Contacts of the helix formed by residues 76 - 90 (chain Z) 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 Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Z LEU* 3.5 24.7 - - + -
73Z ARG* 3.6 2.0 - - - +
75Z SER* 1.4 74.7 + - - +
77Z ALA* 1.3 54.7 + - - +
79Z ALA* 4.0 0.2 - - - +
80Z SER* 2.7 34.7 + - - -
101Z ILE* 3.7 24.4 - - + +
103Z GLY 3.6 16.4 - - - +
105Z ASP* 3.0 31.6 - - - +
110Z GLY 4.0 11.0 - - - -
112Z TYR* 3.4 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R GLU* 3.5 37.0 - - + +
75Z SER* 3.2 9.7 + - - +
76Z VAL* 1.3 78.6 - - - +
78Z ALA* 1.3 56.4 + - - +
80Z SER* 3.0 16.7 + - - -
81Z LYS* 3.1 10.3 + - - +
105Z ASP* 4.8 1.2 + - - -
112Z TYR* 3.9 15.4 - - - +
120Z ARG* 3.0 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R VAL* 4.0 31.9 - - + +
99R GLU* 4.4 6.5 - - + +
66Z TYR* 5.3 2.2 - - - +
74Z ILE* 3.8 16.4 - - + -
75Z SER* 3.4 16.8 + - - +
77Z ALA* 1.3 76.7 - - - +
79Z ALA* 1.4 59.6 + - - +
81Z LYS* 3.3 5.9 + - - +
82Z LEU* 2.9 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Z ILE* 4.8 5.4 - - + -
41Z LEU* 4.3 10.3 - - + -
59Z LEU* 3.8 8.8 - - + +
63Z CYS* 4.6 9.0 - - - -
74Z ILE* 4.1 19.7 - - + -
75Z SER 2.7 23.5 + - - +
76Z VAL 4.0 3.1 - - - +
78Z ALA* 1.4 69.3 - - - +
80Z SER* 1.4 64.1 + - - +
82Z LEU* 3.6 1.4 + - - +
83Z LEU* 3.1 23.6 + - - +
101Z ILE* 4.1 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76Z VAL 2.7 21.7 + - - -
77Z ALA 3.0 11.4 + - - -
79Z ALA* 1.4 78.7 - - - +
81Z LYS* 1.3 55.6 + - - +
82Z LEU 3.5 0.2 - - - -
83Z LEU* 3.4 4.0 - - - +
84Z ALA* 2.9 29.6 + - - +
101Z ILE* 3.8 15.6 - - - +
112Z TYR* 3.3 18.7 - - - -
114Z VAL* 3.7 23.4 - - - +
120Z ARG* 3.1 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96R LEU* 3.1 25.1 - - - +
97R THR 3.3 18.6 - - - +
98R VAL 4.9 0.2 - - - -
99R GLU* 4.7 8.3 - - - +
54Y VAL* 5.2 6.5 + - - +
55Y GLN* 3.8 12.7 + - - +
58Y GLU* 3.2 28.8 + - - -
77Z ALA 3.1 19.2 + - - +
78Z ALA* 3.6 6.3 - - - +
79Z ALA 3.2 0.4 - - - -
80Z SER* 1.3 74.7 + - - +
82Z LEU* 1.4 63.6 + - - +
83Z LEU 3.1 0.2 - - - -
84Z ALA* 3.3 2.2 + - + +
85Z ASN* 2.8 49.8 + - - +
120Z ARG* 3.6 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R THR* 3.3 29.4 - - - +
98R VAL* 4.1 14.4 - - + -
59Z LEU* 4.4 9.9 - - + -
62Z GLN* 4.5 25.6 - - + +
63Z CYS* 6.0 0.4 - - - -
66Z TYR* 5.5 5.8 - - + -
74Z ILE* 4.4 17.3 - - + -
78Z ALA 2.9 32.5 + - - +
79Z ALA* 4.0 5.4 - - - +
81Z LYS* 1.4 74.5 - - - +
83Z LEU* 1.4 56.2 + - - +
85Z ASN* 3.5 8.0 + - - +
86Z MET* 3.1 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Z TRP* 4.8 19.3 - - + +
56Z GLU* 5.4 2.0 - - + -
59Z LEU* 3.7 28.7 - - + +
79Z ALA 3.1 16.9 + - - +
80Z SER 3.4 4.0 - - - +
82Z LEU* 1.4 75.3 - - - +
