Contacts of the helix formed by residues 126 - 137 (chain E) in PDB entry 5JKL
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 126 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASN* 3.3 20.0 + - - +
12E TYR* 3.7 12.5 - - - -
13E HIS 4.8 1.0 + - - +
16E SER* 4.6 3.4 + - - +
76E ARG* 2.9 37.2 + - - -
121E ALA* 2.9 17.5 + - + +
122E THR* 5.1 0.2 - - - +
124E LYS* 4.3 8.5 - - + +
125E ASN* 1.3 75.4 - - - +
127E PRO* 1.3 59.6 - - - +
128E HIS* 3.5 4.0 + - - +
129E LEU* 3.0 26.0 + - + +
130E CYS* 3.0 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASN* 3.9 8.5 - - - +
125E ASN 3.2 13.5 - - - +
126E ASP* 1.3 83.1 - - - +
128E HIS* 1.4 60.9 + - - +
130E CYS* 3.6 9.6 - - + +
131E ASP* 2.9 30.1 + - - +
115F LEU* 3.7 21.8 - - + +
118F HIS* 3.4 44.2 - - + +
134F GLU* 4.2 6.1 - - + +
138F LEU* 3.7 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LEU* 3.7 27.1 - - + +
75E GLN* 5.3 0.4 - - - -
76E ARG* 3.1 38.3 + - - +
126E ASP* 3.2 2.3 + - - +
127E PRO* 1.4 82.1 - - - +
129E LEU* 1.3 56.8 + - - +
131E ASP* 3.4 9.0 + - - +
132E PHE* 2.9 31.4 + + + +
115F LEU* 5.2 4.0 - - + +
138F LEU* 3.8 20.0 - - + +
139F ASN* 2.8 44.8 + - + -
142F VAL* 3.7 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E TYR* 4.4 7.4 - - + -
16E SER* 3.7 31.4 - - - +
20E ILE* 3.9 27.8 - - + -
72E LEU* 4.2 17.7 - - + -
76E ARG* 4.0 4.5 - - - +
117E LEU* 4.8 7.4 - - + -
121E ALA* 3.9 19.7 - - + -
126E ASP* 3.0 28.3 + - - +
128E HIS* 1.3 74.2 + - - +
130E CYS* 1.3 66.9 + - - +
132E PHE* 3.2 9.2 + - + -
133E ILE* 3.0 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E HIS* 3.6 25.0 - - + +
121E ALA* 3.6 18.2 - - - -
122E THR* 3.5 30.3 - - - -
126E ASP 3.0 19.4 + - - +
127E PRO* 3.6 11.7 - - + +
129E LEU* 1.3 76.3 - - - +
131E ASP* 1.3 56.3 + - - +
133E ILE* 3.2 2.0 + - - -
134E GLU* 3.0 38.5 + - - +
134F GLU* 5.4 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E PRO 2.9 18.8 + - - +
128E HIS* 3.6 10.1 + - + +
130E CYS* 1.3 75.6 - - - +
132E PHE* 1.3 60.8 + - - +
134E GLU* 4.5 6.5 - - - -
135E THR* 2.8 50.7 + - - +
136E HIS* 5.9 0.7 + - - -
202E MG 3.4 14.9 - - - -
134F GLU* 3.7 43.2 + - + +
135F THR* 4.5 2.8 + - - -
138F LEU* 6.2 0.4 - - + -
139F ASN* 4.9 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ILE* 5.2 0.2 - - + -
68E LYS* 3.9 24.2 - - + -
69E LEU* 3.7 19.7 - - + -
72E LEU* 3.7 46.2 - - + -
75E GLN* 5.4 2.7 - - - -
128E HIS* 2.9 22.3 + + + +
129E LEU* 3.2 12.8 + - + +
131E ASP* 1.3 80.8 + - - +
133E ILE* 1.3 74.0 + - + +
136E HIS* 3.1 45.1 + + - +
137E TYR* 3.4 32.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ILE* 5.6 0.2 - - + -
69E LEU* 6.3 0.2 - - + -
114E LEU* 4.0 24.0 - - + +
117E LEU* 3.8 33.7 - - + +
118E HIS* 3.9 26.7 - - + +
121E ALA* 4.6 0.4 - - + -
129E LEU* 3.0 33.2 + - + +
130E CYS* 3.7 3.8 - - - +
132E PHE* 1.3 88.6 - - + +
134E GLU* 1.4 59.4 + - - +
137E TYR* 2.9 28.7 + - + +
138E LEU* 3.0 33.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D PRO* 4.1 11.7 - - - +
130D CYS* 5.7 1.3 - - - +
131D ASP* 3.6 43.1 + - - +
134D GLU* 4.4 6.8 - - - +
203D MG 3.8 14.0 - - - -
118E HIS* 2.7 34.1 + - + +
130E CYS* 3.0 24.3 + - - +
131E ASP* 3.9 3.8 - - - +
133E ILE* 1.4 78.1 - - - +
135E THR* 1.3 63.7 + - - +
136E HIS 3.6 0.2 + - - -
138E LEU* 3.8 26.8 + - + +
139E ASN* 4.1 9.2 + - - +
202E MG 4.3 7.6 - - - -
134F GLU* 4.3 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D ASP* 4.8 3.5 + - - -
131E ASP* 2.8 36.5 + - - +
134E GLU* 1.3 78.4 - - - +
136E HIS* 1.3 85.6 + - + +
137E TYR 3.6 0.2 - - - -
139E ASN* 5.8 2.3 + - - +
140E GLU* 5.5 2.3 - - - +
202E MG 4.1 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E HIS* 5.6 3.6 - - - -
68E LYS* 3.3 36.8 + - + +
131E ASP* 5.9 0.6 + - - -
132E PHE* 3.1 36.2 + + - +
135E THR* 1.3 98.4 + - + +
137E TYR* 1.3 85.2 + - + +
140E GLU* 3.4 21.4 - - - +
139F ASN* 6.1 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E GLU* 4.2 8.5 - - - -
65E HIS* 2.7 52.7 + + + -
68E LYS* 3.4 19.8 - - + +
69E LEU* 3.4 21.4 + - + +
114E LEU* 3.9 35.4 - - + -
132E PHE* 3.4 36.6 - + - -
133E ILE* 2.9 16.4 + - + +
135E THR 3.6 0.6 - - - -
136E HIS* 1.3 98.2 - - + +
138E LEU* 1.3 65.4 + - - +
139E ASN 3.4 2.0 - - - +
140E GLU* 3.2 6.8 + - + +
141E GLN* 3.0 29.4 + - - +
----------------------------------------------------------
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