Contacts of the helix formed by residues 69 - 83 (chain A) in PDB entry 5JGH
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 ARG 69 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR 3.7 2.4 + - - +
68A LEU* 1.3 76.7 - - - +
70A PRO* 1.3 77.7 - - + +
71A ALA* 3.3 8.7 - - + +
72A GLU* 2.8 39.6 + - - +
73A ILE* 3.1 12.7 + - - +
12F A 4.9 2.2 - - - +
13F A 4.0 39.3 + - - +
14F A 4.2 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 4.4 4.8 + - - +
68A LEU 4.5 1.3 - - - +
69A ARG* 1.3 86.9 - - + +
71A ALA* 1.3 62.0 + - - +
73A ILE* 3.2 16.5 + - + +
74A SER* 3.4 14.6 + - - -
12E A 4.4 4.5 - - + -
13E T 4.3 1.8 - - - -
10F A 4.2 13.1 - - + +
11F T 3.2 49.8 - - + +
12F A 3.6 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 3.3 5.8 - - + +
70A PRO* 1.3 79.4 - - - +
72A GLU* 1.3 62.6 + - - +
73A ILE 3.3 0.3 + - - -
74A SER* 3.6 4.7 + - - -
75A LYS* 3.5 16.8 + - - +
12E A 4.0 26.0 + - - +
13E T 3.2 50.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR 4.8 0.2 - - - +
68A LEU* 3.5 28.3 - - + +
69A ARG* 2.8 50.0 + - + +
71A ALA* 1.3 80.4 - - - +
73A ILE* 1.3 57.1 + - - +
75A LYS* 3.2 9.3 + - - +
76A ILE* 3.1 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 4.4 17.0 - - - +
61A PHE* 3.9 25.8 - - + +
62A VAL* 3.4 36.6 - - + -
65A ASN* 3.6 26.2 - - + +
68A LEU* 3.6 23.1 - - + +
69A ARG 3.1 14.3 + - - +
70A PRO* 3.2 9.1 + - + +
72A GLU* 1.3 73.2 - - - +
74A SER* 1.3 55.2 + - - +
75A LYS 3.1 0.9 - - - -
76A ILE* 3.0 8.8 + - + +
77A ALA* 2.7 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 3.0 12.8 + - - -
54A LEU* 5.4 0.7 - - - -
58A ARG* 3.6 14.1 + - - +
70A PRO 3.4 6.2 + - - -
71A ALA 3.6 3.8 - - - -
73A ILE* 1.3 78.2 - - - +
75A LYS* 1.3 57.0 + - - -
77A ALA* 3.3 2.4 + - - -
78A GLY 2.9 22.3 + - - -
13E T 2.7 30.7 + - - -
14E A 3.0 40.0 + - - +
10F A 4.2 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA 3.5 8.0 + - - +
72A GLU* 3.2 11.1 + - - +
73A ILE 3.1 0.8 - - - -
74A SER* 1.3 74.7 - - - +
76A ILE* 1.3 73.9 + - + +
78A GLY 3.0 1.8 + - - -
79A GLU* 3.0 59.3 + - + +
82A GLN* 6.3 0.2 - - - +
13E T 5.1 5.1 + - - +
14E A 3.6 34.5 + - - +
15E T 4.9 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 4.4 11.7 - - + -
65A ASN* 4.5 16.4 - - + +
68A LEU* 3.8 25.4 - - + -
72A GLU 3.1 13.6 + - - +
73A ILE* 3.0 10.7 + - + +
75A LYS* 1.3 79.9 - - + +
77A ALA* 1.3 64.4 + - - +
79A GLU* 3.2 9.1 + - + +
80A LYS* 3.0 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 3.2 24.0 - - + +
53A TYR* 4.1 4.4 - - + -
54A LEU* 3.7 23.6 - - + -
61A PHE* 3.8 25.0 - - + -
73A ILE* 2.7 16.0 + - + +
74A SER 3.6 3.1 - - - +
76A ILE* 1.3 72.9 - - - +
78A GLY* 1.3 56.7 + - - +
80A LYS* 3.3 4.4 + - - +
81A TRP* 2.8 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 3.5 13.2 + - - -
74A SER 2.9 12.4 + - - -
75A LYS* 3.0 4.8 + - - -
77A ALA* 1.3 76.2 - - - +
79A GLU* 1.3 56.3 + - - +
81A TRP* 3.0 3.6 + - - +
82A GLN* 2.8 35.6 + - - +
14E A 3.4 26.2 - - - -
15E T 4.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 3.0 43.4 + - + +
76A ILE* 3.7 11.7 - - + +
78A GLY* 1.3 75.3 - - - +
80A LYS* 1.3 63.8 + - + +
82A GLN* 3.4 11.2 + - - +
83A ASN* 3.2 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.4 20.8 + - - +
61A PHE* 3.3 37.1 - - + -
64A GLU* 3.6 24.6 + - - -
65A ASN* 5.5 0.4 - - - +
76A ILE* 3.0 32.8 + - - +
77A ALA 3.5 5.6 - - - +
79A GLU* 1.3 77.2 - - + +
81A TRP* 1.3 57.9 + - - +
83A ASN* 3.4 3.9 + - - -
84A LEU* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.9 21.5 - - + -
50A TYR* 3.6 27.8 - + + -
53A TYR* 3.4 46.1 - + + -
77A ALA 2.8 14.1 + - - +
78A GLY 3.0 7.2 + - - +
80A LYS* 1.3 74.1 - - - +
82A GLN* 1.3 91.4 + - - +
84A LEU* 3.2 26.0 + - + +
89A LYS* 3.4 50.7 - - + +
92A TYR* 4.0 9.6 - + + -
93A ILE* 4.0 14.6 - - + -
15E T 3.4 14.5 + - - -
16E T 3.1 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 6.3 0.4 - - - +
78A GLY 2.8 21.6 + - - +
79A GLU* 3.4 15.9 + - - +
80A LYS 3.4 0.2 - - - -
81A TRP* 1.3 96.6 - - - +
83A ASN* 1.3 66.6 + - - +
84A LEU 3.5 2.1 + - - +
89A LYS* 3.8 21.3 + - - +
15E T 3.0 28.5 + - - +
16E T 3.6 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.2 32.1 + - - +
80A LYS* 3.5 3.8 - - - +
82A GLN* 1.3 81.0 - - - +
84A LEU* 1.3 64.4 + - - +
85A GLU* 3.6 1.9 + - - -
----------------------------------------------------------
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