Contacts of the strand formed by residues 52 - 57 (chain F) in PDB entry 4NL3
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 52 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E PRO 3.1 18.4 + - - +
67E GLN* 2.9 29.8 + - - +
68E LYS* 4.5 0.2 - - - +
69E ASN* 3.5 16.8 + - - +
47F LEU 3.6 0.3 - - - +
48F ASP* 3.6 2.0 - - - -
49F VAL* 2.8 44.1 + - + +
50F GLU 3.1 3.9 + - - +
51F GLY* 1.3 82.1 - - - +
53F GLN* 1.3 68.9 + - - +
54F GLN* 4.8 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E TYR* 2.9 32.0 + - - +
65E SER* 5.1 0.2 - - - -
66E PRO* 3.4 21.6 - - + +
69E ASN* 3.3 28.8 + - - +
70E VAL* 2.7 48.0 + - - +
72E LEU* 4.5 7.9 - - - +
38F VAL* 5.9 3.7 - - + +
46F LEU* 4.2 19.6 - - + +
47F LEU 3.4 5.6 - - - +
48F ASP* 4.9 3.1 - - - +
52F LYS* 1.3 76.4 - - - +
54F GLN* 1.3 70.1 + - - +
55F LEU 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E PHE* 5.5 2.3 - - - -
63E THR* 3.5 21.9 - - + +
64E PHE 3.9 1.6 - - - -
65E SER* 2.3 29.6 + - - -
33F LEU* 3.7 32.6 - - + +
45F VAL 3.4 3.6 - - - +
46F LEU* 4.0 2.7 - - - +
47F LEU* 2.6 52.5 + - + +
49F VAL* 4.1 17.7 - - + +
52F LYS* 4.5 8.7 + - - +
53F GLN* 1.3 87.7 + - - +
55F LEU* 1.3 61.1 + - - +
56F VAL* 3.5 1.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 3.7 30.1 - - + -
9E GLN* 5.0 3.6 - - + -
12E TYR* 3.4 45.2 + - + -
13E LEU* 4.7 9.6 - - + -
63E THR* 3.3 2.8 - - - -
64E PHE* 2.7 63.0 + - + +
44F THR* 3.8 26.0 - - + +
45F VAL 3.8 8.1 - - - +
46F LEU* 4.1 10.4 - - + +
54F GLN* 1.3 69.6 - - - +
56F VAL* 1.3 61.2 + - - +
57F PHE* 4.1 3.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E SER 3.5 12.3 - - - +
63E THR* 3.9 13.9 - - + +
25F VAL* 5.8 0.7 - - + -
27F LEU* 3.9 16.2 - - + -
33F LEU* 4.1 18.4 - - + -
44F THR* 3.3 2.7 - - - -
45F VAL* 2.7 43.2 + - - +
47F LEU* 3.7 25.8 - - + -
54F GLN* 3.9 5.2 - - + +
55F LEU* 1.3 76.8 - - - +
57F PHE* 1.3 66.1 + - - +
60F ALA* 4.7 1.1 - - + -
61F ILE* 3.6 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E GLN* 3.3 27.1 - - + -
13E LEU* 5.1 2.9 - - + -
45E VAL* 5.6 0.2 - - + -
58E LYS* 4.0 22.7 - - + -
61E ILE* 3.5 42.0 - - + +
62E SER 3.0 11.6 + - - +
63E THR 4.8 0.2 - - - -
64E PHE* 3.8 23.8 - + - -
43F PHE 3.5 7.0 - - - -
44F THR* 3.7 17.7 - - + +
55F LEU* 5.0 3.8 - - + -
56F VAL* 1.3 74.7 - - - +
58F LYS* 1.3 59.2 + - - +
59F HIS* 3.3 34.3 - + + +
60F ALA* 2.9 24.7 + - - +
61F ILE* 3.5 7.1 + - - +
29Z U 3.9 10.5 - - - -
----------------------------------------------------------
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