Contacts of the helix formed by residues 66 - 76 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 3.1 20.8 - - - +
65B ASN* 1.3 87.5 - - + +
67B ALA* 1.3 64.1 + - - +
68B ASP* 3.6 26.6 - - - +
69B GLN* 3.4 8.7 + - - +
70B CYS* 4.0 2.4 + - - -
89B PHE* 4.0 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 4.5 4.9 - - + -
66B THR* 1.3 72.3 - - - +
68B ASP* 1.3 64.0 + - - +
70B CYS* 2.8 31.7 + - - +
71B ALA* 3.1 5.2 + - - +
87B PHE* 4.1 2.5 - - + -
89B PHE* 3.5 43.8 - - + -
119B TYR* 4.0 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN 3.5 18.0 + - - +
39B ILE* 3.1 38.8 - - - +
66B THR* 3.6 19.2 + - - +
67B ALA* 1.3 81.0 + - - +
69B GLN* 1.3 60.6 + - - +
71B ALA* 3.1 2.8 + - - +
72B ASP* 2.6 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 3.3 31.2 - - + -
66B THR* 3.4 6.7 + - - +
67B ALA 3.2 0.2 - - - -
68B ASP* 1.3 77.6 - - - +
70B CYS* 1.3 64.8 + - - +
72B ASP* 3.2 7.2 + - - +
73B ARG* 2.9 25.9 + - - +
96B CYS* 4.6 0.2 - - - -
98B TRP* 5.0 0.4 - - - -
7K IDS 4.2 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B THR 4.1 1.6 - - - -
67B ALA* 2.8 15.3 + - - +
69B GLN* 1.3 80.3 - - - +
71B ALA* 1.3 51.5 + - - +
74B CYS* 2.8 31.2 + - - +
87B PHE* 3.3 26.5 - - + -
89B PHE* 3.7 22.9 - - - -
96B CYS* 2.0 55.6 - - + -
98B TRP* 2.9 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B THR* 3.3 16.8 - - - +
39B ILE* 3.4 34.5 - - + +
42B PHE* 3.9 3.5 - - + -
67B ALA 3.1 1.4 + - - -
68B ASP* 3.1 9.1 + - - +
70B CYS* 1.3 79.3 - - - +
72B ASP* 1.3 54.0 + - - +
74B CYS* 2.9 4.5 + - - +
75B THR* 2.5 37.5 + - - -
87B PHE* 3.5 18.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 3.9 25.3 + - - +
38B THR* 3.4 16.4 + - - +
68B ASP* 2.6 28.0 + - - +
69B GLN* 3.7 8.1 - - - +
71B ALA* 1.3 69.8 - - - +
73B ARG* 1.3 57.2 + - - +
75B THR* 3.1 4.0 + - - -
76B ARG* 2.7 81.4 + - - +
8K SGN 5.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 5.5 0.2 - - - -
62B LYS* 4.9 0.6 - - - +
69B GLN 2.9 17.3 + - - +
70B CYS 3.4 4.0 - - - +
72B ASP* 1.3 74.4 - - - +
74B CYS* 1.3 57.6 + - - +
76B ARG* 5.2 2.0 - - - +
77B ASN* 2.8 28.8 + - - -
78B LYS* 2.4 36.1 + - + +
79B GLY 3.7 13.3 + - - -
80B LEU* 3.6 14.5 - - - +
98B TRP* 3.2 39.7 - - + -
5K IDS 2.8 36.2 + - - -
6K SGN 2.9 27.7 + - - +
7K IDS 3.0 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 3.6 22.7 - - + -
70B CYS 2.8 14.1 + - - +
71B ALA 3.3 6.7 - - - +
73B ARG* 1.3 75.4 - - - +
75B THR* 1.3 66.9 + - - +
77B ASN* 3.3 11.6 + - - +
80B LEU* 4.3 1.8 - - - -
84B CYS* 2.0 67.0 - - - +
86B ALA 4.5 3.1 - - - -
87B PHE* 3.9 11.7 - - + -
98B TRP* 3.8 6.5 - - + +
121B ASN* 4.6 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 5.2 5.0 - - - +
38B THR* 3.2 36.6 + - + -
41B GLU* 4.6 10.1 + - - +
42B PHE* 3.5 13.6 - - - -
71B ALA 2.5 20.6 + - - -
72B ASP* 3.6 3.6 - - - -
74B CYS* 1.3 75.7 - - - +
76B ARG* 1.3 65.2 + - + +
77B ASN* 3.0 7.5 + - - +
121B ASN* 5.4 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 5.1 5.0 - - - +
148A LYS* 6.1 2.4 - - - +
37B ASN* 5.3 3.2 - - - +
38B THR* 5.8 3.0 - - + +
72B ASP* 2.7 56.3 + - - +
73B ARG* 5.2 0.7 - - - +
75B THR* 1.3 76.6 - - + +
77B ASN* 1.3 59.3 + - - +
78B LYS* 2.7 27.1 + - + +
8K SGN 3.2 42.4 + - - -
----------------------------------------------------------
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