Contacts of the strand formed by residues 49 - 54 (chain E) in PDB entry 2SGQ
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 THR 49 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E SER* 1.3 132.4 + - - +
50E TYR* 1.3 66.0 - - - +
51E TYR* 3.0 38.7 - - + +
107E ARG* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E SER* 3.2 60.6 + - - +
49E THR* 1.3 72.3 - - - +
51E TYR* 1.3 63.2 + - - +
107E ARG* 3.7 6.6 - - - +
108E TYR* 2.9 43.3 + + + +
115E LYS* 4.1 19.5 - - + -
242E TYR* 3.5 44.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E ASN* 3.7 0.7 - - - +
48E VAL* 3.0 43.0 + + + +
49E THR* 3.0 40.1 - - + +
50E TYR* 1.3 75.8 - - - +
52E PHE* 1.3 60.3 + - - +
89E SER* 4.1 14.1 - - - -
105E ILE* 3.5 34.3 - - + -
106E VAL 3.2 8.3 - - - +
107E ARG* 3.5 35.6 - - + -
108E TYR* 3.6 14.9 - - - -
239E VAL* 4.2 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ILE* 3.6 37.0 - - + -
44E LEU* 3.9 17.9 - - + -
46E PHE 3.3 7.9 - - - +
47E ASN* 3.5 16.6 - - - +
48E VAL* 4.6 0.4 - - - -
51E TYR* 1.3 74.3 - - - +
53E LEU* 1.3 75.6 + - - +
54E THR* 4.0 4.3 - - + -
66E TRP* 4.2 10.3 - - + -
85E LEU* 4.1 25.1 - - + -
105E ILE* 3.4 4.3 - - - +
106E VAL* 2.9 73.4 + - + -
108E TYR* 3.7 23.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E GLY* 2.7 35.3 + - - -
46E PHE* 2.8 20.7 + - + +
48E VAL* 4.0 14.6 - - + -
52E PHE* 1.3 78.1 - - - +
54E THR* 1.3 56.4 + - - +
104E GLY 3.5 14.8 - - - +
105E ILE* 4.1 24.5 - - + -
212E LEU* 3.9 15.9 - - + -
231E VAL* 3.7 29.2 - - + -
234E ALA* 4.3 15.7 - - + -
235E LEU* 4.0 20.4 - - + -
237E TYR* 4.2 11.9 - - + -
239E VAL* 5.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ILE* 3.8 14.5 - - + +
42E CYS* 4.3 5.5 - - - +
43E SER 2.9 22.9 + - - -
52E PHE* 4.0 17.3 - - + -
53E LEU* 1.3 77.7 - - - +
55E ALA* 1.3 69.8 + - - +
58E CYS* 4.3 5.1 - - + +
59E THR* 3.7 27.4 - - + -
66E TRP* 5.0 1.3 - - + -
103E TYR* 3.6 4.3 - - - -
104E GLY 3.0 23.3 + - - +
106E VAL* 4.7 2.5 - - + -
195E SER 4.3 1.6 + - - -
196E GLY* 3.6 13.0 - - - -
212E LEU* 3.8 11.2 - - - +
----------------------------------------------------------
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