Contacts of the helix formed by residues 150 - 159 (chain D) in PDB entry 4MNE
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 150 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D GLY* 1.3 74.4 - - - -
151D LEU* 1.3 60.0 + - - +
152D ASP* 3.2 12.0 - - - +
153D GLN* 3.0 21.6 + - - +
154D VAL* 2.8 30.6 + - - +
194D SER* 3.3 30.2 - - - -
196D ILE 3.5 4.9 - - - -
197D LEU* 3.5 6.5 - - - -
198D VAL* 5.1 0.2 - - - -
901D ACP 3.2 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D SER* 1.3 69.8 - - - +
152D ASP* 1.3 57.4 + - - +
154D VAL* 4.0 9.6 - - + -
155D LEU* 2.6 37.2 + - - +
161D ILE* 4.2 16.7 - - + +
165D ILE* 6.2 0.4 - - + -
169D VAL* 3.6 28.0 - - + -
193D PRO* 3.2 9.8 + - + +
196D ILE* 2.8 44.2 + - + +
198D VAL* 4.0 26.0 - - + -
256D MET* 3.4 30.5 - - - -
371D PHE* 5.4 5.6 - - + -
374D TRP* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D SER* 3.2 12.7 + - - +
151D LEU* 1.3 79.5 - - - +
153D GLN* 1.3 65.2 + - - +
155D LEU* 3.5 6.3 + - - +
156D LYS* 3.4 46.1 + - - +
193D PRO* 3.3 14.7 + - + +
194D SER* 3.5 26.0 - - - +
227D ARG* 4.0 19.0 + - - -
255D GLU* 5.3 3.6 - - - +
901D ACP 4.0 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D LEU* 2.8 28.5 + - - +
75D GLY* 5.0 1.2 - - - -
148D GLY 4.6 1.4 - - - +
149D GLY* 3.6 18.7 - - - -
150D SER* 3.0 11.2 + - - +
152D ASP* 1.3 84.0 - - - +
154D VAL* 1.3 64.8 + - + +
156D LYS* 3.5 23.6 + - + +
157D LYS* 3.9 22.1 + - - +
379D ILE* 6.0 0.4 - - + -
901D ACP 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D GLY 3.6 19.5 - - - +
150D SER 2.8 19.7 + - - +
151D LEU* 3.7 10.3 - - + +
153D GLN* 1.3 74.6 - - - +
155D LEU* 1.3 67.9 + - - +
157D LYS* 2.9 17.5 + - - +
158D ALA* 3.1 10.0 + - + +
161D ILE* 4.6 5.4 - - + -
198D VAL* 4.1 10.5 - - + -
374D TRP* 4.0 32.1 - - + -
375D LEU* 3.8 21.5 - - + -
378D THR* 4.4 9.8 - - + +
379D ILE* 3.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU 2.6 22.1 + - - +
152D ASP* 3.6 7.0 - - - +
154D VAL* 1.3 73.0 - - - +
156D LYS* 1.3 63.8 + - + +
157D LYS 3.2 0.2 + - - -
158D ALA* 3.2 1.0 + - - +
159D GLY* 2.9 53.3 + - - +
160D ARG* 4.2 1.8 - - - -
161D ILE* 4.3 14.1 - - + +
193D PRO* 5.2 3.6 - - + -
255D GLU* 3.7 37.7 - - + +
256D MET* 3.8 35.2 - - + +
259D GLY* 4.1 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D ASP* 3.4 41.2 + - - +
153D GLN* 3.6 15.5 - - + +
154D VAL 3.2 0.8 - - - -
155D LEU* 1.3 80.7 - - + +
157D LYS* 1.3 62.2 + - + +
159D GLY* 4.1 5.4 + - - -
227D ARG* 5.8 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D GLN* 4.0 22.5 + - - +
154D VAL 2.9 7.5 + - - +
156D LYS* 1.3 81.2 - - + +
158D ALA* 1.3 60.8 + - - +
159D GLY 3.5 0.2 - - - -
378D THR* 4.1 21.6 - - + +
379D ILE* 3.4 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D VAL 3.1 12.2 + - - +
155D LEU 4.2 1.8 - - - +
157D LYS* 1.3 77.7 - - - +
159D GLY* 1.3 59.0 + - - +
160D ARG 3.0 25.9 + - - +
161D ILE* 4.8 2.2 - - + -
374D TRP* 4.2 17.9 - - + -
378D THR* 3.7 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D LEU* 2.9 28.3 + - - +
156D LYS 4.1 4.5 + - - -
157D LYS 3.5 2.2 - - - -
158D ALA* 1.3 72.5 - - - +
160D ARG* 1.3 61.6 + - - -
259D GLY* 3.3 16.5 - - - +
----------------------------------------------------------
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