Contacts of the helix formed by residues 76 - 89 (chain V) in PDB entry 5M32
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 V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41V ILE* 3.7 29.4 - - + -
74V PRO 4.1 0.2 + - - -
75V ARG* 1.3 73.4 - - - +
77V VAL* 1.3 64.6 + - - +
78V THR 3.3 0.9 - - - -
79V ALA* 3.5 1.3 + - - +
80V ASN* 3.3 19.9 + - - +
100V LEU* 4.7 9.6 - - + +
101V GLY* 3.9 7.2 - - - -
102V GLY* 3.7 30.3 - - - +
103V VAL 5.9 0.2 - - - +
104V ASP* 3.5 9.4 + - + +
109V HIS* 3.3 47.6 - - + +
111V TYR* 4.1 6.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105U TYR 5.7 0.2 - - - +
106U GLY* 4.4 21.3 - - - -
107U TYR* 5.1 4.3 - - + +
75V ARG* 3.4 22.8 - - + +
76V VAL* 1.3 79.6 - - + +
78V THR* 1.3 57.8 + - - +
80V ASN* 3.2 11.6 + - + +
81V ARG* 2.9 34.0 + - + +
104V ASP* 4.9 2.2 - - - +
109V HIS* 4.0 23.1 - - + +
111V TYR* 4.0 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105U TYR* 3.4 49.6 + - - -
107U TYR* 4.9 4.5 - - + -
63V LEU* 4.6 6.3 - - + -
66V HIS* 4.6 15.3 - - + +
74V PRO* 5.2 0.7 - - + -
75V ARG* 3.3 31.4 - - + +
77V VAL* 1.3 76.8 - - - +
79V ALA* 1.3 60.9 + - - +
81V ARG* 4.2 5.6 - - - +
82V MET* 2.9 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37V ILE* 5.2 2.5 - - + -
41V ILE* 4.2 16.4 - - + -
59V ILE* 4.4 5.8 - - + +
63V LEU* 3.6 25.8 - - + -
76V VAL 3.5 7.3 + - - +
77V VAL 3.2 0.8 - - - -
78V THR* 1.3 79.5 - - - +
80V ASN* 1.3 60.4 + - - +
82V MET* 4.2 2.4 - - - +
83V LEU* 3.0 35.0 + - - +
100V LEU* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76V VAL 3.3 5.0 + - - +
77V VAL* 3.2 11.6 + - - +
79V ALA* 1.3 79.3 - - - +
81V ARG* 1.3 57.2 + - - +
83V LEU* 3.6 2.5 + - - +
84V LYS* 2.9 27.4 + - - +
100V LEU* 4.1 9.1 - - + +
111V TYR* 3.2 56.8 - - + -
113V ILE* 3.3 8.8 - - - +
119V THR* 3.3 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102U LYS* 5.0 7.4 + - - +
103U TYR* 3.4 23.3 + - - +
104U LYS 4.2 6.7 - - - +
106U GLY* 3.7 30.8 + - - +
77V VAL* 2.9 22.3 + - + +
78V THR* 4.2 6.3 - - - +
79V ALA 3.3 0.2 - - - -
80V ASN* 1.3 75.4 - - + +
82V MET* 1.3 61.3 + - - +
84V LYS* 3.7 22.4 - - - +
85V GLN* 2.9 44.7 + - + +
57b ASP* 2.6 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104U LYS* 4.5 11.7 - - + +
105U TYR* 4.2 20.0 - - + -
59V ILE* 3.8 19.7 - - + +
62V ASN* 4.3 25.6 - - - +
63V LEU* 3.8 41.1 - - + -
66V HIS* 5.4 2.0 - - + -
78V THR* 2.9 37.1 + - + +
79V ALA* 4.2 2.5 - - - +
81V ARG* 1.3 75.7 - - - +
83V LEU* 1.3 60.1 + - - +
85V GLN* 5.0 1.8 - - - -
86V MET* 2.9 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37V ILE* 5.0 6.1 - - + -
