Contacts of the helix formed by residues 68 - 78 (chain E) in PDB entry 1GEC
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 GLN 68 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E TRP* 5.2 2.0 - - + -
29E SER* 5.5 0.4 - - - +
30E THR* 4.3 6.5 - - + -
67E TYR* 1.3 71.7 - - - +
69E SER* 1.3 64.1 + - - +
71E SER* 3.0 16.1 + - - -
72E LEU* 3.1 21.7 + - + +
131E SER* 3.3 36.9 + - - +
132E VAL 4.1 6.9 + - - -
133E VAL* 4.4 7.4 - - - +
160E ALA* 4.6 14.1 - - + -
209E SER* 2.6 51.8 + - - -
211E TYR* 3.5 18.4 - - + -
1I PHQ 4.0 16.0 + - - +
3I VAL* 5.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E TYR* 4.4 6.1 - - - +
68E GLN* 1.3 80.6 - - - +
70E THR* 1.3 58.9 + - - +
72E LEU* 3.7 5.9 - - - +
73E GLN* 2.7 36.1 + - - +
110E VAL* 4.6 5.4 - - - +
211E TYR* 3.8 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E ASP* 2.7 34.6 + - - +
59E GLN* 3.6 32.5 - - + +
60E SER* 3.3 3.8 + - - -
67E TYR* 3.2 33.3 - - + +
68E GLN 3.4 0.6 - - - -
69E SER* 1.3 79.9 + - - +
71E SER* 1.3 60.1 + - - +
73E GLN* 3.7 13.8 + - - +
74E TYR* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E TRP* 3.8 21.8 + - - -
30E THR* 3.2 26.9 + - - +
53E LEU* 3.7 14.3 - - - +
57E ASP* 3.7 6.1 - - - -
67E TYR 2.4 26.3 + - - -
68E GLN 3.0 9.7 + - - -
70E THR* 1.3 75.9 + - - +
72E LEU* 1.3 64.8 + - - +
74E TYR* 3.3 8.2 + - - +
75E VAL* 3.3 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E THR* 3.5 24.2 - - + -
33E THR* 3.9 15.9 - - - +
34E VAL* 4.3 9.4 - - + -
68E GLN 3.1 19.6 + - - +
69E SER 3.7 4.5 - - - +
71E SER* 1.3 79.1 - - - +
73E GLN* 1.3 60.6 + - - +
75E VAL* 3.5 5.6 + - - +
76E ALA* 3.1 21.3 + - - +
107E THR* 4.5 2.1 + - - -
109E GLY 4.8 0.9 - - - +
110E VAL* 3.7 21.8 - - + +
131E SER* 4.8 4.5 - - - -
211E TYR* 3.2 37.2 - - + +
212E TYR* 4.0 10.3 - - - +
213E PRO* 4.0 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E GLN* 5.1 9.9 - - - +
69E SER 2.7 18.9 + - - +
70E THR* 3.8 18.2 + - - +
72E LEU* 1.3 75.8 - - - +
74E TYR* 1.3 65.8 + - - +
76E ALA* 3.2 7.6 + - + +
77E GLN* 2.9 51.8 + - - +
110E VAL* 4.1 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E GLU* 2.7 36.4 + - + -
53E LEU* 3.4 24.2 - - + -
56E CYS* 3.3 46.1 - - + +
57E ASP* 4.1 8.1 - - + +
58E LEU 5.5 0.2 - - - -
70E THR 3.0 17.2 + - - +
71E SER* 3.4 9.6 - - - +
73E GLN* 1.3 75.9 - - - +
75E VAL* 1.3 55.7 + - + +
77E GLN* 3.2 1.8 + - - -
78E ASN* 2.7 61.7 + - + +
79E GLY 3.7 13.2 - - - -
80E ILE* 5.3 0.7 - - + -
95E CYS* 4.4 0.7 - - - -
97E ALA* 3.5 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E THR* 6.2 0.9 - - - -
34E VAL* 4.1 20.9 - - + -
53E LEU* 4.3 9.4 - - + -
71E SER 3.3 13.4 + - - +
72E LEU* 3.9 6.7 - - - +
73E GLN 3.4 0.2 - - - -
74E TYR* 1.3 74.6 - - + +
76E ALA* 1.3 60.4 + - - +
79E GLY* 2.8 33.4 + - - +
80E ILE* 3.9 46.0 - - + -
105E VAL 4.3 1.8 - - - +
106E LYS* 3.4 5.9 - - - +
107E THR* 3.6 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LEU 3.1 13.2 + - - +
73E GLN* 3.5 13.2 - - + +
75E VAL* 1.3 76.3 - - - +
77E GLN* 1.3 70.3 + - - +
106E LYS* 3.9 5.9 - - - +
107E THR* 3.3 30.1 + - - +
108E ASN* 4.1 5.9 - - - -
109E GLY* 3.9 26.0 - - - +
110E VAL* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E GLN* 2.9 44.4 + - - +
74E TYR* 4.7 0.7 - - - -
76E ALA* 1.3 89.0 - - - +
78E ASN* 1.3 77.1 + - - +
79E GLY 3.8 0.4 - - - -
106E LYS* 4.0 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E GLU* 5.4 0.2 - - - +
74E TYR* 2.7 50.7 + - + +
77E GLN* 1.3 88.0 + - - +
79E GLY* 1.3 65.0 + - - +
103E PRO* 3.2 32.2 - - + +
106E LYS* 3.7 6.1 - - - +
----------------------------------------------------------
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