Contacts of the helix formed by residues 106 - 119 (chain E) in PDB entry 3KHU
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 LEU 106 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C PHE* 3.8 34.5 + - + +
325C THR* 4.1 11.6 - - + -
91E THR* 4.4 3.6 - - + -
104E ALA 3.8 4.8 + - - +
105E ASP* 1.3 72.3 + - - +
107E LYS* 1.3 64.3 + - - +
108E TYR 3.2 2.6 + - - -
109E ILE* 3.2 29.0 + - + +
110E GLU* 2.9 24.2 + - + +
133E PRO* 3.8 38.6 - - + -
135E ARG 5.6 0.7 - - - +
136E ALA* 4.2 15.0 - - + +
139E SER* 4.3 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C THR* 3.8 15.4 - - + +
327C THR* 4.6 27.7 + - + +
92E PRO* 4.8 7.0 - - - -
96E TYR* 5.3 2.0 + - - -
105E ASP* 3.1 34.9 + - - +
106E LEU* 1.3 77.0 - - - +
108E TYR* 1.3 102.4 + - + +
110E GLU* 3.5 4.9 + - - +
111E ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E VAL* 3.7 18.4 - - + -
90E ASN* 3.3 45.8 - - - +
91E THR* 5.9 0.2 - - + -
92E PRO* 4.0 11.0 - - + -
105E ASP 4.7 0.4 + - - -
106E LEU 3.3 0.6 - - - -
107E LYS* 1.3 113.6 + - + +
109E ILE* 1.3 67.6 + - - +
111E ALA* 3.4 6.4 + - + +
112E CYS* 3.0 27.2 + - - -
502E UPG 3.5 31.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ILE* 3.6 26.5 - - + +
89E VAL* 3.9 14.1 - - + +
91E THR* 3.4 30.3 - - + +
106E LEU* 3.2 23.6 + - + +
108E TYR* 1.3 75.0 - - - +
110E GLU* 1.3 58.6 + - - +
112E CYS* 3.2 6.9 + - - +
113E ALA* 2.9 26.5 + - - +
128E GLU* 5.9 1.6 - - + -
130E SER* 6.0 1.1 - - - -
132E VAL* 4.0 17.9 - - + -
136E ALA* 5.2 5.6 - - + +
139E SER* 6.1 2.5 - - - -
140E ILE* 3.8 34.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
323C PHE* 3.4 18.7 - - + -
325C THR* 3.7 8.7 - - - +
329C LYS* 2.8 39.3 + - - -
409C HIS* 3.9 1.6 - - - -
106E LEU* 2.9 16.6 + - + +
107E LYS* 3.7 5.3 - - - +
109E ILE* 1.3 78.9 - - - +
111E ALA* 1.3 57.6 + - - +
113E ALA* 3.1 2.5 + - - +
114E ARG* 2.9 68.8 + - - +
143E ILE* 3.7 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E LYS 3.0 17.5 + - - +
108E TYR* 3.8 9.4 - - + +
109E ILE 3.3 0.2 - - - -
110E GLU* 1.3 79.3 - - - +
112E CYS* 1.3 55.4 + - - +
114E ARG* 3.5 7.5 + - - +
115E ARG* 3.0 29.3 + - - +
502E UPG 5.1 1.8 - - - +
613E EDO 3.9 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ILE* 3.8 27.8 - - + +
87E ILE* 4.1 20.2 - - + -
89E VAL* 3.7 31.9 - - - -
108E TYR 3.0 22.7 + - - -
109E ILE 3.5 7.0 - - - +
111E ALA* 1.3 73.9 - - - +
113E ALA* 1.3 59.1 + - - +
115E ARG* 3.2 4.0 + - - +
116E ILE* 2.8 35.5 + - - +
502E UPG 5.1 0.2 - - - -
613E EDO 4.1 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ILE* 4.6 2.2 - - + +
109E ILE 2.9 13.3 + - - +
110E GLU* 3.1 8.0 + - - +
112E CYS* 1.3 74.7 - - - +
114E ARG* 1.3 62.9 + - - +
116E ILE* 3.3 5.8 + - - -
117E VAL* 3.1 24.6 + - - +
140E ILE* 4.2 18.4 - - + -
143E ILE* 3.9 22.7 - - + -
144E PHE* 3.4 25.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C PHE* 4.8 3.0 - - - -
409C HIS* 3.7 25.6 + - - -
433C LEU* 4.5 13.3 - - - +
434C LYS 2.8 36.0 + - - +
435C PRO* 4.1 11.5 + - - +
110E GLU* 2.9 52.0 + - + +
111E ALA* 3.9 6.7 - - - +
113E ALA* 1.3 75.6 - - - +
115E ARG* 1.3 62.3 + - - +
117E VAL* 3.2 11.4 - - + +
118E GLN* 3.0 30.1 + - - +
143E ILE* 3.9 17.2 - - + +
147E ASN* 4.2 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ILE* 5.7 0.9 - - + -
37E VAL* 4.3 7.7 - - - +
75E ILE* 3.6 36.2 - - + +
76E ASP* 2.9 34.9 + - - -
79E ILE* 3.7 20.0 - - + -
111E ALA 3.0 20.3 + - - +
112E CYS* 3.6 6.1 - - - +
114E ARG* 1.3 76.3 - - - +
116E ILE* 1.3 62.1 + - - +
118E GLN* 3.3 10.0 + - - +
119E ASN* 2.9 34.6 + - - +
613E EDO 3.6 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ILE* 3.9 17.9 - - + -
79E ILE* 4.0 14.3 - - + +
85E VAL* 3.7 28.0 - - + -
87E ILE* 3.9 26.2 - - + -
112E CYS 2.8 25.0 + - - +
113E ALA* 3.6 7.4 - - - +
115E ARG* 1.3 73.5 - - - +
117E VAL* 1.3 60.6 + - - +
119E ASN 3.2 2.9 + - - -
120E SER* 2.6 41.4 + - - +
124E LYS* 5.5 0.2 - - + -
126E VAL* 4.0 28.5 - - + -
144E PHE* 4.2 7.9 - - + -
154E LEU* 4.5 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E ALA 3.1 12.5 + - - +
114E ARG* 3.2 23.3 - - - +
116E ILE* 1.3 79.9 - - - +
118E GLN* 1.3 51.5 + - - +
119E ASN 3.4 0.5 + - - -
120E SER* 3.5 4.7 + - - +
143E ILE* 4.4 5.2 - - + -
144E PHE* 4.2 19.3 - - + +
147E ASN* 3.0 46.4 - - + +
149E LYS* 2.7 34.4 + - - -
152E LEU* 3.9 14.2 - - + +
154E LEU* 4.4 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E ARG* 3.0 25.5 + - - +
115E ARG* 3.5 11.2 - - - +
116E ILE 3.2 0.2 - - - -
117E VAL* 1.3 79.0 - - - +
119E ASN* 1.3 62.5 + - - +
149E LYS* 3.2 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ASP* 3.1 51.8 + - - +
79E ILE* 4.0 15.5 - - + +
80E LYS* 3.5 46.5 + - - +
115E ARG* 2.9 35.3 + - - +
116E ILE 3.2 0.4 + - - -
118E GLN* 1.3 81.2 - - - +
120E SER* 1.3 60.7 + - - +
121E ASN* 5.2 2.6 + - - -
149E LYS* 4.6 0.2 - - - -
----------------------------------------------------------
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