Contacts of the strand formed by residues 76 - 92 (chain V) in PDB entry 4EDW
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 TRP 76 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71V ILE* 4.1 16.1 - - + +
72V ASP* 2.9 33.7 + - + +
73V SER* 3.6 14.7 + - - +
75V HIS* 1.3 94.5 + - + +
77V ASN* 1.4 64.3 + - - +
78V SER 4.3 0.2 + - - -
112V LEU* 3.8 37.0 - - + -
113V SER 3.7 20.0 - - - -
114V ARG* 4.2 21.3 - - + -
115V LYS* 3.3 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 77 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76V TRP* 1.4 74.0 - - - +
78V SER* 1.3 63.2 + - - +
112V LEU* 3.5 2.3 - - - -
113V SER* 2.9 44.9 + - - +
114V ARG 3.5 17.4 + - - -
115V LYS* 3.3 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67V GLY* 3.2 20.4 + - - -
68V CYS* 3.3 26.1 + - - -
71V ILE* 3.4 18.5 - - - +
76V TRP 5.0 0.2 + - - -
77V ASN* 1.3 77.3 - - - +
79V TYR* 1.3 69.5 + - - +
110V CYS* 3.8 0.4 - - - -
111V VAL 3.3 13.5 - - - -
112V LEU* 3.7 15.5 - - - +
113V SER* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 79 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62V ASN* 4.1 17.0 - - + -
67V GLY 4.4 3.8 - - - +
68V CYS* 3.5 8.3 - - - -
77V ASN 6.1 0.2 - - - -
78V SER* 1.3 80.9 - - - +
80V CYS* 1.3 71.1 + - - +
81V THR* 3.8 22.0 + - - +
109V VAL 3.8 0.7 - - - +
110V CYS* 3.5 0.7 - - - -
111V VAL* 3.1 53.8 + - + +
113V SER* 6.0 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 80 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14V VAL 3.9 0.9 - - - -
15V CYS* 2.0 51.8 - - - -
16V ASP 5.7 0.4 - - - +
58V CYS* 3.6 4.5 - - + -
62V ASN* 3.3 40.4 + - - +
64V VAL* 3.7 24.7 - - + -
68V CYS* 3.9 6.3 - - - -
79V TYR* 1.3 77.7 - - - +
81V THR* 1.3 60.1 + - - +
108V CYS* 3.7 13.7 - - - -
109V VAL 3.4 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58V CYS* 3.4 5.8 - - - -
62V ASN* 4.8 1.3 - - - -
79V TYR* 3.8 18.9 - - + +
80V CYS* 1.3 75.6 - - - +
82V THR* 1.3 68.2 + - - +
83V THR* 3.6 7.4 + - + -
108V CYS* 3.4 0.9 - - - -
109V VAL* 2.7 50.2 + - + +
111V VAL* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57V LYS* 3.7 11.9 - - + +
58V CYS* 3.0 29.0 + - - +
62V ASN* 4.8 2.2 + - - -
81V THR* 1.3 78.9 + - - +
83V THR* 1.3 67.5 + - - +
84V HIS* 3.5 17.0 - - - +
105V ASP* 3.5 35.2 - - + +
107V ALA 3.2 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81V THR* 3.6 7.4 + - + +
82V THR* 1.3 80.4 - - - +
84V HIS* 1.3 71.4 + - - +
106V THR* 2.9 22.8 + - - +
107V ALA* 3.0 32.4 + - - +
109V VAL* 3.6 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 84 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82V THR* 3.5 24.7 + - + +
83V THR* 1.3 78.2 + - - +
85V THR* 1.3 61.1 + - - +
103V ARG* 3.7 34.1 - - + -
104V ILE* 3.2 11.0 - - - +
105V ASP* 3.2 34.9 + - - -
106V THR* 3.5 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54V PHE 5.9 0.2 - - - +
84V HIS* 1.3 74.8 - - - +
86V PHE* 1.3 72.5 + - - +
87V VAL* 3.8 12.9 + - + +
102V ILE 3.5 0.3 - - - +
103V ARG* 3.5 7.0 - - - +
104V ILE* 2.9 50.6 + - + -
106V THR* 3.4 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 86 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31V ILE* 3.7 46.2 - - + -
85V THR* 1.3 84.6 + - - +
87V VAL* 1.3 65.9 + - - +
101V PHE* 3.8 27.5 - - + -
102V ILE 3.2 15.9 - - - -
103V ARG* 3.6 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53V PHE* 3.8 22.0 - - + -
85V THR* 3.8 12.3 - - + +
86V PHE* 1.3 77.9 - - - +
88V LYS* 1.3 73.2 + - - +
101V PHE* 3.8 4.5 - - - -
102V ILE* 2.8 38.2 + - + +
104V ILE* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51V GLN* 4.7 0.3 - - - +
53V PHE* 3.9 4.0 - - - -
87V VAL* 1.3 87.5 - - - +
89V ALA* 1.3 60.0 + - - +
99V TRP* 3.2 78.7 + - + +
100V ARG* 3.4 10.6 - - - +
101V PHE* 3.6 49.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38V VAL* 4.6 2.5 - - + -
51V GLN* 3.4 7.0 - - - +
53V PHE* 3.6 25.8 - - + -
88V LYS* 1.3 75.7 - - - +
90V LEU* 1.3 63.4 + - - +
91V THR* 3.3 12.5 + - + +
98V ALA 3.3 1.2 - - - +
99V TRP* 3.5 8.2 - - - -
100V ARG 2.8 30.2 + - - +
102V ILE* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38V VAL* 3.9 1.7 - - - +
39V LEU* 2.9 32.1 + - + +
41V GLU 3.4 21.8 - - - +
42V VAL* 3.1 28.5 - - + -
43V ASN* 5.3 1.3 - - - +
51V GLN* 2.8 27.2 + - - +
89V ALA* 1.3 69.8 - - - +
91V THR* 1.3 61.2 + - - +
97V ALA* 4.3 11.2 - - + -
98V ALA* 3.7 28.3 - - - +
99V TRP* 3.4 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 91 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36V VAL* 3.6 24.0 - - + +
37V MET 3.2 13.5 - - - +
38V VAL* 4.1 9.2 - - + -
39V LEU* 3.3 16.2 - - - +
89V ALA* 3.5 14.6 - - + +
90V LEU* 1.3 74.6 - - - +
92V MET* 1.3 62.8 + - - +
97V ALA* 3.6 1.4 - - - -
98V ALA* 2.8 41.2 + - - +
100V ARG* 3.9 20.6 - - + +
102V ILE* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 92 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36V VAL* 4.3 5.8 - - - +
37V MET* 2.9 52.7 + - + +
39V LEU* 4.6 19.3 - - + -
91V THR* 1.3 75.3 - - - +
93V ASP* 1.4 63.4 - - - +
94V GLY 3.4 18.8 - - - +
95V LYS* 3.4 23.1 - - - +
96V GLN 4.0 10.5 - - - +
97V ALA* 4.5 10.1 - - - -
----------------------------------------------------------
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