Contacts of the helix formed by residues 73 - 85 (chain A) in PDB entry 1GDT
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 73 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG 4.1 0.2 + - - -
72A ASP* 1.3 81.0 + - - +
74A ALA* 1.3 61.9 + - - +
76A MET* 2.9 45.2 + - + +
77A ILE* 2.9 16.5 + - - +
111A LEU* 4.4 24.7 - - + +
115A ALA* 4.0 18.5 - - + +
114B VAL* 5.4 7.0 - - + +
118B GLU* 5.4 14.4 - - + +
121B ARG* 5.4 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 2.9 12.4 + - + +
73A THR* 1.3 81.3 + - - +
75A ASP* 1.3 63.0 + - - +
77A ILE* 3.5 16.4 + - + +
78A GLN* 3.2 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 4.3 6.9 + - - -
45A ARG* 4.5 14.2 + - - -
70A GLY* 3.6 9.4 - - - -
71A ARG* 3.6 49.3 + - - +
72A ASP* 2.6 25.6 + - - +
74A ALA* 1.3 70.4 - - - +
76A MET* 1.3 57.5 + - - +
78A GLN* 3.7 1.7 + - - +
79A LEU* 2.9 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.6 47.1 - - + +
67A ASP* 4.9 7.2 - - + +
69A LEU* 4.5 8.3 - - + -
70A GLY* 4.0 22.0 - - - +
71A ARG 5.0 5.6 - - - +
72A ASP 3.4 2.9 + - - +
73A THR* 2.9 43.8 + - + +
75A ASP* 1.3 76.8 - - - +
77A ILE* 1.3 67.3 + - - +
79A LEU* 3.1 5.8 + - - -
80A ILE* 2.7 36.7 + - + +
92A PHE* 5.7 0.9 - - - -
111A LEU* 3.7 19.5 - - + -
114B VAL* 6.5 0.4 - - - -
117B ALA* 5.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR 2.9 15.1 + - - +
74A ALA* 3.5 23.3 - - + +
75A ASP 3.3 0.2 - - - -
76A MET* 1.3 79.2 - - - +
78A GLN* 1.3 81.4 + - - +
80A ILE* 3.6 3.1 - - - +
81A LYS* 2.9 33.8 + - + +
108A VAL* 3.8 14.6 - - + +
111A LEU* 3.6 26.7 - - + +
112A SER* 3.7 36.8 - - - +
115A ALA* 5.2 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 3.2 25.3 + - - +
75A ASP 4.5 0.7 - - - +
77A ILE* 1.3 99.8 - - - +
79A LEU* 1.3 56.4 + - - +
81A LYS* 3.1 28.9 + - + +
82A GLU* 2.7 35.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
45A ARG* 5.7 1.8 - - - +
48A LEU* 3.8 20.4 - - + -
52A ARG* 4.2 26.7 - - - +
69A LEU* 3.1 44.4 - - + +
70A GLY* 4.8 0.7 - - - -
75A ASP* 2.9 35.2 + - - +
76A MET* 3.6 3.6 - - - +
78A GLN* 1.3 76.6 - - - +
80A ILE* 1.3 61.9 + - - +
82A GLU* 3.3 11.7 - - - +
83A PHE* 3.2 44.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 5.7 0.4 - - + -
69A LEU* 4.4 13.2 - - + -
76A MET* 2.7 29.9 + - + +
77A ILE 3.6 2.9 - - - +
79A LEU* 1.3 70.3 - - - +
81A LYS* 1.3 65.7 + - - +
82A GLU 2.9 2.5 + - - -
83A PHE* 3.0 8.8 + - + +
84A ASP* 2.8 46.7 + - - +
90A ILE* 4.7 9.2 - - + -
92A PHE* 4.5 16.2 - - + -
99A THR* 4.0 16.4 - - + -
104A GLY 4.4 1.8 - - - +
107A VAL* 4.1 15.5 - - + -
108A VAL* 3.6 13.7 - - + -
111A LEU* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 2.9 22.5 + - + +
78A GLN* 3.1 43.5 + - + +
80A ILE* 1.3 76.3 - - - +
82A GLU* 1.3 63.5 + - - +
84A ASP* 3.7 8.4 - - - +
85A ALA* 3.2 22.5 + - - +
108A VAL* 4.3 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 2.9 59.2 + - - +
78A GLN 2.7 12.5 + - - +
79A LEU* 3.3 16.1 - - - +
81A LYS* 1.3 76.4 - - - +
83A PHE* 1.3 71.9 + - + +
84A ASP 3.0 1.4 + - - -
85A ALA* 3.2 4.0 + - - +
86A GLN* 3.0 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.3 13.9 - - + -
51A LEU* 4.9 0.9 - - + -
52A ARG* 3.6 31.9 - - + -
55A VAL* 4.1 17.5 - - + -
61A ILE* 3.3 30.7 - - + -
69A LEU* 4.6 4.9 - - + -
79A LEU* 3.2 39.4 + - + -
80A ILE* 3.0 6.1 + - - +
82A GLU* 1.3 81.8 - - + +
84A ASP* 1.3 55.1 + - - +
86A GLN* 3.5 4.9 + - + -
87A GLY 3.3 2.8 + - - -
88A VAL* 2.6 57.0 + - + +
90A ILE* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 2.8 36.2 + - - +
81A LYS* 3.7 8.2 - - - +
83A PHE* 1.3 74.7 - - - +
85A ALA* 1.3 59.2 + - - +
87A GLY* 2.7 25.1 + - - -
88A VAL 3.6 7.7 - - - +
90A ILE* 5.9 0.2 - - - +
99A THR* 3.7 26.5 + - - +
101A GLY 5.1 4.5 - - - +
104A GLY* 3.5 25.0 - - - +
105A LYS* 4.1 7.9 + - + +
108A VAL* 4.5 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS 3.2 13.9 + - - +
82A GLU* 3.2 4.8 + - - +
84A ASP* 1.3 78.4 - - - +
86A GLN* 1.3 57.4 + - - +
87A GLY* 3.0 5.9 + - - -
----------------------------------------------------------
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