Contacts of the helix formed by residues 104 - 115 (chain E) in PDB entry 5BXD
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 104 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D ARG* 5.0 9.3 + - - -
98D ILE 4.8 3.0 - - - -
99D PRO* 3.5 31.4 - - - +
82E GLN* 5.5 0.7 - - - +
83E MET* 3.6 26.8 - - + +
102E PHE* 3.4 30.7 - - + -
103E LYS* 1.3 84.5 - - - +
105E TYR* 1.3 64.0 + - - +
106E THR 3.3 2.9 + - - -
107E LEU* 3.3 11.2 + - + +
108E LEU 3.0 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ASP* 5.0 9.4 + - - +
96E LEU* 6.2 0.2 - - + -
98E ILE* 5.4 2.0 - - + -
102E PHE* 3.6 11.3 - - + +
103E LYS 3.5 3.4 + - - -
104E ASP* 1.3 78.0 - - - +
106E THR* 1.3 69.7 + - + +
108E LEU 3.3 0.3 + - - -
109E TYR* 2.8 66.4 + + + +
124E MET* 3.2 53.1 + - + +
125E GLU* 3.8 4.0 + - - -
127E TRP* 3.5 33.0 - + + -
128E LYS* 3.5 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU 4.9 1.5 + - - -
97D LEU* 3.6 29.1 - - - +
98D ILE 3.7 18.5 + - - -
100D ASP* 4.4 15.0 + - - +
103E LYS 5.6 0.2 + - - -
104E ASP 4.9 1.0 - - - -
105E TYR* 1.3 87.6 - - + +
107E LEU* 1.3 64.0 + - - +
109E TYR* 3.8 3.7 - - - +
110E GLU* 3.3 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D ARG* 3.5 31.2 - - - +
86D TYR* 5.9 1.6 - - + -
89D ASN* 3.7 29.4 - - - +
97D LEU* 3.6 43.1 - - + +
98D ILE* 6.0 1.1 - - - +
80E ASP* 3.8 2.9 - - + +
83E MET* 3.5 18.2 - - + -
104E ASP* 3.3 13.6 + - + +
105E TYR 3.3 0.4 - - - -
106E THR* 1.3 80.1 + - - +
108E LEU* 1.3 64.5 + - - +
110E GLU* 3.2 3.3 + - - +
111E GLU* 3.1 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E MET* 3.8 31.6 - - + +
86E TYR* 3.8 25.1 - - + -
87E ILE* 4.2 9.0 - - + -
96E LEU* 4.3 1.6 - - + -
98E ILE* 3.8 30.1 - - + -
102E PHE* 3.8 8.5 - - + -
104E ASP 3.0 16.8 + - - +
107E LEU* 1.3 76.8 - - - +
109E TYR* 1.3 57.5 + - - +
111E GLU* 3.1 2.9 + - + +
112E ALA* 2.9 27.5 + - - +
120E MET* 4.0 17.7 - - + -
124E MET* 3.6 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E TYR* 2.8 53.8 + + + +
106E THR* 3.8 5.2 - - - +
108E LEU* 1.3 72.3 - - - +
110E GLU* 1.3 60.6 + - - +
112E ALA* 3.3 2.1 + - - +
113E LYS* 2.8 48.3 + - + +
121E LEU* 3.6 43.9 - - + +
124E MET* 3.6 15.4 - - + +
125E GLU* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D THR* 3.6 38.7 - - + +
95D LYS* 2.9 39.4 + - - +
97D LEU* 3.7 14.3 - - + +
79E ARG* 3.7 6.4 + - - +
106E THR 3.3 11.0 + - - +
107E LEU 3.2 8.8 + - - +
109E TYR* 1.3 83.2 - - - +
111E GLU* 1.3 56.1 + - - +
113E LYS* 3.3 16.1 + - - +
114E TYR* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ASN* 5.0 2.1 - - - +
92D ARG* 5.9 0.5 - - - -
93D THR* 4.6 2.8 - - - +
79E ARG* 2.9 54.5 + - - +
80E ASP* 3.9 15.7 + - - +
83E MET* 3.8 24.0 - - + -
84E PHE 5.8 0.4 - - - +
87E ILE* 4.0 15.3 - - + -
107E LEU* 3.1 28.2 + - + +
108E LEU* 3.1 8.0 + - - +
110E GLU* 1.3 78.0 - - - +
112E ALA* 1.3 57.4 + - - +
114E TYR* 3.2 2.1 + - - +
115E PHE* 2.9 43.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ILE* 3.7 10.0 - - + +
108E LEU 2.9 15.4 + - - +
109E TYR 3.8 0.4 - - - +
111E GLU* 1.3 76.5 - - - +
113E LYS* 1.3 55.8 + - - +
115E PHE* 3.5 1.9 + - - +
116E GLN* 3.0 22.2 + - - -
117E LEU* 3.1 15.4 + - + +
120E MET* 4.0 28.3 - - + -
121E LEU* 3.6 24.5 - - + +
124E MET* 4.3 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D LYS* 4.1 15.7 - - - +
109E TYR* 2.8 31.9 + - + +
110E GLU* 3.5 21.3 - - - +
112E ALA* 1.3 75.1 - - - +
114E TYR* 1.3 65.1 + - - +
116E GLN* 3.1 19.4 + - - +
118E GLN* 5.1 0.9 + - - -
121E LEU* 3.8 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ARG* 2.7 71.6 + - - +
59E LEU* 5.7 2.0 - - + +
77E ILE* 4.9 4.2 - - + +
79E ARG* 3.5 58.5 - - + +
110E GLU* 2.9 17.6 + - - +
111E GLU 3.5 2.9 - - - +
113E LYS* 1.3 78.8 - - - +
115E PHE* 1.3 75.8 + + - +
116E GLN* 3.0 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E SER* 3.3 5.9 - - - -
55E ARG* 2.9 26.8 + - - -
56E ILE* 3.6 42.5 + - + -
59E LEU* 4.8 3.8 - - + -
77E ILE* 4.0 23.6 - - + -
79E ARG* 4.0 10.8 - - + -
84E PHE* 3.8 30.1 - + - -
87E ILE* 4.0 20.4 - - + -
111E GLU* 2.9 44.2 + - + +
112E ALA 4.3 2.9 - - - +
114E TYR* 1.3 92.2 - + - +
116E GLN* 1.3 66.1 + - - +
117E LEU* 3.3 11.5 + - + +
----------------------------------------------------------
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