Contacts of the helix formed by residues 76 - 89 (chain H) in PDB entry 5A0Q
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 VAL 76 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ILE* 3.9 11.7 - - + -
74H PRO 4.8 1.1 - - - +
75H LEU* 1.4 76.2 - - + +
77H HIS* 1.4 57.7 + - - +
79H ALA* 3.1 5.9 + - - +
80H ALA* 3.0 24.7 + - - +
100H ILE* 4.5 5.6 - - + +
101H ALA* 3.6 25.4 - - - +
102H GLY* 3.7 4.7 - - - -
103H TRP 3.7 31.9 - - - +
110H GLN* 3.7 37.9 - - + +
112H TYR* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 77 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G PHE 4.4 9.0 - - - -
103G GLY* 4.9 4.0 - - - -
104G TYR* 3.6 24.0 + - + +
75H LEU* 3.7 37.8 - - + +
76H VAL* 1.4 75.9 + - - +
78H THR* 1.3 56.7 + - - +
80H ALA* 3.6 8.3 - - - +
81H SER* 2.8 37.8 + - - -
110H GLN* 4.5 5.6 + - - -
112H TYR* 3.8 27.9 + - + +
120H MET* 3.7 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ASN 4.4 0.3 - - - +
102G PHE* 3.0 52.2 + - + -
104G TYR* 3.1 21.1 - - - -
63H LEU* 4.4 7.4 - - + -
66H HIS* 3.8 17.3 - - + +
75H LEU* 3.1 22.6 + - - +
77H HIS* 1.3 76.3 - - - +
79H ALA* 1.3 60.0 + - - +
81H SER* 3.2 4.0 + - - -
82H LEU* 3.0 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 4.7 0.9 - - + -
41H ILE* 3.9 20.0 - - + -
59H VAL* 4.0 4.3 - - + +
63H LEU* 3.5 39.0 - - + +
75H LEU 3.2 2.2 + - - -
76H VAL 3.1 9.7 + - - +
78H THR* 1.3 76.5 - - - +
80H ALA* 1.3 58.2 + - - +
82H LEU* 3.1 10.5 + - - +
83H PHE* 3.0 31.7 + - - -
100H ILE* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H VAL 3.0 15.2 + - - +
77H HIS* 3.7 6.3 - - - +
79H ALA* 1.3 76.0 - - - +
81H SER* 1.4 54.7 + - - +
83H PHE* 3.2 4.2 + - - +
84H LYS* 2.9 22.2 + - - +
100H ILE* 3.9 20.4 - - + +
112H TYR* 3.9 20.4 - - + -
114H VAL* 4.3 0.9 - - - +
120H MET* 3.2 35.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G SER 4.9 3.4 - - - -
101G ASN 4.0 13.5 - - - -
102G PHE 4.0 14.8 + - - -
103G GLY* 4.2 7.4 + - - -
77H HIS* 2.8 23.8 + - - +
78H THR 3.2 6.5 + - - -
80H ALA* 1.4 71.1 - - - +
82H LEU* 1.4 59.7 + - - +
84H LYS* 3.2 14.5 + - - +
85H GLU* 3.0 32.4 + - - +
120H MET* 3.3 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ASN* 3.4 23.1 - - + +
102G PHE* 4.2 20.0 - - + -
59H VAL* 4.1 24.9 - - + +
62H GLN* 3.6 40.4 - - + +
63H LEU* 4.2 21.1 - - + +
66H HIS* 5.9 0.2 - - + -
78H THR 3.0 14.4 + - - +
79H ALA* 3.1 7.6 + - - +
81H SER* 1.4 75.1 - - - +
83H PHE* 1.4 56.8 + - - +
85H GLU* 3.2 10.1 + - + +
86H MET* 2.9 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 3.5 26.2 - - + -
43H CYS* 3.6 17.9 - - - -
55H VAL* 3.5 33.9 - - + -
56H ALA* 3.7 8.7 - - - -
59H VAL* 3.7 21.8 - - + -
79H ALA 3.0 24.2 + - - -
80H ALA 3.2 6.7 + - - +
82H LEU* 1.4 73.1 - - - +
84H LYS* 1.3 63.6 + - - +
86H MET* 4.5 1.6 - - - +
87H CYS* 3.0 32.2 + - - +
98H ILE* 3.9 17.3 - - + -
100H ILE* 2.8 42.8 - - + -
114H VAL* 3.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H ALA 2.9 14.9 + - - +
81H SER* 3.2 17.6 + - - +
83H PHE* 1.3 75.3 - - - +
85H GLU* 1.4 59.6 + - - +
87H CYS* 4.9 0.2 - - - -
88H TYR* 2.6 54.2 + - + +
114H VAL* 4.7 8.0 - - - +
118H GLY 4.2 12.5 - - - +
120H MET* 3.8 36.3 - - + +
61N GLN* 4.2 29.2 + - + +
65N GLN* 3.5 35.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G SER* 3.0 30.1 - - - +
101G ASN* 3.7 19.9 - - + +
81H SER 3.0 21.5 + - - +
82H LEU* 3.2 14.3 + - + +
84H LYS* 1.4 80.5 + - - +
86H MET* 1.4 65.3 + - + +
88H TYR* 3.8 7.1 - - - +
89H ARG* 3.0 28.1 + - - +
65N GLN* 3.9 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H ALA* 4.5 2.7 - - + +
55H VAL* 4.0 30.3 - - + +
58H ALA* 4.1 21.1 - - + -
59H VAL* 4.1 16.8 - - + -
62H GLN* 4.5 20.4 - - - +
82H LEU* 2.9 20.2 + - + +
83H PHE* 4.1 4.7 - - - +
85H GLU* 1.4 78.8 - - + +
87H CYS* 1.3 64.1 - - - +
89H ARG* 3.9 42.1 + - - +
90H TYR* 3.6 15.9 + - - +
94H LEU* 4.0 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H VAL* 4.7 10.1 - - - -
83H PHE* 3.0 27.3 + - - +
84H LYS 4.4 0.2 - - - +
86H MET* 1.3 79.3 - - - +
88H TYR* 1.3 61.4 + - - +
90H TYR 2.7 22.9 - - - +
91H ARG* 3.3 10.9 + - - +
94H LEU* 3.4 23.8 - - + -
96H ALA* 4.2 16.2 - - - -
98H ILE* 5.3 1.3 - - - -
114H VAL* 4.2 12.8 - - + -
116H MET 4.4 5.1 - - - +
117H GLY 3.9 3.2 - - - +
118H GLY* 4.1 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H LYS* 2.6 39.4 + - + +
85H GLU* 3.8 8.7 - - - +
87H CYS* 1.3 80.4 - - - +
89H ARG* 1.3 61.8 + - - +
90H TYR 3.5 0.3 + - - -
91H ARG* 3.7 23.9 + - - -
117H GLY 4.4 6.5 - - - -
118H GLY* 3.7 15.9 - - - +
58N ALA* 3.3 26.9 + - + -
59N ASP* 3.7 9.4 + - - -
61N GLN* 6.1 0.4 - - + -
62N TYR* 1.9 73.4 - + + +
65N GLN* 5.3 4.3 - - - -
99N ARG* 5.6 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H GLU 3.0 18.1 + - - +
86H MET* 3.9 45.8 + - - +
88H TYR* 1.3 77.9 - - - +
90H TYR* 1.3 98.1 + - + +
91H ARG* 4.0 9.9 + - - +
92H GLU* 5.4 0.3 - - - +
----------------------------------------------------------
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