Contacts of the helix formed by residues 73 - 80 (chain A) in PDB entry 3GBN
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 ASN 73 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY* 2.9 14.8 + - - +
72A GLY* 1.3 77.8 - - - +
74A PRO* 1.3 68.9 - - - +
75A GLU* 2.7 39.6 + - - +
76A CYS* 2.9 35.6 + - - +
77A ASP* 3.9 4.0 - - - +
95A GLY* 3.4 33.5 + - - +
97A CYS* 3.6 9.1 - - - +
148A TYR* 3.6 10.4 - - + -
149A ARG* 4.7 0.2 - - - -
330A NAG 3.1 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY 3.3 3.1 - - - +
73A ASN* 1.3 93.5 - - - +
75A GLU* 1.3 55.8 + - - +
76A CYS 3.2 0.9 - - - -
77A ASP* 2.9 30.8 + - - +
97A CYS* 4.1 13.2 - - - -
139A CYS* 3.7 26.2 - - + +
140A SER 3.8 15.9 - - - +
141A TYR* 3.9 17.0 - - + -
147A PHE 3.6 18.4 - - - +
148A TYR 4.6 0.2 - - - +
149A ARG* 3.6 22.0 - - - +
330A NAG 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 2.6 59.9 + - - +
64A CYS* 3.8 2.4 - - - -
73A ASN* 2.7 15.5 + - - +
74A PRO* 1.3 70.7 - - - +
76A CYS* 1.3 56.7 + - - -
77A ASP 3.5 1.5 + - - -
78A LEU* 5.9 0.9 - - - +
95A ASN* 3.4 21.4 - - + +
140A SER 4.5 10.1 - - - +
141A TYR* 5.8 3.2 - - - -
330A NAG 3.4 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A CYS* 2.0 48.5 - - - -
68A GLY 3.7 15.5 - - - +
69A TRP* 4.8 0.7 - - - -
72A GLY* 5.3 1.1 - - - -
73A ASN* 2.9 36.6 + - - +
75A GLU* 1.3 78.6 - - - +
77A ASP* 1.3 53.6 + - - +
78A LEU* 3.1 4.3 - - - -
79A LEU* 2.7 46.0 + - + +
80A LEU* 4.0 3.1 + - - +
95A ASN 3.9 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN 3.9 1.4 - - - +
74A PRO* 2.9 24.3 - - - +
75A GLU 3.5 3.0 - - - -
76A CYS* 1.3 77.5 - - - +
78A LEU* 1.3 62.7 + - + +
79A LEU 3.1 0.7 + - - -
80A LEU* 3.2 38.8 + - + +
81A THR* 4.9 0.9 + - - +
141A TYR* 4.1 18.4 + - + +
149A ARG* 3.0 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLU 5.9 0.7 - - - +
76A CYS* 4.5 2.5 - - - +
77A ASP* 1.3 79.0 - - + +
79A LEU* 1.3 68.2 + - + +
80A LEU 3.4 0.7 + - - -
81A THR* 4.0 12.0 + - - -
82A ALA* 5.0 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 4.5 10.8 - - + -
60A GLN 3.8 22.0 - - - +
61A LEU* 3.4 33.9 - - + +
64A CYS* 4.1 11.7 - - + -
69A TRP* 3.6 36.5 + - + +
76A CYS* 2.7 37.6 + - + +
78A LEU* 1.3 81.6 - - + +
80A LEU* 1.3 62.4 + - - +
81A THR 3.2 2.9 - - - -
82A ALA* 3.0 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP 6.1 0.7 - - - +
72A GLY* 5.3 6.5 - - - -
76A CYS 4.7 1.8 - - - +
77A ASP* 3.2 44.0 + - + +
78A LEU 3.4 0.2 - - - -
79A LEU* 1.3 78.9 - - - +
81A THR* 1.3 65.0 + - + +
82A ALA 3.6 4.0 + - - +
118A PHE* 6.0 0.5 - - - -
120A LYS* 3.4 44.3 + - - +
149A ARG* 3.9 28.0 - - + -
150A ASN* 4.5 4.7 - - - +
----------------------------------------------------------
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