Contacts of the helix formed by residues 85 - 106 (chain H) in PDB entry 6O81
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 85 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H TYR* 4.0 4.9 - - - +
84H SER* 1.3 81.8 - - - +
86H TYR* 1.3 60.7 + - - +
87H SER* 3.5 6.3 - - - +
88H LYS* 4.9 8.2 - - + +
89H CYS* 3.3 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLY 3.2 28.6 + - - -
40H GLU* 3.7 22.0 - - + -
41H THR 3.6 20.9 - - - -
42H ILE* 4.5 9.6 - - + -
45H LEU* 3.4 20.2 - - + +
80H SER* 5.9 8.3 - - - -
84H SER 3.7 2.1 + - - +
85H ASP* 1.3 73.4 - - - +
87H SER* 1.3 60.5 + - - +
88H LYS 3.4 0.4 - - - -
89H CYS* 3.6 10.1 - - + -
90H LYS* 2.9 41.6 + - + +
93H MET* 5.2 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H ASP* 3.5 4.9 - - - +
86H TYR* 1.3 81.0 - - - +
88H LYS* 1.3 61.4 + - - +
90H LYS* 3.8 9.1 + - - +
91H LYS* 4.0 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H TYR* 5.5 9.9 - - + -
85H ASP* 4.3 10.8 + - + +
87H SER* 1.3 77.9 - - - +
89H CYS* 1.3 60.1 + - - +
90H LYS 3.4 0.2 + - - -
91H LYS* 3.4 6.7 + - - +
92H ILE* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H ALA* 4.3 12.3 - - - +
80H SER* 5.5 3.1 - - - -
83H TYR* 3.8 21.7 - - + +
85H ASP 3.3 21.0 + - - +
86H TYR* 3.2 15.8 + - + +
88H LYS* 1.3 77.0 - - - +
90H LYS* 1.3 59.6 + - - +
92H ILE* 3.8 7.3 - - - +
93H MET* 2.8 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H TYR* 2.9 34.0 + - + +
87H SER* 4.1 6.5 - - - +
88H LYS 3.3 0.4 - - - -
89H CYS* 1.3 76.6 - - - +
91H LYS* 1.3 57.7 + - - +
93H MET* 3.4 8.4 + - - +
94H ILE* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H SER 4.0 6.8 + - - +
88H LYS* 3.4 9.0 + - - +
90H LYS* 1.3 75.1 - - - +
92H ILE* 1.3 60.1 + - - +
94H ILE* 3.3 7.5 + - - +
95H GLU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H ALA* 5.8 0.2 - - - -
83H TYR* 3.7 37.2 - - + +
88H LYS 2.9 19.0 + - - +
89H CYS* 3.8 4.0 - - - +
91H LYS* 1.3 78.5 - - - +
93H MET* 1.3 56.0 + - - +
95H GLU* 3.5 4.5 + - - +
96H ARG* 2.9 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 4.6 3.9 - - + +
34H LEU* 5.6 9.0 - - - -
49H LEU* 5.7 2.2 - - - -
72H PHE* 5.5 10.9 - - + -
75H PHE* 4.7 9.0 - - + -
76H ILE* 3.9 35.4 - - + +
79H ALA* 3.8 32.3 - - + +
80H SER* 4.7 6.5 - - - +
86H TYR* 5.2 15.9 - - + +
89H CYS* 2.8 22.3 + - + +
90H LYS* 3.8 6.1 - - - +
92H ILE* 1.3 73.7 - - - +
94H ILE* 1.3 59.7 + - - +
96H ARG* 3.8 5.2 - - - +
97H GLY* 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 4.6 14.6 - - + +
35H LYS* 6.2 4.5 - - + -
90H LYS 2.9 17.2 + - - +
91H LYS* 3.7 8.7 - - - +
92H ILE 3.3 0.2 - - - -
93H MET* 1.3 77.0 - - - +
95H GLU* 1.3 57.2 + - - +
97H GLY* 3.4 1.6 + - - -
98H GLU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H LYS 2.9 16.1 + - - +
92H ILE* 4.0 4.9 - - - +
94H ILE* 1.3 77.1 - - - +
96H ARG* 1.3 58.5 + - + +
98H GLU* 3.3 6.0 + - - +
99H LEU* 2.9 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H PHE* 3.6 31.4 - - + -
78H LEU* 4.2 22.6 - - - +
79H ALA* 4.3 13.6 - - - +
82H GLU* 4.4 8.3 - - - +
