Contacts of the helix formed by residues 66 - 82 (chain A) in PDB entry 1DSB
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 GLY 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN 4.4 5.4 + - - +
63A PHE 5.4 0.8 - - - -
64A MET* 3.3 4.9 - - - +
65A GLY* 1.3 75.1 - - - +
67A ASP* 1.3 63.3 + - - -
69A GLY* 3.3 7.3 + - - -
70A LYS* 3.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY 3.2 1.6 + - - -
66A GLY* 1.3 68.7 - - - -
68A LEU* 1.3 67.2 + - - +
70A LYS* 3.1 10.6 + - - +
71A ASP* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.6 27.6 - - + -
65A GLY 3.3 9.4 + - - +
67A ASP* 1.3 77.6 - - - +
69A GLY* 1.3 56.2 + - - +
71A ASP* 3.0 11.4 + - - +
72A LEU* 2.8 34.0 + - + +
96A VAL* 5.5 0.7 - - + -
102A ILE* 3.5 33.2 - - + +
103A ARG* 4.0 14.6 - - - +
104A SER* 4.0 22.7 - - - +
108A ILE* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.0 9.1 - - - -
60A HIS* 3.6 9.7 - - - -
61A VAL 4.0 0.8 - - - +
62A ASN* 4.5 6.3 - - - -
64A MET 3.3 25.4 - - - -
65A GLY 3.2 7.7 + - - -
66A GLY 3.6 3.4 - - - -
67A ASP 3.1 1.6 - - - -
68A LEU* 1.3 78.6 - - - +
70A LYS* 1.3 60.4 + - - +
72A LEU* 3.4 3.0 + - - -
73A THR* 3.2 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN* 3.6 43.3 - - + +
66A GLY 3.3 13.4 + - - +
67A ASP* 3.1 9.6 + - - +
69A GLY* 1.3 73.9 - - - +
71A ASP* 1.3 66.3 + - - +
73A THR* 3.2 3.3 + - - -
74A GLN* 3.1 21.5 + - - +
135A VAL* 6.3 1.1 - - - -
139A GLU* 4.2 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 3.1 20.6 + - - +
68A LEU* 3.0 17.2 + - + +
70A LYS* 1.3 77.6 - - - +
72A LEU* 1.3 56.6 + - - +
74A GLN* 3.2 7.5 + - - +
75A ALA* 2.8 27.7 + - - +
105A ALA* 3.8 25.3 + - - +
108A ILE* 3.8 17.2 - - + +
126A TRP* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 4.0 34.4 - - + -
29A PHE* 3.6 33.2 - - + -
60A HIS* 3.5 22.5 + - + +
68A LEU* 2.8 17.7 + - + +
69A GLY 3.7 0.2 - - - +
71A ASP* 1.3 73.2 - - - +
73A THR* 1.3 60.3 + - - +
75A ALA* 3.5 4.6 - - + +
76A TRP* 2.8 30.7 + - - +
92A LEU* 4.3 16.8 - - + -
96A VAL* 4.0 13.5 - - + -
102A ILE* 5.2 0.7 - - + -
108A ILE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS* 2.8 34.8 + - - +
61A VAL 3.2 8.8 + - - -
62A ASN* 3.0 30.1 + - - +
69A GLY 3.2 6.6 + - - -
70A LYS 3.2 5.5 + - - -
72A LEU* 1.3 75.0 - - - +
74A GLN* 1.3 62.4 + - - +
76A TRP* 3.5 0.9 + - - +
77A ALA* 3.1 17.0 + - - +
135A VAL* 4.6 15.0 - - + +
138A GLN* 3.3 35.1 + - + +
139A GLU* 5.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS 3.1 12.7 + - - +
71A ASP* 3.5 10.5 - - - +
72A LEU 3.2 0.2 - - - -
73A THR* 1.3 75.8 - - - +
75A ALA* 1.3 59.5 + - - +
77A ALA* 3.1 6.2 + - - +
78A VAL* 2.9 26.0 + - - +
126A TRP* 2.8 63.4 + - + +
131A VAL* 3.9 15.3 - - + +
132A LYS* 4.9 9.1 - - - +
