Contacts of the helix formed by residues 159 - 170 (chain E) in PDB entry 3ECS
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 159 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E GLU* 3.1 41.5 - - + +
155E SER 2.9 7.2 + - - +
156E GLN* 3.8 29.2 - - - +
157E PRO 3.2 8.7 - - - +
158E ASP* 1.3 80.7 - - - +
160E SER* 1.3 61.5 + - - +
161E GLY 3.1 5.4 - - - -
162E LYS* 3.2 43.0 + - + +
163E LYS* 3.7 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ALA* 3.7 12.5 - - - +
130E TYR* 3.2 24.9 + - - +
154E GLU 3.4 1.0 + - - -
155E SER* 4.1 0.3 + - - -
158E ASP* 3.1 25.2 + - - -
159E LEU* 1.3 75.2 - - - +
161E GLY* 1.3 64.9 + - - +
162E LYS 3.2 0.2 - - - -
163E LYS* 3.3 15.8 + - - +
164E MSE 3.0 17.2 + - - -
209E LYS* 3.5 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ALA* 3.7 18.2 - - - +
152E VAL* 3.7 8.1 - - - +
153E THR 3.2 26.5 - - - -
154E GLU* 2.9 8.6 + - - -
160E SER* 1.3 82.7 + - - +
162E LYS* 1.3 56.0 + - - +
164E MSE 3.2 3.8 + - - +
165E ALA* 3.0 25.3 + - - +
177E VAL* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D LYS* 3.3 38.3 - - - +
154E GLU* 3.7 35.6 + - + -
159E LEU* 3.2 39.8 + - + +
161E GLY* 1.3 73.1 - - - +
163E LYS* 1.3 66.6 + - - +
165E ALA* 3.0 17.7 + - - +
166E LYS* 3.0 25.6 + - - +
177E VAL* 4.5 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E PRO* 6.4 0.2 - - - +
130E TYR* 3.6 33.3 - - + +
159E LEU 3.7 2.5 + - - +
160E SER* 3.3 19.8 + - - +
162E LYS* 1.3 78.1 - - - +
164E MSE 1.3 61.8 + - - +
166E LYS* 3.3 13.0 + - - +
167E ALA* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 164 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E THR* 4.9 4.7 - - - +
129E ALA 3.4 21.1 - - - +
130E TYR* 3.4 17.7 - - + -
131E SER 3.6 29.2 - - - +
134E VAL* 3.8 22.2 - - + -
135E LEU* 3.7 31.0 - - + -
138E LEU* 4.4 3.4 - - + -
152E VAL* 4.3 9.6 - - + -
160E SER 3.0 10.9 + - - +
161E GLY 3.3 10.1 - - - +
163E LYS* 1.3 77.2 - - - +
165E ALA* 1.3 55.7 + - - +
167E ALA* 3.3 4.5 + - - +
168E LEU* 3.0 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D ASP* 3.6 13.6 - - - +
152E VAL* 4.2 2.0 - - + -
161E GLY 3.0 8.2 + - - +
162E LYS* 3.0 10.4 + - - +
164E MSE 1.3 74.5 - - - +
166E LYS* 1.3 64.9 + - - +
168E LEU* 3.3 1.6 + - - +
169E CYS* 3.0 23.2 + - - +
175E VAL* 3.5 25.3 - - + +
177E VAL* 3.4 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D ASP* 4.3 8.1 - - - +
162E LYS* 3.0 23.3 + - - +
163E LYS* 3.3 12.1 + - - +
165E ALA* 1.3 76.3 - - - +
167E ALA* 1.3 63.3 + - - +
169E CYS* 3.1 9.3 + - - +
170E HIS* 3.0 35.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E TYR* 4.5 7.6 - - + +
135E LEU* 4.2 27.0 - - + +
163E LYS 3.1 13.7 + - - +
164E MSE 3.4 13.0 - - - +
165E ALA 3.1 0.2 - - - -
166E LYS* 1.3 78.6 - - - +
168E LEU* 1.3 61.5 + - - +
170E HIS* 3.4 17.4 + - - +
171E LEU* 3.6 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D GLN* 3.9 0.2 - - - -
127E THR* 5.5 1.6 - - - +
135E LEU* 4.5 2.5 - - + -
138E LEU* 3.7 30.3 - - + -
150E VAL* 3.8 33.0 - - + -
152E VAL* 5.4 1.1 - - + -
164E MSE 3.0 46.3 + - + +
165E ALA 3.3 4.5 + - - +
167E ALA* 1.3 73.3 - - - +
169E CYS* 1.3 63.6 + - - +
171E LEU* 3.2 24.0 + - + +
173E VAL* 3.0 42.2 + - + +
175E VAL* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 169 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D GLN* 2.6 45.8 + - - +
265D ASP* 4.2 24.5 - - + -
165E ALA 3.0 13.8 + - - +
166E LYS* 3.1 13.7 + - - +
168E LEU* 1.3 78.7 - - - +
170E HIS* 1.3 64.1 + - - +
172E ASN* 2.7 12.6 + - - -
173E VAL 4.2 2.2 - - - -
175E VAL* 4.2 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 170 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E LYS* 3.0 25.5 + - + +
167E ALA* 3.8 11.6 - - - +
168E LEU 3.3 0.6 - - - -
169E CYS* 1.3 83.7 - - - +
171E LEU* 1.3 62.1 + - + +
172E ASN* 3.1 9.7 + - - +
----------------------------------------------------------
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