Contacts of the strand formed by residues 44 - 49 (chain I) 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 THR 44 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I PHE* 3.5 4.0 - - - +
41I ASP* 2.7 60.1 + - - +
42I ASN 3.8 0.2 - - - -
43I PHE* 1.3 80.8 - - - +
45I VAL* 1.3 66.5 + - - +
46I LEU 4.3 0.2 - - - -
55I LEU* 3.9 18.6 - - + -
56I VAL 3.3 8.5 - - - +
57I PHE* 3.8 19.1 - - + -
58I LYS* 4.1 0.8 - - - -
8L LEU* 3.3 12.3 - - - +
9L GLN* 3.4 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I LEU* 4.5 8.5 - - + -
37I VAL* 4.4 12.6 - - + -
39I SER 3.8 7.4 - - - +
40I PHE* 4.3 6.3 - - + -
44I THR* 1.3 79.6 - - - +
46I LEU* 1.3 65.8 + - - +
47I LEU* 3.6 23.1 + - + -
54I GLN 3.3 3.3 - - - +
55I LEU* 4.0 3.4 - - - -
56I VAL* 2.7 42.3 + - + +
58I LYS* 4.1 17.5 - - + -
61I ILE* 3.8 26.2 - - + -
64I PHE* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I VAL* 3.9 4.0 - - - -
38I VAL* 3.0 40.6 + - + -
39I SER* 2.8 37.8 + - - +
44I THR 4.3 0.4 - - - -
45I VAL* 1.3 70.9 - - - +
47I LEU* 1.3 67.2 + - - +
53I GLN* 4.3 11.9 - - + +
54I GLN 3.8 20.9 - - - +
55I LEU* 4.0 8.6 - - + +
8L LEU* 4.1 13.8 - - + +
12L TYR* 3.6 29.4 - - + +
72L LEU* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I VAL* 3.7 32.1 - - + -
33I LEU* 4.0 24.0 - - + +
35I GLY 4.7 3.8 - - - +
36I ARG 3.5 22.2 - - - +
37I VAL* 4.2 8.3 - - + +
38I VAL* 4.3 3.9 - - - +
45I VAL* 4.0 18.8 - - + -
46I LEU* 1.3 81.5 - - - +
48I ASP* 1.3 60.1 + - - +
49I VAL* 3.8 9.0 - - + -
53I GLN* 3.3 10.2 - - - +
54I GLN* 2.7 45.2 + - + +
56I VAL* 4.2 15.9 - - + -
64I PHE* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I GLY* 3.2 4.0 - - - -
36I ARG* 2.6 56.2 + - + +
38I VAL* 3.8 17.0 - - + +
47I LEU* 1.3 71.6 - - - +
49I VAL* 1.3 59.7 + - - +
50I GLU* 3.6 3.3 + - - -
51I GLY* 3.2 37.0 + - - +
52I LYS 3.6 2.4 - - - +
53I GLN* 5.0 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I LEU* 4.2 18.4 - - + -
34I ARG 3.4 26.5 - - - +
47I LEU* 4.4 13.5 - - + -
48I ASP* 1.3 73.0 - - - +
50I GLU* 1.3 73.7 + - + +
51I GLY 3.3 0.2 - - - -
52I LYS* 2.6 31.1 + - + +
54I GLN* 3.9 31.6 - - + +
----------------------------------------------------------
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