Contacts of the strand formed by residues 47 - 54 (chain C) in PDB entry 5DIR
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 PHE 47 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 3.2 45.4 + - + -
43C ILE* 2.8 58.2 + - + +
46C LEU* 1.3 79.4 - - + +
48C SER* 1.3 78.4 + - - +
49C TRP* 3.7 36.8 - + - -
126C ILE* 3.5 26.0 - - + -
127C LEU 3.6 4.3 - - - -
128C VAL* 3.8 21.3 - - + -
129C HIS* 4.1 1.0 + - - -
201C OLC 5.5 5.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
39C GLN* 2.9 44.6 + - - -
40C ILE 3.5 8.5 - - - -
41C VAL* 3.7 12.3 - - - +
42C VAL* 4.1 1.3 - - - +
43C ILE 4.4 2.1 + - - -
44C PRO 4.9 0.7 + - - -
47C PHE* 1.3 88.9 + - - +
49C TRP* 1.3 62.7 + - - +
127C LEU* 2.8 41.2 + - - +
129C HIS* 4.1 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 3.5 34.1 - + + -
34C LEU* 4.4 2.5 - - + -
39C GLN* 3.3 7.1 - - - +
40C ILE* 2.9 52.5 + - + +
42C VAL* 3.3 25.8 - - + +
47C PHE* 3.7 30.1 - + - -
48C SER* 1.3 73.9 - - - +
50C THR* 1.3 61.4 + - - +
125C PHE* 3.2 36.8 - + - -
126C ILE* 3.9 12.6 - - + -
201C OLC 3.7 32.9 + - + -
204C OLC 3.0 43.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 4.4 0.2 - - - -
34C LEU* 3.3 13.9 - - - +
37C TYR* 3.8 17.3 + - - -
38C GLN 3.0 17.6 + - - -
39C GLN* 4.6 2.1 - - - +
49C TRP* 1.3 76.6 - - - +
51C LEU* 1.3 70.3 + - - +
52C ALA* 4.7 2.4 - - + +
124C ASP 4.1 4.7 - - - +
125C PHE* 2.7 44.7 + - - +
127C LEU* 3.8 30.8 - - + +
138C ALA* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 3.5 24.2 - - + +
31C GLN* 3.4 31.9 - - - +
34C LEU* 3.2 34.8 - - + +
35C SER* 3.6 17.0 - - - +
36C MET* 3.7 10.2 - - + +
37C TYR* 2.7 31.4 + - - -
38C GLN 3.6 3.6 + - - -
50C THR* 1.3 82.1 + - - +
52C ALA* 1.3 61.3 + - - +
53C TYR* 4.5 15.0 - - + +
123C VAL* 3.8 17.0 - - + -
124C ASP 3.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C MET* 4.8 1.8 - - - -
37C TYR* 4.1 23.3 - - + -
50C THR* 4.8 3.6 - - + -
51C LEU* 1.3 76.3 - - - +
53C TYR* 1.3 70.0 + - - +
54C ASN* 3.9 0.4 - - + -
122C VAL 3.4 2.3 - - - +
123C VAL* 3.6 0.3 - - - +
124C ASP* 2.9 47.5 + - + +
138C ALA* 4.5 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLN* 2.6 45.9 + - - -
36C MET* 3.5 41.7 - - + +
37C TYR* 4.8 8.3 + - - -
51C LEU* 4.5 9.7 - - + +
52C ALA* 1.3 81.1 - - - +
54C ASN* 1.3 60.5 + - - +
55C THR* 3.5 9.8 + - + +
121C HIS* 3.5 49.1 - + + +
122C VAL 3.5 1.6 - - - -
123C VAL* 4.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA* 3.9 1.1 + - + -
53C TYR* 1.3 69.5 - - - +
55C THR* 1.3 58.8 + - - +
56C GLY* 2.9 29.8 + - - -
57C ALA 4.3 1.9 + - - -
116C ARG* 5.2 1.9 + - - -
121C HIS* 3.8 1.0 - - - -
122C VAL* 2.7 39.9 + - + +
124C ASP* 3.3 25.1 + - - +
137C PRO* 6.0 1.2 - - - +
138C ALA 4.8 1.4 + - - -
203F SER* 3.2 19.6 - - - +
204F ALO 3.2 33.9 + - - -
301F OLC 3.9 2.2 + - - -
----------------------------------------------------------
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