Contacts of the helix formed by residues 67 - 81 (chain A) in PDB entry 2Q9Q
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 ASP 67 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 3.9 6.1 - - - +
65A TRP 2.5 7.8 + - - +
66A MET* 1.3 75.1 - - - +
68A VAL* 1.3 68.1 + - - +
69A GLU* 3.1 15.4 + - - +
70A LYS* 3.2 48.2 + - + +
71A LEU* 2.8 35.2 + - - +
113A ILE* 4.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 1.3 77.6 + - - +
69A GLU* 1.3 63.0 + - + +
72A GLU* 3.0 35.1 + - - +
108A PRO 4.9 0.4 - - - +
109A LYS* 3.5 57.9 - - + +
112A GLU* 3.9 23.6 - - + +
113A ILE* 3.9 15.2 - - + +
116A LEU* 3.5 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 3.2 12.6 + - - +
68A VAL* 1.3 81.9 - - + +
70A LYS* 1.3 68.0 + - + +
72A GLU* 3.4 10.2 + - - +
73A LYS* 3.0 53.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
64A GLU* 3.1 43.2 + - - +
65A TRP* 4.1 7.0 - - - +
67A ASP* 3.1 22.9 + - + +
69A GLU* 1.3 78.4 - - + +
71A LEU* 1.3 61.2 + - - +
73A LYS* 2.9 13.7 + - + +
74A MET* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 3.6 22.4 - - + +
66A MET* 4.3 3.8 - - + -
67A ASP 2.8 31.2 + - - +
70A LYS* 1.3 73.2 - - - +
72A GLU* 1.3 57.2 + - - +
74A MET* 3.2 20.5 + - + +
75A ARG* 2.9 31.9 + - - +
88A PRO* 4.7 2.5 - - + -
92A TYR* 6.5 0.7 - - + -
113A ILE* 3.7 35.9 - - + +
116A LEU* 4.0 13.2 - - + -
117A VAL* 3.8 14.8 - - + -
120A MET* 3.2 30.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
68A VAL* 3.0 25.5 + - - +
69A GLU* 3.5 9.8 - - - +
70A LYS 3.1 0.2 - - - -
71A LEU* 1.3 78.7 - - - +
73A LYS* 1.3 59.9 + - + +
75A ARG* 3.7 22.5 + - - +
76A ASP* 3.3 33.4 + - - +
116A LEU* 4.0 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 3.0 53.0 + - - +
70A LYS* 2.9 12.1 + - + +
72A GLU* 1.3 77.6 - - + +
74A MET* 1.3 59.5 + - + +
76A ASP* 3.4 6.5 + - - +
77A HIS* 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 3.8 15.0 - - + +
70A LYS* 2.9 42.6 + - + +
71A LEU* 3.6 24.5 - - + +
73A LYS* 1.3 78.1 - - + +
75A ARG* 1.3 57.3 + - - +
77A HIS* 3.1 8.9 + - - +
78A GLU* 2.9 30.7 + - - +
85A THR* 5.0 3.1 + - - +
86A PRO 5.6 3.8 - - - +
87A MET* 5.9 0.4 - - + -
88A PRO* 3.0 37.7 - - + -
120A MET* 4.0 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU 2.9 16.9 + - - +
72A GLU* 3.8 26.4 + - - +
74A MET* 1.3 76.9 - - - +
76A ASP* 1.3 82.6 + - - +
78A GLU* 3.5 3.9 + - - +
79A ARG* 3.2 52.8 + - + +
115A THR* 5.6 2.8 - - - +
116A LEU* 3.4 28.6 - - + +
119A ASP* 3.5 36.4 + - + -
120A MET* 3.8 21.5 - - + +
123A THR* 5.1 1.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 3.3 20.6 + - - +
73A LYS* 3.9 6.3 - - - +
74A MET 3.3 0.6 - - - -
75A ARG* 1.3 99.8 + - - +
77A HIS* 1.3 64.9 + - - +
79A ARG* 3.4 12.5 + - - +
80A LYS* 3.0 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS 3.0 18.7 + - - +
74A MET* 3.1 9.0 + - - +
76A ASP* 1.3 77.6 - - - +
78A GLU* 1.3 62.8 + - - +
80A LYS* 3.2 9.9 + - + +
81A GLU* 3.1 53.9 + - + +
85A THR* 3.7 27.4 + - + +
86A PRO* 5.0 7.0 - - + -
27G ASP* 4.3 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A MET 2.9 16.3 + - - +
75A ARG* 3.7 8.3 - - - +
76A ASP 3.4 0.2 - - - -
77A HIS* 1.3 76.0 - - - +
79A ARG* 1.3 61.5 + - - +
81A GLU 3.2 3.1 + - - +
84A PHE* 3.5 5.0 - - - -
85A THR* 2.6 43.3 + - - +
87A MET* 4.3 4.5 - - - +
120A MET* 4.9 4.7 - - + +
123A THR* 3.9 16.1 + - + +
124A ARG* 3.0 46.5 + - + -
127A LYS* 2.7 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 3.2 47.8 + - - +
76A ASP* 3.8 11.6 + - - +
77A HIS 3.2 0.2 - - - -
78A GLU* 1.3 79.4 - - - +
80A LYS* 1.3 62.3 + - + +
81A GLU 3.5 4.3 + - - +
119A ASP* 3.6 30.9 + - - +
123A THR* 4.0 24.4 - - + +
127A LYS* 5.7 0.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
76A ASP* 3.0 31.1 + - - +
77A HIS* 3.2 10.1 + - + +
79A ARG* 1.3 78.5 - - + +
81A GLU* 1.3 69.9 + - - +
82A GLU* 3.5 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A HIS* 3.1 38.1 + - - +
78A GLU 3.2 3.9 + - - +
79A ARG 3.3 4.3 - - - +
80A LYS* 1.3 88.2 - - - +
82A GLU* 1.3 65.4 + - - +
83A THR* 3.5 23.1 + - - +
85A THR* 3.7 11.7 - - + -
127A LYS* 2.8 24.8 + - - -
27G ASP* 2.8 39.5 + - - +
----------------------------------------------------------
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