - - +
58E PRO 2.3 29.3 + - - -
61E VAL* 4.3 1.5 - - + +
62E GLY* 1.3 74.4 - - - +
64E THR* 1.3 60.4 + - - +
66E ILE* 4.0 0.4 - - - +
67E ALA 3.6 5.5 + - - -
255E PHE* 3.7 6.5 - - + -
308E SER* 3.7 29.6 - - - +
309E GLY* 4.2 8.6 - - - -
310E ALA* 5.1 0.8 - - - +
333E LEU* 3.5 21.1 - - + +
454E ATP 3.1 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E GLY 3.1 0.2 - - - -
63E LYS* 1.3 73.8 - - - +
65E GLU* 1.3 53.6 + - - +
67E ALA* 3.1 2.1 + - - +
68E ARG* 2.7 56.4 + - + +
78E PHE* 5.2 2.2 - - + -
80E LYS* 3.4 34.7 + - + +
255E PHE* 3.3 24.5 - - + -
454E ATP 2.6 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E HIS* 4.8 5.8 - - - +
17E ILE* 4.0 15.3 - - + -
62E GLY* 3.0 7.7 + - - +
64E THR* 1.3 76.2 - - - +
66E ILE* 1.3 58.2 + - - +
68E ARG* 2.9 17.6 + - - +
69E ARG* 2.6 77.8 + - - +
454E ATP 3.4 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E LEU* 4.2 10.5 - - + +
17E ILE* 3.7 28.0 - - + +
20E GLN* 3.9 17.0 - - + +
23E ALA* 3.9 24.5 - - + +
24E LYS* 4.6 9.4 - - + +
27E VAL* 3.8 26.2 - - + -
55E MET* 4.3 13.0 - - + -
62E GLY* 2.9 27.4 + - - +
63E LYS* 4.0 3.6 - - - +
65E GLU* 1.3 74.5 - - - +
67E ALA* 1.3 57.1 + - - +
69E ARG* 3.7 2.1 - - - +
70E LEU* 2.9 30.0 + - - +
333E LEU* 3.9 9.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
27E VAL* 5.3 0.4 - - - -
55E MET* 4.4 2.5 - - + -
63E LYS 3.6 7.0 + - - +
64E THR 3.1 7.3 + - - +
65E GLU 3.0 0.8 - - - -
66E ILE* 1.3 79.1 - - - +
68E ARG* 1.3 66.5 + - - +
70E LEU* 3.2 7.3 + - - +
71E ALA* 3.0 23.7 + - - +
78E PHE* 3.6 14.7 - - + -
253E ILE* 5.1 1.2 - - - +
255E PHE* 3.6 31.2 - - + -
306E ILE* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E THR* 2.7 42.4 + - - +
65E GLU* 3.6 18.7 + - - +
67E ALA* 1.3 73.4 - - - +
69E ARG* 1.3 59.0 + - + +
71E ALA* 3.4 3.6 - - - +
72E LYS* 2.9 27.5 + - - +
78E PHE* 3.9 33.1 - - + -
80E LYS* 3.9 17.2 - - - +
287F GLU* 4.5 13.9 + - - +
288F GLY 4.6 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E LEU* 3.9 14.6 - - + -
16E HIS* 3.4 45.5 + - + +
17E ILE* 4.1 11.7 - - + -
65E GLU* 2.6 55.3 + - - +
66E ILE* 3.7 3.6 - - - +
68E ARG* 1.3 71.5 - - - +
70E LEU* 1.3 57.9 + - - +
72E LYS* 2.8 26.5 + - - +
73E LEU* 2.7 38.1 + - + +
349E HIS 5.9 0.2 + - - -
47F GLU* 3.5 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ILE* 4.1 16.6 - - + -
13E LEU* 4.1 2.9 - - + +
27E VAL* 3.4 54.3 - - + +
31E LEU* 3.5 31.9 - - + -
66E ILE 2.9 19.0 + - - +
67E ALA* 3.4 5.8 - - - +
69E ARG* 1.3 75.9 - - - +
71E ALA* 1.3 65.0 + - - +
73E LEU* 3.3 10.8 - - + +
74E ALA* 3.2 23.3 + - + +
253E ILE* 4.8 9.6 - - + -
304E LEU* 4.5 11.7 - - + -
306E ILE* 4.3 11.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
67E ALA 3.0 2.2 + - - +
68E ARG 3.4 7.9 - - - +
70E LEU* 1.3 81.4 - - - +
72E LYS* 1.3 57.1 + - - +
74E ALA* 3.0 3.0 + - - -
75E ASN 2.8 23.6 + - - -
76E ALA* 3.0 18.2 + - - +
78E PHE* 3.3 48.9 - - + -
253E ILE* 3.9 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ARG 2.9 13.9 + - - +
69E ARG* 2.8 37.0 + - - +
71E ALA* 1.3 70.9 - - - +
73E LEU* 1.3 59.6 + - - +
75E ASN* 2.8 22.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
3E GLU* 5.2 4.4 - - - +
4E MET* 3.9 29.6 - - + +
9E ILE* 3.8 23.6 - - + -
12E GLU* 3.7 30.7 - - + +
13E LEU* 3.4 33.0 - - + -
31E LEU* 4.0 13.0 - - + -
69E ARG* 2.7 17.4 + - + +
70E LEU* 3.3 10.8 - - - +
72E LYS* 1.3 73.6 - - - +
74E ALA* 1.3 59.8 + - - +
75E ASN* 3.3 0.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
3E GLU* 5.3 11.2 - - - +
31E LEU* 3.4 33.0 - - + -
70E LEU 3.2 17.3 + - - +
71E ALA 3.0 3.9 + - - +
72E LYS 3.0 0.6 - - - -
73E LEU* 1.3 77.8 - - - +
75E ASN* 1.3 75.7 + - - +
76E ALA* 3.1 12.4 + - + +
251E ASN* 5.2 4.2 + - + +
253E ILE* 5.9 0.9 - - + -
----------------------------------------------------------
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