84Z ALA* 1.3 64.3 + - - +
86Z MET* 3.2 7.5 + - + +
87Z VAL* 3.1 27.2 + - + +
97Z MET* 5.9 0.2 - - - -
99Z THR* 3.6 33.9 - - + +
101Z ILE* 3.7 32.8 - - + -
114Z VAL* 4.0 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Y GLN* 4.9 1.5 - - - +
80Z SER 2.9 18.8 + - - +
81Z LYS* 3.7 7.2 - - + +
83Z LEU* 1.3 72.0 - - - +
85Z ASN* 1.3 67.9 + - - +
87Z VAL* 3.5 11.3 - - - +
88Z TYR* 3.1 23.2 + - - +
114Z VAL* 4.2 7.0 - - + -
118Z GLY* 4.2 13.0 - - - +
120Z ARG* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 85 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96R LEU* 4.0 28.0 + - - +
97R THR* 4.1 18.6 + - - +
55Y GLN* 3.5 18.0 + - - +
81Z LYS* 2.8 43.5 + - - +
82Z LEU* 3.7 7.8 - - - +
83Z LEU 3.2 0.2 - - - -
84Z ALA* 1.3 77.3 - - - +
86Z MET* 1.4 65.5 + - + +
88Z TYR* 3.3 15.3 + - - +
89Z GLN* 3.6 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 86 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Z TRP* 5.2 11.3 - - + +
58Z LEU* 4.5 30.3 - - + +
59Z LEU* 5.3 7.2 - - - -
62Z GLN* 4.0 33.2 - - + +
82Z LEU* 3.1 26.2 + - + +
83Z LEU* 3.2 9.6 + - + +
85Z ASN* 1.4 78.6 - - + +
87Z VAL* 1.3 58.9 + - - +
89Z GLN* 3.9 20.7 + - - +
90Z TYR* 3.6 23.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Z TRP* 4.7 9.2 - - + +
83Z LEU* 3.1 20.4 + - + +
84Z ALA* 3.5 15.0 - - - +
86Z MET* 1.3 75.2 - - - +
88Z TYR* 1.3 68.9 + - - +
89Z GLN 3.3 0.4 - - - -
90Z TYR* 3.3 18.5 + - + -
91Z LYS 3.6 0.2 + - - -
95Z LEU* 4.2 4.3 - - + +
97Z MET* 3.6 38.4 - - + -
99Z THR* 6.2 1.3 - - + -
114Z VAL* 5.0 3.4 - - + -
115Z ASP 3.8 17.3 - - - +
116Z SER* 3.5 30.5 - - - +
118Z GLY* 4.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Y GLY* 5.3 0.9 - - - -
52Y ASP* 1.9 34.2 + - - -
55Y GLN* 2.7 57.4 - - + -
96Y THR* 4.3 3.5 + - - -
98Y TYR* 2.9 25.4 - + - -
84Z ALA 3.1 18.6 + - - +
85Z ASN 3.3 8.0 + - - +
87Z VAL* 1.3 79.8 - - - +
89Z GLN* 1.3 56.1 + - + +
91Z LYS* 2.7 53.9 + - + +
116Z SER 4.7 2.2 - - - -
117Z GLU 4.3 9.2 - - - +
118Z GLY* 5.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85Z ASN* 3.6 20.2 + - - +
86Z MET* 4.1 20.9 - - - +
87Z VAL 3.3 0.8 - - - -
88Z TYR* 1.3 78.8 - - + +
90Z TYR* 1.3 79.7 + - + +
91Z LYS 3.2 2.7 + - - +
93Z MET* 3.8 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Z TRP* 3.9 26.2 - + + -
86Z MET 3.6 20.0 - - - -
87Z VAL* 3.3 12.3 + - - +
88Z TYR 3.0 0.8 - - - -
89Z GLN* 1.3 93.2 + - + +
91Z LYS* 1.3 60.0 - - - +
92Z GLY 3.5 0.3 + - - -
93Z MET* 3.4 33.8 + - + +
94Z GLY 4.2 2.9 + - - -
95Z LEU* 3.6 38.2 + - + +
116Z SER 5.3 0.2 - - - +
101a PHE* 4.2 18.4 - + - -
----------------------------------------------------------
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