Contacts of the strand formed by residues 47 - 53 (chain C) in PDB entry 5J1T
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 GLU 47 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B TYR* 5.7 0.4 - - - -
38C TYR* 3.2 7.7 - - - -
39C ARG* 2.9 77.1 + - + +
44C LYS* 5.3 8.3 - - - +
45C GLN 4.2 7.4 - - - +
46C ARG* 1.4 75.0 - - - +
48C LEU* 1.3 71.9 + - - +
49C VAL* 4.0 0.2 - - - +
63C SER* 4.8 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 4.1 25.6 - - + -
349B LEU* 4.2 28.0 - - + -
350B GLU* 4.2 23.1 + - - +
353B TYR* 6.1 0.2 - - - -
37C TRP 3.7 4.7 - - - +
38C TYR* 3.5 37.2 - - + +
47C GLU* 1.3 79.4 - - - +
49C VAL* 1.3 66.9 + - - +
50C ALA* 3.6 27.4 - - - +
51C ALA* 4.3 7.6 - - + -
59C THR* 4.8 6.5 - - + -
61C ALA* 3.3 22.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
37C TRP* 2.8 19.6 + - + +
38C TYR 4.0 1.8 - - - -
39C ARG* 3.5 53.6 - - + +
47C GLU 4.9 0.2 - - - -
48C LEU* 1.3 78.6 - - - +
50C ALA* 1.3 61.5 + - + +
60C TYR* 3.5 2.4 - - - -
61C ALA* 3.0 26.7 + - - -
64C VAL* 3.6 12.0 - - + +
68C PHE* 3.5 37.0 - - + -
81C LEU* 4.3 11.2 - - + -
94C TYR* 4.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLY* 3.2 2.3 - - - -
37C TRP* 2.8 29.1 + - + +
48C LEU* 3.6 7.2 - - - +
49C VAL* 1.3 84.3 - - + +
51C ALA* 1.3 63.8 + - - +
59C THR 3.3 6.7 - - - -
60C TYR* 3.6 27.8 - - + +
70C ILE* 3.8 17.5 - - + -
81C LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 4.5 2.9 - - + -
349B LEU* 3.4 33.7 - - + -
34C VAL* 3.8 7.0 - - + -
35C MET 3.3 11.7 - - - +
36C GLY* 4.3 1.6 - - - -
48C LEU* 4.3 6.7 - - + -
50C ALA* 1.3 77.1 - - - +
52C ILE* 1.3 63.4 + - - +
58C THR* 3.3 4.0 - - - -
59C THR* 3.0 36.4 + - + +
70C ILE* 3.7 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 4.7 0.4 - - - -
34C VAL* 3.5 4.2 - - - -
35C MET* 2.9 43.1 + - + +
51C ALA* 1.3 76.7 - - - +
53C THR* 1.3 75.1 + - - +
56C ASP* 3.7 27.1 - - + +
57C THR 3.3 12.3 - - - +
58C THR* 3.7 18.6 - - + -
70C ILE* 3.7 20.4 - - + +
71C SER* 4.0 17.7 - - - -
72C ARG* 3.3 32.2 + - + -
79C VAL* 4.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A HIS* 4.6 7.6 - - + -
142A SER* 2.7 28.4 + - - +
143A ASN* 3.5 18.8 - - - +
345B LEU* 3.9 29.2 - - + -
33C ASN 3.4 8.5 - - - +
34C VAL* 4.7 1.3 - - + -
52C ILE* 1.3 83.7 - - - +
54C SER* 1.3 65.1 + - - +
55C GLY 3.3 5.5 + - - -
56C ASP* 3.1 9.5 + - - -
57C THR* 2.9 32.8 + - + +
72C ARG* 3.4 8.7 + - - -
----------------------------------------------------------
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