55V THR* 3.7 21.8 - - + +
56V THR* 5.1 1.6 - - + -
59V ILE* 3.7 31.6 - - + -
79V ALA 3.0 20.3 + - - +
80V ASN 4.0 2.9 - - - +
82V MET* 1.3 75.8 - - - +
84V LYS* 1.3 55.5 + - - +
86V MET* 5.0 1.3 - - + -
87V LEU* 2.7 41.4 + - + +
98V LEU* 3.9 32.5 - - + -
100V LEU* 3.7 29.8 - - + -
113V ILE* 4.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80V ASN* 2.9 21.7 + - - +
81V ARG* 3.7 30.7 - - - +
82V MET 3.3 0.2 - - - -
83V LEU* 1.3 77.4 - - - +
85V GLN* 1.3 64.2 + - + +
87V LEU* 3.8 0.8 - - - -
88V PHE* 2.9 33.8 + - + +
113V ILE* 5.1 2.0 - - - +
117V GLY* 3.8 21.5 - - - +
119V THR* 3.6 34.0 + - + +
50b ALA 6.0 0.2 - - - +
53b GLN* 4.0 26.7 + - + +
54b ALA* 5.9 4.0 - - + +
57b ASP* 3.5 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103U TYR* 3.2 54.8 + - - +
104U LYS* 4.6 10.7 - - - +
81V ARG* 2.9 35.1 + - + +
82V MET* 4.6 2.1 - - - +
84V LYS* 1.3 83.5 - - + +
86V MET* 1.3 61.9 + - - +
88V PHE* 3.6 5.8 + - - +
89V ARG* 3.5 31.3 + - - +
54b ALA* 6.5 0.9 - - + -
57b ASP* 3.6 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 86 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55V THR* 3.2 32.3 - - - +
58V LEU* 3.8 30.1 - - + -
59V ILE* 3.8 24.2 - - + -
82V MET* 2.9 20.7 + - + +
83V LEU* 5.1 1.1 - - + -
85V GLN* 1.3 79.2 - - - +
87V LEU* 1.3 64.1 + - - +
88V PHE 3.6 0.3 + - - -
89V ARG* 3.4 41.1 + - - +
90V TYR* 4.2 26.6 - - + -
94V ILE* 5.2 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55V THR* 4.8 13.7 - - - +
83V LEU* 2.7 23.2 + - + +
84V LYS 4.2 0.2 - - - +
86V MET* 1.3 78.7 - - + +
88V PHE* 1.3 64.0 + - - +
90V TYR* 4.0 8.9 + - - +
92V GLY* 4.3 10.6 + - - -
94V ILE* 4.8 18.7 - - + +
96V ALA* 4.0 23.8 - - + +
98V LEU* 4.0 10.1 - - + -
113V ILE* 3.9 18.6 - - + -
114V TYR 3.4 17.5 - - - +
115V PRO 3.3 29.1 - - - +
116V HIS 4.4 0.2 - - - +
117V GLY* 3.6 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84V LYS* 2.9 21.2 + - + +
85V GLN* 4.0 6.7 - - - +
86V MET 3.3 0.6 - - - -
87V LEU* 1.3 75.6 - - - +
89V ARG* 1.3 63.8 + - + +
90V TYR 3.1 4.9 - - - -
91V GLN* 2.9 41.4 + - - -
116V HIS 3.4 21.7 - - - +
117V GLY* 4.7 4.3 - - - +
50b ALA* 3.7 14.1 - - + -
51b ASP* 3.7 40.2 - - + -
54b ALA* 4.0 19.5 - - + -
94b LEU* 5.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85V GLN* 3.5 15.4 + - - +
86V MET* 3.4 47.7 - - - +
88V PHE* 1.3 85.1 - - + +
90V TYR* 1.3 82.0 + - + +
91V GLN* 3.2 14.1 + - - +
----------------------------------------------------------
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