Contacts of the helix formed by residues 396 - 401 (chain A) in PDB entry 1MU5
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 ASP 396 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLU 3.4 4.0 + - - +
395A LEU* 1.3 72.6 - - - +
397A TRP* 1.3 59.0 + - - +
398A LYS* 3.0 29.8 + - - +
399A ARG* 3.0 49.0 + - + +
400A TYR* 3.5 8.7 - - - -
471A CA 4.2 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A VAL* 5.2 4.3 - - + -
368A PRO* 4.5 2.4 - - + +
392A VAL* 3.4 29.5 + - + +
395A LEU* 3.4 28.7 + - + +
396A ASP* 1.3 69.3 + - - +
398A LYS* 1.3 60.9 + - - +
399A ARG 3.1 0.4 - - - -
400A TYR* 2.8 31.5 + - + +
402A ILE* 3.2 50.8 + - + +
407A TYR* 4.3 17.7 - - + +
409A MET* 3.7 26.1 - - + +
411A VAL* 3.9 17.3 - - + -
444A LEU* 3.8 30.5 - - + -
447A VAL* 5.8 0.7 - - + -
448A ALA* 3.7 26.5 - - + -
451A LEU* 4.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP* 3.0 16.5 + - - +
397A TRP* 1.3 72.5 - - + +
399A ARG* 1.3 62.7 + - + +
400A TYR 2.9 6.0 + - - -
401A GLY* 3.4 9.5 + - - -
402A ILE* 3.4 21.9 - - + +
403A GLU* 3.1 28.5 + - + +
404A SER 4.3 11.4 - - - -
405A ASP* 4.5 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 5.4 1.4 - - - +
396A ASP* 3.0 35.3 + - - +
398A LYS* 1.3 77.5 - - + +
400A TYR* 1.3 100.6 + - + +
401A GLY 3.5 0.4 - - - -
445A MET* 4.7 11.9 - - - +
452A LYS* 3.4 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 3.8 23.6 - - + -
396A ASP 3.5 15.0 - - - -
397A TRP* 2.8 21.5 + + + +
399A ARG* 1.3 124.0 + - + +
401A GLY* 1.3 58.8 + - - +
402A ILE* 3.5 1.4 + - + -
445A MET* 3.8 25.4 - - + +
448A ALA* 3.5 43.5 - - + +
449A ARG* 3.7 28.4 + - + +
451A LEU* 4.2 3.4 - - + +
452A LYS* 3.1 33.3 + - + -
455A LEU* 3.9 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LYS 3.4 8.5 + - - -
399A ARG 3.5 1.2 + - - -
400A TYR* 1.3 79.4 - - - +
402A ILE* 1.3 55.8 + - - +
403A GLU* 4.5 2.5 - - - -
452A LYS* 4.1 7.4 - - - +
455A LEU* 3.6 14.0 - - - +
459A ARG* 2.6 46.6 + - - -
----------------------------------------------------------
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