Contacts of the strand formed by residues 47 - 52 (chain A) in PDB entry 2F4N
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 LYS 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP 2.9 8.2 + - - +
14A ILE* 3.7 11.8 - - + +
15A ILE* 3.1 28.8 + - - +
46A ALA* 1.3 76.3 - - - +
48A ILE* 1.3 60.7 + - - +
49A ILE* 4.0 15.2 + - + -
36B LEU* 4.2 26.5 - - + -
39B LEU* 6.3 0.2 - - - -
45B ASP* 3.5 18.8 + - - +
46B ALA 2.9 31.0 + - - +
47B LYS* 4.6 12.0 - - - +
48B ILE* 5.0 4.9 - - - +
47C LYS* 4.6 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.4 22.9 - - + +
17A LEU* 4.3 25.1 - - + -
32A LYS* 4.3 21.5 - - + +
35A ILE* 3.6 23.6 - - + -
36A LEU* 3.1 38.8 - - + -
39A LEU* 5.2 2.2 - - + -
46A ALA 4.0 5.1 + - - +
47A LYS* 1.3 76.0 - - - +
49A ILE* 1.3 70.8 + - - +
50A ASP* 4.3 0.9 + - - -
47C LYS* 5.1 4.1 - - - +
49C ILE* 5.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 4.2 10.1 - - + -
15A ILE 3.0 5.9 + - - +
16A THR* 3.0 15.7 - - + -
17A LEU* 3.0 26.0 + - - +
47A LYS* 4.5 16.2 - - + -
48A ILE* 1.3 83.3 - - - +
50A ASP* 1.3 73.0 + - - +
51A ILE* 5.4 0.2 - - + -
74A PHE* 4.1 18.6 - - + -
29B GLY* 5.8 0.2 - - - -
32B LYS* 3.4 34.3 - - + +
36B LEU* 3.8 31.6 - - + -
48B ILE* 5.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.9 8.7 - - - +
32A LYS* 2.6 37.3 + - - -
48A ILE* 4.3 1.7 + - - +
49A ILE* 1.3 84.4 - - - +
51A ILE* 1.3 63.9 + - - +
52A SER* 4.7 1.6 - - - +
53A HIS* 2.8 37.5 + - + +
28B VAL* 5.4 0.9 - - - +
29B GLY* 4.8 1.9 - - - -
32B LYS* 3.4 27.5 + - - +
50C ASP* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.5 37.7 - - + +
17A LEU 3.1 5.3 + - - -
18A THR* 3.2 20.4 - - - +
50A ASP* 1.3 77.6 - - - +
52A SER* 1.3 65.5 + - - +
66A VAL* 3.6 29.2 - - + +
67A LEU* 4.7 3.6 - - + -
70A ALA* 3.9 24.7 - - + -
71A ILE* 4.0 24.0 - - + -
74A PHE* 4.6 9.2 - - + -
79A HIS* 4.5 0.2 - - - +
23B THR* 4.3 10.1 - - - +
25B GLU 4.7 4.0 - - - +
26B GLY* 4.8 1.8 - - - -
28B VAL* 5.2 4.3 - - - +
29B GLY* 4.5 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 3.7 0.2 - - - +
18A THR* 3.3 8.3 + - - +
19A THR 3.0 21.5 + - - -
50A ASP* 3.6 1.3 - - - +
51A ILE* 1.3 84.9 - - - +
53A HIS* 1.3 70.8 + - - +
54A GLU* 3.3 12.8 + - - +
55A ILE* 4.1 8.5 + - - +
66A VAL* 4.3 20.0 - - - -
23B THR* 2.5 37.2 + - - -
25B GLU 4.4 1.8 - - - -
----------------------------------------------------------
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