83H TYR* 3.4 38.6 + - - -
92H ILE* 2.9 24.7 + - - +
93H MET* 3.9 4.7 - - - +
95H GLU* 1.3 76.3 - - + +
97H GLY* 1.3 57.6 + - - +
99H LEU* 3.5 6.0 + - - +
100H PHE* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 4.0 20.0 - - - -
72H PHE* 5.3 5.2 - - - -
75H PHE* 4.1 8.2 - - - -
93H MET 2.9 17.5 + - - -
94H ILE 3.8 1.3 - - - -
96H ARG* 1.3 74.6 - - - +
98H GLU* 1.3 58.2 + - - +
100H PHE* 3.7 8.7 - - - +
101H LEU* 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 4.1 8.4 - - + +
94H ILE 3.0 18.2 + - - +
95H GLU* 3.3 8.5 + - - +
97H GLY* 1.3 77.3 - - - +
99H LEU* 1.3 60.8 + - + +
101H LEU* 3.4 6.1 + - - +
102H ARG* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H GLU* 2.9 30.6 + - + +
96H ARG* 3.9 6.5 - - - +
98H GLU* 1.3 80.4 - - + +
100H PHE* 1.3 58.4 + - - +
102H ARG* 3.3 11.5 + - + +
103H ARG* 2.9 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H ILE* 4.2 34.5 - - + -
71H LEU* 5.6 16.6 - - + -
72H PHE* 5.6 10.1 - + + -
75H PHE* 4.8 25.6 - + + -
96H ARG 2.8 18.8 + - - +
97H GLY* 3.7 9.0 - - - +
99H LEU* 1.3 74.6 - - - +
101H LEU* 1.3 61.3 + - - +
103H ARG* 3.3 7.8 + - + -
104H ILE* 2.9 59.0 + - + +
232H SER* 6.3 2.0 - - - -
233H PHE* 5.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H VAL* 4.4 9.4 - - + +
27H ILE* 3.8 29.2 - - + -
28H ARG* 3.7 47.8 - - + +
31H LEU* 3.7 29.6 - - + -
97H GLY 2.9 12.9 + - - +
98H GLU* 3.4 6.0 + - - +
100H PHE* 1.3 74.3 - - + +
102H ARG* 1.3 58.6 + - - +
104H ILE* 3.9 11.9 - - + +
105H SER* 2.7 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H GLU 2.9 17.4 + - - +
99H LEU* 3.6 15.5 - - + +
101H LEU* 1.3 77.9 - - - +
103H ARG* 1.3 60.9 + - + +
105H SER* 3.6 12.4 + - - -
106H LEU* 3.3 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H LEU* 2.9 24.7 + - + +
100H PHE* 3.7 9.9 - - + +
102H ARG* 1.3 77.0 - - + +
104H ILE* 1.3 65.4 - - + +
106H LEU* 3.5 36.5 + - - +
107H SER* 3.8 7.4 + - - -
287H ASP* 4.2 20.7 + - - +
288H LEU* 5.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H VAL* 3.7 29.8 - - + -
27H ILE* 5.5 3.1 - - + -
100H PHE* 2.9 53.8 + - + +
101H LEU* 3.9 12.1 - - + +
103H ARG* 1.3 78.1 - - + +
105H SER* 1.3 64.8 + - - +
107H SER* 3.1 25.7 + - - -
108H ARG* 4.6 2.9 + - - +
232H SER* 4.6 17.3 - - - +
233H PHE* 3.7 30.1 - - + +
287H ASP* 5.6 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 105 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H VAL* 6.1 1.2 - - - +
28H ARG* 5.9 1.4 + - - -
101H LEU* 2.7 27.8 + - - +
102H ARG* 4.0 7.4 - - - -
103H ARG 3.4 0.6 - - - -
104H ILE* 1.3 78.0 - - - +
106H LEU* 1.3 57.1 + - - +
107H SER 3.4 0.4 + - - -
108H ARG* 4.7 8.3 + - - +
109H ASN* 5.0 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H ARG* 3.3 18.1 + - + +
103H ARG* 3.5 33.7 - - - +
104H ILE 3.2 0.8 - - - -
105H SER* 1.3 76.6 - - - +
107H SER* 1.3 64.7 + - - +
108H ARG 3.4 2.7 - - - -
109H ASN* 3.5 23.0 + - + +
110H LYS* 3.4 18.6 + - + +
----------------------------------------------------------
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