Contacts of the strand formed by residues 45 - 51 (chain N) in PDB entry 4R2G
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 45 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36M TYR* 5.5 3.8 - - + -
38M HIS* 3.9 13.2 - - + +
44M PRO* 3.9 35.9 - - + -
87M TYR* 3.5 45.7 + - + -
98M PHE* 3.5 37.5 + - + +
99M GLY 5.5 1.0 - - - +
37N ILE* 4.4 9.4 - - + -
38N ARG 3.8 4.5 - - - +
39N GLN* 3.5 27.6 - - + -
44N GLY* 1.3 73.7 - - - -
46N GLU* 1.3 59.4 + - - +
91N PHE* 4.7 1.8 - - + -
103N TRP* 5.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M PHE* 4.3 0.4 - - - -
37N ILE* 3.3 7.2 - - - +
38N ARG* 2.7 81.5 + - + +
40N SER* 5.9 4.0 - - - +
44N GLY 3.6 3.2 + - - +
45N LEU* 1.3 73.8 - - - +
47N TRP* 1.3 71.2 + - - +
48N ILE 3.8 0.2 + - - -
60N ASN* 4.4 5.8 - - - +
62N SER* 2.9 26.8 + - - +
63N LEU* 3.8 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M HIS* 4.0 10.5 - + - -
91M TRP* 3.7 15.9 - + - -
95M SER* 3.4 52.0 - + - -
96M TRP* 3.5 34.7 + + + +
98M PHE* 3.5 17.9 - + + -
35N THR* 2.5 30.1 + - - -
36N TRP 3.4 13.5 - - - -
37N ILE* 3.5 11.2 - - + +
46N GLU* 1.3 76.3 - - - +
48N ILE* 1.3 60.7 + - - +
49N GLY 4.0 4.7 + - - -
50N TYR* 4.3 15.3 - + + -
60N ASN* 3.0 29.1 + - - +
63N LEU* 4.6 0.3 - - - +
95N ALA* 5.5 0.7 - - + -
100N MET* 3.4 40.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N TRP* 3.0 20.9 + - + +
38N ARG* 3.8 33.2 - - + +
47N TRP* 1.3 75.0 - - - +
49N GLY* 1.3 60.9 + - - +
59N TYR* 3.7 5.2 - - - +
60N ASN* 3.0 25.9 + - - +
63N LEU* 3.9 28.8 - - + +
67N ALA* 4.2 17.0 - - + -
69N ILE* 5.3 0.9 - - + -
80N LEU* 3.6 34.3 - - + -
82N LEU* 5.4 3.1 - - + -
90N TYR* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M TRP* 4.3 8.1 - - - -
35N THR* 2.9 17.5 + - - -
36N TRP 3.0 14.1 + - - -
47N TRP* 3.7 3.9 - - - -
48N ILE* 1.3 82.0 - - - +
50N TYR* 1.3 63.0 + - - -
58N THR 3.1 13.9 - - - -
59N TYR* 4.2 3.6 - - - -
69N ILE* 3.5 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M PHE* 3.7 25.1 - + - -
96M TRP* 4.1 9.4 - + - -
33N TYR* 4.0 23.6 - + + -
34N TRP 3.2 13.5 - - - +
35N THR* 3.6 12.1 - - - +
47N TRP* 4.3 12.8 - + + -
49N GLY* 1.3 75.7 - - - +
51N ILE* 1.3 64.5 + - - +
52N SER* 5.2 2.7 - - - -
56N THR 3.9 1.3 - - - +
57N THR* 3.4 2.3 - - - -
58N THR* 2.8 66.6 + - + +
69N ILE* 3.8 6.7 - - - +
95N ALA* 5.2 3.4 - - + -
100N TYR* 3.0 43.7 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N TYR* 3.4 4.5 - - - +
34N TRP* 2.8 51.0 + - + +
50N TYR* 1.3 75.2 - - - +
52N SER* 1.3 70.5 + - - +
55N GLU* 3.8 21.3 - - + +
56N THR 3.2 4.9 - - - +
57N THR* 3.7 18.8 - - + +
69N ILE* 4.0 15.0 - - + +
70N SER* 4.0 5.4 - - - -
71N ARG* 3.8 37.2 - - + +
78N LEU* 3.7 25.4 - - + -
----------------------------------------------------------
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