Contacts of the helix formed by residues 134 - 147 (chain E) in PDB entry 1F9N
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 THR 134 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E HIS* 3.6 6.5 - - + -
132E CYS* 4.2 0.2 - - - +
133E ARG* 1.3 91.2 - - + +
135E PRO* 1.3 70.8 - - + +
136E GLU* 3.2 16.4 + - - +
137E ASP* 3.0 30.2 + - - +
138E THR* 2.9 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E SER* 3.0 31.5 - - - +
92E HIS* 3.4 23.3 - - + +
134E THR* 1.3 90.0 - - + +
136E GLU* 1.3 74.4 + - - +
138E THR* 3.3 3.5 + - - -
139E GLU* 3.2 22.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
134E THR* 3.2 22.1 + - - +
135E PRO* 1.3 89.5 - - - +
137E ASP* 1.3 65.6 + - - +
139E GLU* 3.6 6.7 + - - +
140E GLY* 3.2 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E GLU* 3.8 33.6 - - + +
132E CYS* 4.3 3.8 - - + -
133E ARG* 3.7 20.4 - - - +
134E THR* 3.0 29.4 + - - +
136E GLU* 1.3 79.0 - - - +
138E THR* 1.3 62.5 + - - +
140E GLY* 4.0 1.0 - - - -
141E VAL* 3.1 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E SER* 4.1 7.9 - - - -
90E ALA 3.4 19.7 - - - +
91E SER 2.7 21.8 + - - -
92E HIS* 3.4 5.3 - - - -
93E MET 4.2 5.4 - - - +
94E ILE* 3.5 29.1 - - + +
132E CYS* 3.2 21.3 - - - +
134E THR 2.9 10.8 + - - -
135E PRO 3.4 3.6 - - - -
136E GLU 3.2 0.2 - - - -
137E ASP* 1.3 76.0 - - - +
139E GLU* 1.3 66.8 + - - +
141E VAL 3.3 1.7 + - - -
142E LYS* 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E SER* 4.5 9.5 + - - -
135E PRO 3.2 12.7 + - - +
136E GLU* 3.9 7.2 - - - +
138E THR* 1.3 80.3 - - - +
140E GLY* 1.3 60.5 + - - +
142E LYS* 3.6 18.1 + - - +
143E ASN* 2.8 55.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E GLU 3.2 12.2 + - - -
137E ASP* 3.6 3.6 + - - -
138E THR 3.1 0.8 - - - -
139E GLU* 1.3 76.7 - - - +
141E VAL* 1.3 64.5 + - - +
143E ASN* 3.2 10.1 + - - +
144E ARG* 3.0 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ILE* 4.1 12.3 - - + -
115E TRP* 4.1 18.4 - - + -
117E GLU* 3.7 28.9 - - + +
118E MET* 4.6 15.5 - - + -
130E ILE* 4.8 4.0 - - + -
132E CYS* 3.9 9.4 - - - -
137E ASP 3.1 19.1 + - - +
138E THR 3.8 3.8 - - - +
140E GLY* 1.3 74.4 - - - +
142E LYS* 1.3 62.0 + - - +
144E ARG* 3.3 14.9 + - - +
145E LEU* 3.0 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ILE* 4.0 31.0 + - + +
88E ASP* 4.6 8.1 + - - +
89E SER* 2.9 39.5 + - - +
94E ILE* 4.0 12.3 - - + +
138E THR 3.0 16.7 + - - +
139E GLU* 3.6 22.4 + - - +
141E VAL* 1.3 79.5 - - - +
143E ASN* 1.3 62.6 + - - +
145E LEU* 3.3 3.6 + - - +
146E LEU* 3.0 43.5 + - + +
----------------------------------------------------------
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 GLU* 2.8 42.9 + - - +
140E GLY* 3.2 8.6 + - - +
142E LYS* 1.3 74.2 - - - +
144E ARG* 1.3 55.8 + - - +
146E LEU* 3.1 16.0 + - - +
147E GLU* 2.8 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E TRP* 3.3 59.1 - - + +
117E GLU* 3.3 33.9 + - - +
140E GLY* 3.0 23.4 + - - +
141E VAL* 3.5 14.6 - - - +
143E ASN* 1.3 77.5 - - - +
145E LEU* 1.3 60.4 + - - +
147E GLU* 3.5 12.2 + - - +
148E LEU* 3.2 26.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
76E LEU* 4.3 12.3 - - + -
80E LEU* 3.8 30.3 - - + +
84E PHE* 5.4 6.3 - - + -
87E ILE* 4.5 19.3 - - + -
94E ILE* 5.1 1.1 - - + -
96E LEU* 5.0 7.9 - - + -
110E MET* 5.0 9.0 - - - -
113E LEU* 5.4 0.2 - - + -
115E TRP* 4.5 12.1 - - + -
130E ILE* 4.1 22.2 - - + -
141E VAL* 3.0 37.8 + - + +
142E LYS* 3.7 4.3 - - - +
143E ASN 3.2 0.2 - - - -
144E ARG* 1.3 73.7 - - - +
146E LEU* 1.3 64.8 + - - +
148E LEU* 3.3 27.8 + - + +
149E LEU* 3.9 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.0 25.4 - - + -
84E PHE* 4.1 10.8 - - + -
87E ILE* 3.8 25.4 - - + -
142E LYS* 3.0 41.3 + - + +
143E ASN* 3.1 17.2 + - - +
145E LEU* 1.3 76.4 - - - +
147E GLU* 1.3 62.0 + - + +
148E LEU 3.1 2.9 + - - -
149E LEU* 3.3 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E LYS* 5.1 1.4 + - - -
143E ASN* 2.8 38.3 + - + +
144E ARG* 3.9 10.9 - - - +
145E LEU 3.2 0.2 - - - -
146E LEU* 1.3 77.9 - - + +
148E LEU* 1.3 61.0 + - - +
149E LEU 3.9 5.4 - - - +
----------------------------------------------------------
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