Contacts of the strand formed by residues 45 - 49 (chain C) in PDB entry 2JA7
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 ALA 45 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 1.3 81.1 - - - +
46C ILE* 1.3 63.7 - - - +
47C ASP* 3.3 3.1 + - - +
68C GLY 3.7 18.6 - - - +
70C ILE 5.3 0.7 - - - +
71C PRO* 6.2 0.7 - - + -
72C LEU* 3.3 14.1 - - + +
159C ALA* 3.7 3.8 - - - -
160C LYS 3.0 28.4 + - - +
169C LYS* 4.0 17.3 - - - +
170C TRP* 3.7 19.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA* 1.3 71.4 - - - +
47C ASP* 1.3 53.9 + - - +
48C SER 3.9 11.2 - - - +
49C VAL* 4.1 10.5 - - + -
67C LEU* 3.0 38.8 - - + +
68C GLY* 3.7 6.6 + - - -
70C ILE* 5.1 1.3 - - + -
72C LEU* 3.3 19.6 - - + +
99C LEU* 5.0 5.6 - - + -
118C LEU* 4.6 19.7 - - + -
157C CYS* 3.4 41.7 - - + -
158C VAL 3.5 6.1 - - - +
159C ALA* 3.9 2.9 - - + +
169C LYS* 2.6 25.3 + - - -
69L ALA* 3.0 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA 3.3 3.5 + - - +
46C ILE* 1.3 72.1 - - - +
48C SER* 1.3 65.5 + - - +
158C VAL 2.8 10.7 + - - +
160C LYS* 4.1 29.4 + - + +
169C LYS* 2.9 18.7 + - - +
170C TRP* 3.4 20.6 - - + -
67L PHE 4.7 0.9 - - - +
68L GLU* 5.1 0.5 - - - -
69L ALA* 2.9 17.1 + - - +
70L ARG* 2.9 35.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 3.6 0.8 - - - -
47C ASP* 1.3 83.2 - - - +
49C VAL* 1.3 62.7 + - - +
50C GLU* 5.2 3.0 + - - -
156C THR 3.7 1.4 - - - +
157C CYS* 3.1 6.8 - - - +
158C VAL* 3.0 47.3 + - - +
160C LYS* 5.1 7.2 - - - -
66L GLN* 4.0 24.9 + - - +
67L PHE 3.9 8.6 + - - -
69L ALA* 3.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 4.1 12.3 - - + -
48C SER* 1.3 78.2 - - - +
50C GLU* 1.3 65.3 + - - +
51C VAL* 3.6 19.8 + - + +
64C ALA* 4.0 31.0 - - + +
67C LEU* 3.7 20.2 - - + -
155C LEU* 3.8 30.5 - - + -
156C THR 3.8 2.0 - - - -
157C CYS* 4.3 2.7 - - - +
66L GLN* 3.7 2.8 - - - +
67L PHE* 2.8 36.6 + - + +
69L ALA* 5.0 4.7 - - + -
----------------------------------------------------------
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