135A VAL* 3.8 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASP 2.8 16.5 + - - +
72A LEU* 3.5 11.9 - - + +
74A GLN* 1.3 73.8 - - - +
76A TRP* 1.3 60.6 + - - +
78A VAL* 3.1 9.7 + - - +
79A ALA 2.8 23.6 + - - -
92A LEU* 5.2 3.1 - - + -
108A ILE* 3.6 30.5 - - + -
112A PHE* 3.5 17.6 - - + -
122A TYR* 4.5 0.9 - - - +
126A TRP* 3.7 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.9 18.8 - + - -
28A PHE* 3.9 28.0 - + + -
58A LYS* 2.9 42.1 + - + -
59A TYR* 4.1 0.4 - - - +
60A HIS* 3.8 19.1 - - + -
72A LEU 2.8 21.0 + - - +
73A THR 3.7 5.6 - - - +
75A ALA* 1.3 72.2 - - - +
77A ALA* 1.3 58.3 + - - +
79A ALA* 3.0 11.5 + - + +
80A MET* 2.8 52.5 + - + +
85A GLU* 3.9 31.9 - - + -
88A VAL* 4.9 2.5 - - + -
89A THR* 3.6 27.6 - - + -
92A LEU* 5.1 3.8 - - + -
138A GLN* 3.2 22.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
73A THR 3.1 13.4 + - - +
74A GLN 3.1 10.5 + - - +
76A TRP* 1.3 76.8 - - - +
78A VAL* 1.3 56.3 + - - +
80A MET* 3.3 13.1 + - - +
81A ALA* 2.9 25.6 + - - +
131A VAL* 3.9 9.9 - - + +
134A LEU* 3.4 27.9 - - + +
135A VAL* 3.8 13.9 - - + -
138A GLN* 3.7 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN 2.9 18.2 + - - +
75A ALA* 3.3 9.6 - - - +
77A ALA* 1.3 74.1 - - - +
79A ALA* 1.3 59.5 + - - +
81A ALA* 3.3 0.9 + - - +
82A LEU* 2.9 49.7 + - + +
112A PHE* 4.2 4.0 - - + -
122A TYR* 4.0 23.3 - - + +
125A ALA* 4.0 9.4 - - + -
126A TRP* 3.8 43.1 - - + +
131A VAL* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA 2.8 12.8 + - - +
76A TRP* 3.0 21.3 + - + +
78A VAL* 1.3 75.3 - - - +
80A MET* 1.3 54.2 + - - +
83A GLY* 2.7 31.0 + - - -
84A VAL* 3.0 22.5 + - + -
85A GLU* 3.6 11.2 - - + +
88A VAL* 3.9 28.3 - - + -
112A PHE* 4.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LYS 3.9 9.0 - - - +
59A TYR* 4.2 13.5 - - + -
76A TRP* 2.8 39.8 + - + +
77A ALA* 3.7 11.4 - - - +
78A VAL 3.3 0.2 - - - -
79A ALA* 1.3 76.6 - - - +
81A ALA* 1.3 62.7 + - - +
83A GLY* 3.2 11.3 + - - -
85A GLU* 3.7 22.5 - - + +
134A LEU* 4.4 19.5 - - + +
137A GLN* 5.8 1.1 - - - +
138A GLN* 3.6 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA 2.9 17.1 + - - +
78A VAL 3.3 3.1 + - - +
80A MET* 1.3 77.5 - - - +
82A LEU* 1.3 66.1 + - + +
125A ALA* 5.5 2.5 - - + -
130A VAL* 4.4 12.8 - - + -
131A VAL* 4.1 14.4 - - + -
134A LEU* 3.7 17.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
78A VAL* 2.9 37.3 + - + +
81A ALA* 1.3 79.6 - - + +
83A GLY* 1.3 62.7 + - - +
84A VAL* 3.5 21.4 + - + +
112A PHE* 5.3 0.7 - - + -
117A ILE* 4.1 33.4 - - + -
121A GLU* 4.4 25.8 - - + +
122A TYR* 4.8 0.7 - - - -
125A ALA* 4.2 18.2 - - + -
----------------------------------------------------------
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