Contacts of the helix formed by residues 131 - 145 (chain E) in PDB entry 5AK9
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 ASN 131 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ASN* 2.8 17.2 + - - +
130E LYS* 1.3 74.1 - - - +
132E LYS* 1.3 63.8 + - - +
133E ALA* 3.3 10.9 + - - +
134E LEU* 3.1 37.5 + - + +
135E LEU* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E LYS 3.3 6.6 + - - +
131E ASN* 1.3 73.2 + - - +
133E ALA* 1.3 55.7 + - - +
135E LEU* 3.1 7.6 + - - +
136E GLU* 2.8 60.8 + - + +
151E ILE* 4.5 13.9 - - + -
161E TYR* 3.7 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E ARG* 5.5 7.6 - - - +
131E ASN* 3.2 9.3 + - - +
132E LYS* 1.3 77.8 - - - +
134E LEU* 1.3 64.2 + - - +
136E GLU* 3.3 15.8 + - - +
137E ILE* 3.2 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ILE* 3.9 25.4 - - + -
95E LEU* 5.6 4.9 - - + -
98E ILE* 4.6 11.0 - - + -
109E PHE* 4.2 26.5 - - + -
113E LEU* 4.5 18.2 - - + -
129E ASN* 4.3 22.4 - - - +
131E ASN* 3.1 32.5 + - + +
133E ALA* 1.3 77.3 - - - +
135E LEU* 1.3 65.0 + - + +
137E ILE* 3.3 18.0 + - + +
138E VAL* 3.2 19.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E LEU* 4.8 11.9 - - + -
127E ILE* 4.3 20.0 - - + +
129E ASN* 3.9 28.3 - - + +
131E ASN 3.1 10.6 + - - +
132E LYS* 3.1 9.7 + - - +
134E LEU* 1.3 78.4 - - + +
136E GLU* 1.3 52.9 + - - +
138E VAL* 3.3 3.2 + - + +
139E SER* 2.7 34.1 + - - -
151E ILE* 3.7 15.5 - - + -
161E TYR* 3.9 31.4 - - + +
162E VAL 4.3 1.3 - - - +
163E LEU* 3.3 37.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E LYS* 2.8 52.1 + - + +
133E ALA* 3.7 15.0 - - - +
134E LEU 3.3 0.2 - - - -
135E LEU* 1.3 75.6 - - - +
137E ILE* 1.3 58.8 + - + +
139E SER* 3.3 4.6 - - - -
140E ARG* 3.0 54.3 + - - +
151E ILE* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ILE* 4.3 16.8 - - + +
99E ARG* 4.2 39.9 - - + +
133E ALA* 3.2 20.2 + - + +
134E LEU* 3.5 15.7 - - + +
135E LEU 3.2 0.2 - - - -
136E GLU* 1.3 74.1 - - + +
138E VAL* 1.3 68.1 + - + +
140E ARG* 3.2 10.8 + - - +
141E TRP* 3.1 62.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E PHE* 4.4 16.4 - - + -
110E ILE* 4.1 26.0 - - + -
113E LEU* 4.1 23.6 - - + -
127E ILE* 4.6 9.0 - - + -
134E LEU* 3.2 13.1 + - + +
135E LEU* 3.7 7.9 - - + +
137E ILE* 1.3 76.7 - - + +
139E SER* 1.3 64.5 + - - +
141E TRP* 3.3 12.3 + - + +
142E LEU* 2.9 45.6 + - + +
163E LEU* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E LEU 2.7 21.2 + - - -
136E GLU* 3.3 9.6 - - - -
137E ILE 3.2 0.2 - - - -
138E VAL* 1.3 73.0 - - - +
140E ARG* 1.3 62.0 + - - +
142E LEU* 3.2 1.7 + - - -
143E ASN* 2.9 37.8 + - - -
149E ASN* 2.8 31.3 + - - +
150E THR* 5.8 0.2 - - - -
151E ILE* 3.9 15.7 - - - +
163E LEU* 3.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E GLU* 3.0 43.9 + - - +
137E ILE* 3.2 8.9 + - - +
139E SER* 1.3 81.4 + - - +
141E TRP* 1.3 70.5 + - + +
143E ASN* 3.1 12.9 + - - +
144E ASN* 2.9 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ILE* 3.2 45.8 - - + -
99E ARG* 4.6 9.5 + - - +
101E PHE* 4.0 10.8 - + + -
106E GLN* 3.4 61.7 - - + +
109E PHE* 4.0 22.4 - + - -
110E ILE* 4.2 16.2 - - + -
137E ILE* 3.1 37.8 + - + +
138E VAL* 3.8 10.1 - - + +
140E ARG* 1.3 80.3 - - + +
142E LEU* 1.3 57.3 + - - +
144E ASN* 3.4 8.1 + - + +
145E LEU* 2.9 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E ILE* 3.8 22.7 - - + -
127E ILE* 5.5 0.7 - - + -
138E VAL* 2.9 41.8 + - + +
139E SER 3.6 3.6 - - - +
141E TRP* 1.3 72.9 - - - +
143E ASN* 1.3 66.7 + - - +
145E LEU* 2.9 15.2 + - + +
146E GLY 2.9 0.3 + - - -
147E VAL* 2.9 32.3 + - + +
149E ASN* 3.7 11.4 - - + +
163E LEU* 3.9 24.7 - - + -
165E ILE* 4.2 16.6 - - + -
173E PHE* 4.1 25.8 - - + -
177E ILE* 4.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E SER* 2.9 30.8 + - - -
140E ARG* 3.1 13.6 + - - +
142E LEU* 1.3 75.2 - - - +
144E ASN* 1.3 57.1 + - - +
146E GLY* 2.9 20.4 + - - -
147E VAL 3.6 7.3 + - - +
148E ARG* 4.2 12.0 - - - +
149E ASN* 3.6 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E MET* 5.3 8.3 - - - +
106E GLN* 4.7 12.1 + - - +
140E ARG 2.9 12.5 + - - +
141E TRP* 3.7 11.3 + - - +
143E ASN* 1.3 76.8 - - - +
145E LEU* 1.3 64.5 + - - +
146E GLY 3.2 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E MET* 4.4 17.9 - - + -
106E GLN* 4.6 10.3 - - + +
107E ILE* 4.0 37.9 - - + -
110E ILE* 4.5 10.5 - - + -
141E TRP 2.9 22.9 + - - +
142E LEU* 2.9 10.5 + - + +
144E ASN* 1.3 83.4 - - - +
146E GLY* 1.3 58.3 + - - +
147E VAL* 3.5 7.6 - - + +
172E LYS* 3.3 19.1 - - - +
176E THR* 4.6 15.6 - - + +
177E ILE* 4.1 13.7 - - + -
----------------------------------------------------------
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