Contacts of the helix formed by residues 68 - 82 (chain A) in PDB entry 4RG7
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 68 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 4.1 14.6 - - + +
66A CYS* 3.6 14.3 - - - -
67A THR* 1.3 79.6 - - - +
69A PRO* 1.3 64.8 - - + +
70A GLN* 3.5 20.4 + - - +
71A CYS* 3.0 27.9 + - - +
72A LYS* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR 3.7 3.8 - - - +
68A THR* 1.3 88.4 - - + +
70A GLN* 1.3 63.1 + - + +
72A LYS* 3.8 5.2 - - + +
73A TYR* 3.0 31.5 + - - +
109A GLU* 3.5 30.1 - - + +
110A PHE* 3.9 31.8 - - + +
113A SER* 5.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 4.2 6.1 - - - +
39A GLU* 4.6 9.9 - - - +
42A PHE* 3.1 58.9 - - + +
68A THR* 3.2 22.6 + - - +
69A PRO* 1.3 81.3 - - + +
71A CYS* 1.3 59.6 + - - +
73A TYR* 4.3 3.9 - - - +
74A LEU* 3.5 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU 3.9 5.2 - - - -
41A LEU* 5.1 3.1 - - - -
42A PHE* 3.9 32.8 - - - -
45A ALA* 6.3 0.7 - - - -
61A LEU* 5.4 10.5 - - + +
66A CYS* 3.7 35.0 - - + +
68A THR* 3.0 22.9 + - - +
70A GLN* 1.3 77.4 - - - +
72A LYS* 1.3 54.7 + - - +
74A LEU* 3.3 3.8 + - - +
75A LEU* 2.7 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A CYS 5.1 4.0 + - - +
67A THR* 4.8 7.0 - - - +
68A THR 2.8 19.7 + - - +
69A PRO* 3.8 9.0 - - + +
71A CYS* 1.3 70.5 - - - +
73A TYR* 1.3 64.5 + - - +
75A LEU* 4.5 1.8 - - - -
76A ALA* 3.0 25.1 + - - +
91A ILE* 3.7 27.2 - - + +
92A LEU* 4.3 2.4 - - + +
109A GLU* 5.2 3.6 - - - +
110A PHE* 4.5 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO 3.0 16.3 + - - +
70A GLN* 4.3 4.7 - - - +
72A LYS* 1.3 76.7 - - - +
74A LEU* 1.3 62.8 + - + +
76A ALA* 3.3 3.3 + - - +
77A LYS* 3.0 50.8 + - + +
92A LEU* 4.5 7.8 - - + +
110A PHE* 5.1 2.4 - - + -
113A SER* 5.5 4.7 - - - -
116A PHE* 3.4 25.5 + - + +
117A THR* 3.4 46.4 - - + -
120A LEU* 4.1 12.7 - - + +
17B ASN 5.7 0.4 - - - -
18B HIS* 2.9 53.1 + + + -
19B TYR* 4.7 5.6 - + - -
20B ALA* 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 4.0 12.8 - - + -
45A ALA* 3.7 31.6 - - + +
46A THR* 3.7 22.2 - - - +
49A TYR* 4.0 25.4 - - + -
57A ALA* 5.2 0.7 - - + -
70A GLN 3.5 15.5 + - - +
71A CYS* 3.3 5.1 + - - +
72A LYS 3.3 0.4 - - - -
73A TYR* 1.3 82.2 - - + +
75A LEU* 1.3 65.9 + - - +
77A LYS* 3.2 6.3 + - + +
78A CYS* 3.0 35.4 + - - -
19B TYR* 4.0 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA 6.0 0.7 - - - -
58A TYR* 4.9 4.3 - - + +
61A LEU* 4.5 21.0 - - + +
62A LYS 6.0 0.4 - - - +
71A CYS 2.7 22.9 + - - +
72A LYS* 4.0 3.8 - - - +
74A LEU* 1.3 73.8 - - - +
76A ALA* 1.3 60.0 + - - +
78A CYS* 3.6 7.0 + - - +
79A CYS* 3.0 30.8 + - - -
91A ILE* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS 3.0 18.8 + - - +
73A TYR 3.5 4.5 - - - +
75A LEU* 1.3 77.2 - - - +
77A LYS* 1.3 56.8 + - - +
79A CYS* 3.2 7.4 - - - +
80A VAL* 3.0 31.1 + - + +
88A GLY* 4.1 12.9 - - - +
91A ILE* 3.8 11.8 - - + +
92A LEU* 3.8 26.7 - - + -
120A LEU* 3.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 3.6 21.7 + - + +
73A TYR* 3.0 38.9 + - + +
74A LEU* 3.2 12.7 + - + +
76A ALA* 1.3 74.3 - - - +
78A CYS* 1.3 64.2 + - - +
80A VAL* 3.3 7.5 + - + +
81A ASP* 2.8 34.5 + - - +
120A LEU* 3.8 27.4 - - + +
18B HIS 3.5 19.3 - - - +
19B TYR* 3.5 26.9 + - + -
20B ALA* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 3.3 29.2 - - - -
54A ALA* 4.0 13.0 - - + +
57A ALA* 3.5 25.8 - - - -
58A TYR* 4.3 14.8 - - + -
74A LEU* 3.0 27.9 + - - +
75A LEU* 3.9 6.7 - - - +
77A LYS* 1.3 75.2 - - - +
79A CYS* 1.3 58.2 + - - +
81A ASP* 3.4 9.7 + - - +
82A LEU* 3.0 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.4 27.1 - - - -
75A LEU* 3.0 21.5 - - - -
76A ALA* 3.2 10.1 + - - +
78A CYS* 1.3 77.2 - - - +
80A VAL* 1.3 63.1 + - - +
82A LEU* 3.0 5.8 + - - -
83A SER 3.0 5.5 + - - -
84A LYS* 2.7 41.7 + - + +
87A GLU* 2.9 43.7 - - - +
88A GLY* 4.4 1.6 - - - -
91A ILE* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA* 3.0 15.9 + - + +
77A LYS* 3.3 9.6 + - + +
79A CYS* 1.3 74.4 - - + +
81A ASP* 1.3 65.6 + - - +
83A SER* 3.1 14.7 + - - +
84A LYS 4.7 3.8 - - - +
85A LEU* 5.4 2.0 - - - +
88A GLY* 5.2 7.2 - - - -
120A LEU* 3.7 29.8 - - + -
123A HIS* 4.2 27.6 - - + +
124A VAL* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 2.4 38.6 + - - -
54A ALA* 4.5 11.2 - - + -
77A LYS* 2.8 26.3 + - - +
78A CYS* 3.4 9.0 - - - +
80A VAL* 1.3 79.1 - - - +
82A LEU* 1.3 60.2 + - + +
83A SER* 3.3 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 4.3 8.3 - - + -
55A TYR* 3.9 40.4 - - + +
58A TYR* 4.2 18.8 - - + -
78A CYS 3.0 21.5 + - - +
79A CYS* 3.0 6.7 + - - +
81A ASP* 1.3 77.5 - - + +
83A SER* 1.3 70.0 + - - +
84A LYS* 3.3 4.9 + - + +
----------------------------------------------------------
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