Contacts of the strand formed by residues 146 - 151 (chain O) in PDB entry 3SDI
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 GLY 146 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140O GLY 3.8 0.7 - - - +
141O HIS* 3.3 19.9 - - - -
142O ASP* 2.9 33.2 + - - +
143O GLU 4.3 2.7 + - - -
144O PHE 3.6 2.4 - - - -
145O ASN* 1.3 78.3 - - - +
147O PHE* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O LYS* 3.6 23.1 + - + +
42O ALA 5.0 1.8 - - - +
43O THR 3.8 14.8 - - - -
44O ASN* 3.6 31.0 - - + -
45O GLY* 3.8 11.9 - - - +
46O VAL* 3.8 16.8 - - + -
140O GLY 3.4 2.5 - - - -
141O HIS* 3.9 33.7 - + + -
145O ASN 3.6 5.7 + - - +
146O GLY* 1.3 73.3 - - - -
147O SER* 1.3 64.3 - - - +
215O ILE* 3.5 27.4 - - + -
216O GLY 3.9 16.2 - - - -
217O ASP* 5.6 1.6 - - - -
220O ARG* 4.6 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 147 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O LYS* 3.8 13.4 - - + +
46O VAL* 3.7 6.5 - - - +
109O THR* 3.6 19.6 - - - +
139O ALA* 3.5 2.3 - - - -
140O GLY 2.8 34.6 + - - +
142O ASP* 4.8 2.4 - - - +
145O ASN* 5.3 5.7 - - + +
146O GLY 4.0 4.6 - - - +
147O PHE* 1.3 78.4 - - - +
148O LEU* 1.3 63.0 + - - +
149O TYR* 3.5 23.4 - - + +
159O PRO* 6.1 0.9 - - + -
63P THR* 6.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O GLY* 3.5 43.3 - - - +
40O ILE 4.3 0.7 - - - +
41O LYS* 4.2 7.9 - - + +
46O VAL* 4.1 10.1 - - + -
48O ILE* 4.1 7.6 - - + -
137O LEU* 4.5 9.9 - - + -
138O ILE 3.5 7.6 - - - +
139O ALA* 4.0 21.3 - - + -
147O SER* 1.3 77.1 - - - +
149O TYR* 1.3 68.6 + - - +
159O PRO* 3.2 7.8 - - - +
160O TRP* 3.0 54.9 + - + +
161O LYS 4.2 3.1 - - - +
162O ALA* 4.2 6.1 - - - -
163O THR* 4.4 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109O THR* 4.0 22.4 - - + -
110O LYS* 3.5 30.7 - - + +
113O VAL* 4.0 23.3 - - + -
136O LEU 3.6 0.3 - - - +
137O LEU* 3.3 6.6 - - - +
138O ILE* 2.8 35.3 + - + +
147O SER* 3.5 27.4 - - + +
148O LEU* 1.3 80.3 - - - +
150O GLN* 1.3 61.5 + - - +
151O VAL* 4.3 0.8 + - + -
157O TYR* 4.0 23.6 - + - -
158O PHE 3.2 19.5 - - - -
159O PRO* 3.7 22.4 - - + -
160O TRP* 4.6 2.7 - - - +
63P THR* 4.1 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 150 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135O SER* 5.0 1.1 - - - -
136O LEU 3.2 5.6 - - - +
137O LEU* 3.6 16.6 - - + -
149O TYR* 1.3 74.1 - - - +
151O VAL* 1.3 63.8 + - - +
152O ASP* 2.9 33.5 + - - +
156O SER 3.7 0.5 - - - +
157O TYR* 3.0 25.6 - - - +
158O PHE* 2.9 26.2 + - + -
160O TRP* 3.4 35.2 + - + +
163O THR* 3.9 10.0 + - - +
164O ALA 5.0 0.2 - - - +
165O ILE* 3.7 25.3 - - + +
----------------------------------------------------------
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