Contacts of the strand formed by residues 51 - 57 (chain D) in PDB entry 4JRX
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 51 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D TYR* 3.4 7.9 - - - -
43D LYS* 2.7 55.4 + - + +
45D PRO* 4.1 19.7 - - + -
49D GLU* 4.3 13.5 - - + +
50D LEU* 1.3 73.5 - - - +
52D PHE* 1.3 71.8 + - - +
53D LEU* 3.5 8.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ARG* 5.8 1.1 - - - -
40D PHE* 3.6 6.7 - + - -
42D TYR* 3.4 36.3 - + + +
50D LEU 4.1 0.6 + - - -
51D VAL* 1.3 78.9 - - - +
53D LEU* 1.3 77.9 + - - +
54D ILE* 3.4 35.2 - - - -
55D ARG* 3.6 4.9 - - + -
110E THR* 3.5 33.4 - - - -
111E GLU* 3.6 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D TRP* 3.1 24.3 + - + +
42D TYR 4.2 3.1 - - - +
43D LYS* 3.8 33.4 - - + +
51D VAL* 3.9 11.7 - - + +
52D PHE* 1.3 95.8 - - - +
54D ILE* 1.3 69.0 + - - +
76D TYR* 3.9 22.2 - - + +
78D TRP* 4.1 17.1 - - + -
90D PHE* 3.8 35.7 - - + -
103D TYR* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D PHE* 3.3 25.6 - - - -
41D TRP* 3.3 17.3 + - + +
52D PHE* 3.4 10.1 - - - -
53D LEU* 1.3 83.2 - - - +
55D ARG* 1.3 62.1 + - - +
56D ARG* 3.8 33.7 - - - +
66D GLU* 4.5 8.5 - - + -
68D SER* 6.0 1.1 - - - -
78D TRP* 3.5 50.9 - - + +
88D PHE* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ARG* 4.2 18.1 + - - +
155A GLN* 5.5 1.0 + - - -
38D TYR* 3.2 50.9 - - + -
39D LEU 3.3 4.0 - - - -
40D PHE* 3.6 15.6 - - + -
52D PHE* 3.6 5.9 - - + -
54D ILE* 1.3 77.2 - - - +
56D ARG* 1.3 73.6 + - - +
57D ASN* 3.0 20.0 + - - +
62D ASP* 4.9 2.3 - - - +
110D PHE* 3.7 19.0 - - - -
108E GLY 3.0 26.3 + - - -
109E GLU* 3.3 27.7 + - - +
110E THR 3.4 23.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D TYR* 3.2 2.2 - - - -
39D LEU* 2.8 39.8 + - + +
54D ILE* 3.8 16.2 - - - +
55D ARG* 1.3 90.6 + - - +
57D ASN* 1.3 69.2 + - - +
62D ASP* 3.7 28.0 + - - -
63D GLU 6.0 0.2 - - - -
64D GLN 4.2 11.4 + - - -
65D ASN* 4.7 4.0 - - - +
66D GLU* 3.5 47.6 + - - +
78D TRP* 3.8 23.0 + - - +
80D PHE* 4.1 29.6 - - + +
88D PHE* 3.6 25.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ARG* 4.3 5.3 - - - +
154A GLU* 3.0 42.0 + - - +
37D TYR 3.7 4.3 - - - -
38D TYR* 3.4 2.3 - - - +
55D ARG* 3.0 27.8 + - - +
56D ARG* 1.3 80.9 - - - +
58D SER* 1.3 65.6 + - - +
59D PHE* 3.7 20.4 - - + -
62D ASP* 3.1 33.8 + - - +
80D PHE* 4.2 2.8 - - - -
110D PHE* 3.2 21.6 - - + -
----------------------------------------------------------
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