Contacts of the helix formed by residues 169 - 178 (chain R) in PDB entry 4M8B
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 SER 169 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R GLN* 3.2 18.2 + - - -
25R PHE* 6.0 0.2 - - - -
125R PHE* 4.6 5.2 - - - -
167R ARG* 3.7 9.9 + - - +
168R PRO* 1.3 75.3 - - - +
170R GLN* 1.3 63.7 + - - +
171R LYS* 3.8 8.7 + - - +
172R LEU* 3.0 30.0 + - - +
173R LEU* 3.2 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 170 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167R ARG* 5.6 1.0 - - - +
168R PRO 3.8 1.6 + - - -
169R SER* 1.3 72.9 - - - +
171R LYS* 1.3 58.3 + - - +
173R LEU* 3.1 26.9 + - - +
174R ASP* 2.8 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 171 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125R PHE* 3.2 27.9 - - + -
126R ASN* 3.1 44.6 + - + +
169R SER* 3.2 7.5 + - - +
170R GLN* 1.3 78.2 - - - +
172R LEU* 1.3 56.6 + - - +
174R ASP* 3.9 7.7 - - - +
175R ALA* 3.1 27.9 + - + +
178R LYS* 5.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18R ALA* 3.4 31.6 - - + +
21R PHE* 4.0 6.3 - - + -
22R GLN* 3.8 26.7 - - + +
25R PHE* 3.8 17.3 - - + -
123R LEU* 3.5 32.8 - - + -
125R PHE* 3.5 12.3 - - + -
168R PRO* 4.3 3.6 - - + -
169R SER* 3.0 20.0 + - - +
171R LYS* 1.3 77.8 - - - +
173R LEU* 1.3 59.6 + - - +
175R ALA* 3.3 1.7 + - - +
176R LEU* 2.9 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R GLU* 4.9 6.5 - - + +
15R GLN* 4.3 18.8 - - - +
18R ALA* 4.3 17.0 - - + -
168R PRO* 4.1 21.1 - - + +
169R SER 3.2 8.1 + - - +
170R GLN* 3.1 31.1 + - - +
172R LEU* 1.3 79.9 - - - +
174R ASP* 1.3 62.4 + - - +
176R LEU* 3.4 9.3 + - + +
177R GLN* 3.2 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 174 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170R GLN* 2.8 48.5 + - - +
171R LYS* 3.9 7.7 - - - +
173R LEU* 1.3 74.2 - - - +
175R ALA* 1.3 64.6 + - - +
177R GLN* 3.0 31.1 + - + +
178R LYS* 3.2 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123R LEU* 4.0 13.1 - - + +
124R LYS 4.5 7.0 - - - +
125R PHE* 3.7 23.1 - - + -
171R LYS* 3.1 19.5 + - + +
172R LEU 3.3 4.5 + - - +
174R ASP* 1.3 75.4 - - - +
176R LEU* 1.3 61.6 + - - +
178R LYS* 3.1 27.1 + - - +
179R VAL* 3.3 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R GLU* 3.4 28.3 - - + +
17R LEU* 4.6 4.7 - - + -
18R ALA* 3.7 38.8 - - + +
21R PHE* 4.3 6.1 - - + -
77R LYS* 2.9 17.0 + - - +
121R PHE* 3.5 34.7 - - + -
123R LEU* 3.7 19.1 - - + -
172R LEU* 2.9 28.5 + - + +
173R LEU* 3.7 9.4 - - + +
174R ASP 3.2 0.4 - - - -
175R ALA* 1.3 78.3 - - - +
177R GLN* 1.3 57.3 + - - +
179R VAL* 3.5 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 177 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R GLU* 3.7 6.5 + - - +
77R LYS* 3.1 19.9 + - - +
173R LEU 3.2 13.2 + - - +
174R ASP* 3.0 24.6 + - - +
176R LEU* 1.3 73.2 - - - +
178R LYS* 1.3 79.0 + - - +
179R VAL 3.1 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 178 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171R LYS 5.0 0.4 + - - -
174R ASP* 3.2 15.5 + - - +
175R ALA* 3.1 41.7 - - - +
176R LEU 3.3 0.2 - - - -
177R GLN* 1.3 92.3 - - - +
179R VAL* 1.3 61.8 + - + +
180R ALA* 3.7 4.2 + - - +
----------------------------------------------------------
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