Contacts of the helix formed by residues 118 - 125 (chain E) in PDB entry 5ANC
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 ALA 118 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E VAL 5.5 0.7 - - - +
79E VAL 3.5 13.4 + - - +
85E TRP* 4.2 15.3 - - + -
87E ARG* 5.3 2.9 - - - +
93E ILE* 5.2 2.2 - - + -
95E PHE* 4.3 13.7 - - + -
116E PRO 4.3 0.4 - - - -
117E VAL* 1.3 74.2 - - - +
119E LYS* 1.3 65.7 + - - +
120E GLU* 3.2 20.2 - - - +
121E CYS* 3.1 32.4 + - - +
122E SER* 3.4 5.5 + - - -
136E VAL* 3.5 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ARG* 4.6 21.2 - - - +
117E VAL 4.4 0.7 - - - -
118E ALA* 1.3 68.7 - - - +
120E GLU* 1.3 58.6 + - - +
122E SER* 3.2 12.7 + - - +
123E ASP* 2.9 50.4 + - - +
135E ILE* 4.4 15.3 - - + +
136E VAL 2.9 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ASN* 3.7 40.4 - - + +
12E ARG 5.5 0.5 - - - +
54E VAL* 4.7 17.5 - - + +
55E GLY 5.9 1.3 - - - +
85E TRP* 3.1 47.3 + - - -
87E ARG* 4.0 22.6 + - - +
118E ALA* 3.8 9.9 - - - +
119E LYS* 1.3 77.9 - - + +
121E CYS* 1.3 60.8 + - - +
123E ASP* 3.2 5.7 + - - +
124E LEU* 2.9 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E VAL 3.4 11.4 - - - -
55E GLY* 3.4 29.2 - - - +
78E VAL 3.8 11.9 - - - +
79E VAL* 3.9 17.5 - - + -
117E VAL* 4.3 9.9 - - + -
118E ALA* 3.1 21.5 + - - +
120E GLU* 1.3 77.4 - - - +
122E SER* 1.3 58.2 + - - +
124E LEU* 3.2 13.3 + - - +
125E TRP* 3.0 33.6 + - + +
128E VAL* 4.6 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E VAL* 3.8 4.5 - - - +
118E ALA 3.4 12.0 + - - -
119E LYS* 3.2 15.0 + - - -
121E CYS* 1.3 76.7 - - - +
123E ASP* 1.3 65.2 - - - +
125E TRP 3.0 25.7 + - - +
126E PRO* 3.8 2.6 - - - +
128E VAL* 4.2 8.0 - - - +
129E ALA* 3.9 25.1 - - - +
135E ILE* 3.3 28.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ALA* 3.9 16.3 - - + +
10E ASN* 3.6 23.2 - - - +
119E LYS* 2.9 38.1 + - - +
120E GLU* 3.2 6.8 + - - +
122E SER* 1.3 78.1 - - - +
124E LEU* 1.3 64.3 + - - +
125E TRP* 4.5 1.2 - - - -
126E PRO* 4.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LYS* 6.1 0.2 - - - +
4E ALA* 3.1 22.3 - - - +
5E GLN* 3.5 32.5 - - + +
6E ALA* 3.7 6.4 - - + +
9E SER 4.2 12.8 - - - +
10E ASN* 3.5 22.2 - - + +
54E VAL* 5.9 2.5 - - + -
55E GLY* 3.9 15.3 - - - +
56E ASP* 3.6 25.6 - - - +
120E GLU* 2.9 28.8 + - + +
121E CYS* 3.4 3.6 - - - +
123E ASP* 1.3 78.6 - - - +
125E TRP* 1.3 78.1 + - + +
126E PRO* 3.7 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E SER* 3.4 32.1 - - - -
3E LYS* 4.2 17.3 - - - -
4E ALA* 4.6 20.2 - - + -
55E GLY 2.8 29.5 + - - -
56E ASP* 4.2 2.5 + - - +
57E MET* 3.5 34.5 - - + -
77E LEU* 3.3 26.1 - - + +
106E LYS 4.7 3.1 - - - -
107E GLY* 3.9 18.4 - - - +
121E CYS* 3.0 11.1 + - + +
122E SER 3.0 11.6 + - - +
124E LEU* 1.3 105.5 - - + +
126E PRO* 1.4 64.1 - - + +
127E LYS* 3.2 4.3 - - + +
128E VAL* 3.0 39.7 + - + +
129E ALA 3.4 0.7 + - - -
----------------------------------------------------------
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