Contacts of the helix formed by residues 45 - 52 (chain X) in PDB entry 4LAH
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 ARG 45 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44X GLY* 1.3 70.4 - - - -
46X LYS* 1.3 93.7 + - - +
48X PHE* 3.3 3.5 + - - +
49X GLU* 3.0 47.9 + - + +
62X VAL* 3.9 10.8 - - - -
63X LEU 3.2 6.7 + - - -
64X THR* 3.9 16.2 - - - +
66X ASP* 5.9 1.1 - - + -
69X PHE* 4.8 11.0 - - + -
202X NAP 2.9 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19X ASN* 4.2 22.5 - - - +
44X GLY 3.2 0.6 - - - -
45X ARG* 1.3 109.1 - - - +
47X THR* 1.3 60.5 + - - +
49X GLU* 3.2 6.5 + - - +
50X SER* 2.9 33.6 + - - -
202X NAP 3.4 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X MET* 4.1 13.5 - - + -
44X GLY 3.4 5.8 + - - -
46X LYS* 1.3 75.7 - - - +
48X PHE* 1.3 62.1 + - - +
50X SER* 3.2 9.9 + - - -
51X ILE* 3.0 40.4 + - + +
93X PHE* 4.2 5.6 - - + +
94X GLY 4.2 1.8 - - - -
95X GLY* 3.0 16.0 + - - -
201X 1VO 4.9 2.2 - - - -
202X NAP 2.6 61.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 48 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X MET* 3.8 19.4 - - + -
44X GLY 3.1 9.2 + - - +
45X ARG 3.7 7.2 - - - +
47X THR* 1.3 76.5 - - - +
49X GLU* 1.3 73.2 + - + +
51X ILE* 3.3 3.4 + - + -
52X GLY* 2.7 37.0 + - - -
53X LYS* 3.6 15.0 - - - -
54X PRO* 3.6 31.0 - - + -
60X ASN* 5.6 0.7 - - + -
62X VAL* 3.6 26.7 - - + -
69X PHE* 3.8 24.2 - + - -
71X VAL* 3.9 16.6 - - + -
74X VAL* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X ARG* 3.0 36.9 + - - +
46X LYS* 3.8 5.8 - - - +
48X PHE* 1.3 96.5 - - - +
50X SER* 1.3 61.6 + - - +
52X GLY* 3.5 14.1 + - - +
69X PHE* 4.0 12.6 - - - -
71X VAL* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19X ASN* 2.8 38.5 + - - +
20X GLN* 3.4 22.9 + - - +
46X LYS 2.9 19.1 + - - -
47X THR* 3.2 12.2 - - - -
48X PHE 3.2 0.2 - - - -
49X GLU* 1.3 76.4 - - - +
51X ILE* 1.3 64.4 + - - +
52X GLY* 4.5 0.2 - - - -
201X 1VO 3.6 18.8 - - - +
202X NAP 4.7 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X MET* 4.1 12.1 - - + -
47X THR* 3.0 28.5 + - + +
48X PHE* 3.8 3.6 - - + +
50X SER* 1.3 76.1 - - - +
52X GLY* 1.3 57.8 + - - +
53X LYS* 3.3 34.3 + - - +
55X LEU* 3.9 23.1 - - + -
93X PHE* 3.6 30.7 - - + -
201X 1VO 3.8 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X PHE* 2.7 28.0 + - - -
49X GLU* 3.7 14.4 - - - -
50X SER 3.3 1.4 - - - -
51X ILE* 1.3 71.7 - - - +
53X LYS* 1.3 60.5 + - - +
----------------------------------------------------------
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