Contacts of the strand formed by residues 85 - 89 (chain N) in PDB entry 4EMG
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 VAL 85 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K PHE* 5.4 0.9 - - + -
81K ARG* 3.0 31.6 - - + +
24N VAL* 4.1 2.7 - - + -
26N LEU* 3.9 17.5 - - + -
27N ARG* 5.8 0.4 - - - -
43N LEU* 4.1 15.7 - - + +
45N MSE 3.4 26.2 - - + -
80N VAL* 4.3 2.0 - - + -
81N ARG 4.0 9.0 - - - +
82N GLY 3.0 15.2 + - - +
83N ASP 3.4 0.2 - - - -
84N SER* 1.3 75.8 - - - +
86N ILE* 1.3 63.0 + - - +
87N LEU 4.0 8.7 - - - +
88N ILE* 3.7 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K LEU* 4.0 15.9 - - + -
27K ARG 6.0 1.6 - - - +
30K ARG* 4.7 13.0 - - - +
79K PHE* 5.5 0.2 - - - -
81K ARG* 2.8 32.6 + - - +
84K SER* 3.8 24.0 - - - +
25N LYS* 2.9 24.1 + - + +
26N LEU 3.6 20.4 - - - +
27N ARG* 3.6 36.6 - - + +
28N GLY 4.9 0.2 - - - +
85N VAL* 1.3 77.1 - - - +
87N LEU* 1.3 74.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K LEU* 4.4 2.5 - - + -
30K ARG* 4.6 4.3 - - - -
32K LEU* 4.3 7.2 - - + -
52K GLU* 3.9 33.4 - - + +
75K TYR* 4.2 7.9 - - - +
78K LEU* 4.0 30.1 - - + -
79K PHE 3.2 10.8 - - - +
80K VAL* 4.1 15.3 - - + -
23N TYR* 4.4 3.1 - - + -
24N VAL* 3.4 5.7 - - - +
25N LYS* 3.0 44.3 + - + +
85N VAL* 4.0 0.2 - - - +
86N ILE* 1.3 99.4 - - + +
88N ILE* 1.3 70.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K LEU* 3.7 2.3 - - - -
79K PHE* 2.7 56.0 + - + +
13N LEU* 4.1 4.7 - - + +
14N VAL* 3.7 33.2 - - + -
17N SER* 5.7 1.6 - - - +
22N VAL* 4.2 24.9 - - + -
23N TYR 3.3 8.3 - - - +
24N VAL* 4.5 7.0 - - + -
36N LEU* 6.1 0.4 - - + -
43N LEU* 4.3 10.1 - - + -
45N MSE 4.0 20.9 - - + -
85N VAL* 3.7 22.2 - - + -
87N LEU* 1.3 79.9 - - - +
89N ALA* 1.3 64.2 + - - +
90N PRO* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75K TYR* 3.5 36.6 - - + -
77K MSE 3.6 9.4 - - - +
78K LEU* 4.2 2.2 - - + -
22N VAL* 3.4 3.7 - - - -
23N TYR* 2.8 48.4 + - + +
88N ILE* 1.3 77.0 - - - +
90N PRO* 1.3 70.5 - - - +
----------------------------------------------------------
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