Contacts of the strand formed by residues 136 - 141 (chain O) in PDB entry 5DST
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 LYS 136 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O LYS 3.6 3.3 + - - +
114O VAL* 3.4 14.1 - - + +
115O VAL* 3.0 23.7 + - - +
135O LYS* 1.3 97.6 - - + +
137O VAL* 1.3 65.5 + - - +
138O PHE* 4.2 27.3 - - + -
159O ASP 5.1 1.0 + - - -
160O ASN 3.3 22.4 + - - -
161O ILE 3.1 22.7 + - - -
163O THR* 3.7 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115O VAL* 3.3 18.4 - - + +
117O ASP* 4.8 2.2 - - + -
126O SER* 3.6 37.0 - - - +
129O ALA* 3.9 6.1 - - + -
130O ALA* 3.9 18.2 - - + +
134O ALA* 3.7 22.0 - - + -
136O LYS* 1.3 79.9 - - - +
138O PHE* 1.3 71.2 + - - +
161O ILE* 3.0 16.4 + - + +
162O ILE* 3.3 11.5 - - + +
163O THR 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114O VAL* 4.0 16.6 - - + -
115O VAL 2.7 11.8 + - - +
116O LEU* 3.3 10.6 - - + +
117O ASP 2.8 30.8 + - - -
136O LYS* 4.2 35.9 - - + -
137O VAL* 1.3 82.2 - - - +
139O GLY* 1.3 53.6 + - - +
163O THR* 3.5 11.2 - - - -
165O PHE* 3.9 24.7 - + + -
174O LEU* 4.0 26.9 - - + -
175O PRO* 3.5 28.3 - - + -
176O VAL* 3.9 30.3 - - + -
179O VAL* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 139 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O ASP* 3.5 11.9 - - - -
120O SER* 3.7 18.2 - - - -
126O SER* 4.2 2.1 + - - -
137O VAL* 4.1 0.8 - - - +
138O PHE* 1.3 73.4 - - - +
140O ILE* 1.3 63.0 + - - +
162O ILE* 5.1 0.2 - - - +
163O THR 3.1 9.1 + - - -
164O ILE* 3.3 13.7 - - - +
165O PHE* 2.8 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116O LEU* 3.6 28.3 - - + -
117O ASP 3.2 8.8 + - - +
118O VAL* 5.8 0.9 - - + -
119O GLY* 3.1 12.8 + - - -
120O SER 2.9 20.0 + - - -
139O GLY* 1.3 77.0 - - - +
141O GLU* 1.3 64.2 + - - +
165O PHE* 3.6 11.9 - - + +
167O GLY 3.4 17.5 - - - +
169O VAL* 3.5 37.0 - - + -
172O VAL* 3.7 29.4 - - + -
174O LEU* 4.4 8.3 - - + -
207O TRP* 4.0 18.2 - - + -
401O SAH 4.0 2.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119O GLY 3.6 2.6 - - - -
120O SER* 3.4 15.7 - - - +
121O GLY 2.9 20.5 + - - +
139O GLY 4.2 0.2 - - - -
140O ILE* 1.3 78.2 - - - +
142O CYS* 1.3 63.5 + - - +
143O SER* 3.0 26.7 + - - +
145O ILE* 3.6 22.9 - - + -
146O SER* 4.0 13.8 - - - +
164O ILE* 4.9 0.9 - - + -
165O PHE 3.3 4.8 + - - +
166O LYS* 3.5 8.5 - - - +
167O GLY 2.9 21.8 + - - -
401O SAH 2.2 58.3 + - - -
----------------------------------------------------------
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