Contacts of the strand formed by residues 150 - 156 (chain O) in PDB entry 2DYS
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 ILE 150 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O PRO* 4.1 2.5 - - - -
94O SER* 6.5 0.2 - - - -
95O LEU* 3.6 30.7 - - + +
97O VAL* 4.2 11.2 - - + -
144O LEU* 4.0 22.4 - - + -
145O PRO* 3.8 33.0 - - + +
148O MET* 3.6 13.7 - - + +
149O THR* 1.3 76.2 - - - +
151O ARG* 1.3 71.1 + - - +
152O MET* 3.8 7.1 + - + +
183O THR* 3.3 6.6 - - - -
184O LEU* 2.8 60.1 + - + +
185O MET* 5.3 0.4 - - - -
186O SER 5.6 0.4 - - - +
213O LEU* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O PRO* 3.4 42.2 - - + +
95O LEU 2.9 9.1 + - - -
96O THR* 3.2 33.2 + - - +
97O VAL 2.9 27.4 + - - +
150O ILE* 1.3 73.1 - - - +
152O MET* 1.3 61.0 + - - +
153O LEU* 4.1 13.2 - - + -
181O GLN* 3.1 42.9 - - + +
182O THR 3.8 3.1 - - - +
183O THR* 4.7 5.8 - - + +
14U ALA* 2.7 33.7 + - - +
15U PRO 3.9 1.4 + - - -
16U PHE* 3.8 20.2 - - - +
63U LEU* 3.8 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 152 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O VAL* 3.3 36.6 - - + +
98O LYS 4.7 0.9 - - - -
99O THR* 3.7 30.7 - - + +
108O TYR* 4.8 2.9 - - + -
142O VAL* 5.5 1.8 - - - -
144O LEU* 5.3 6.3 - - - -
150O ILE* 3.8 5.1 + - + -
151O ARG* 1.3 73.7 - - - +
153O LEU* 1.3 63.9 + - - +
154O VAL* 5.1 1.1 - - + -
163O TRP* 3.7 36.6 - - + -
180O ASN 3.6 0.9 - - - +
181O GLN* 3.4 4.5 - - - +
182O THR* 2.8 52.3 + - + +
184O LEU* 3.9 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O THR* 3.6 25.6 - - + -
97O VAL 2.9 6.9 + - - -
98O LYS* 3.3 17.0 - - + +
99O THR* 2.9 30.1 + - - +
151O ARG* 4.1 5.6 - - + -
152O MET* 1.3 76.6 - - - +
154O VAL* 1.3 59.7 + - - +
179O LEU* 3.9 16.4 - - + -
180O ASN 3.2 3.8 - - - +
181O GLN* 3.5 42.2 - - + +
25U GLN* 4.1 11.4 - - + -
63U LEU* 3.8 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O THR* 3.5 24.0 - - + -
106O TRP* 4.6 0.9 - - + -
152O MET* 4.9 5.4 - - + +
153O LEU* 1.3 79.8 - - - +
155O SER* 1.3 68.3 + - - +
163O TRP* 4.0 19.3 - - + -
172O THR* 3.8 39.0 - - + +
173O ASP 3.7 4.8 - - - +
174O ALA* 3.4 30.3 - - + -
175O ILE 5.0 0.3 + - - -
178O ARG 3.4 1.9 - - - +
179O LEU* 3.6 1.2 - - - -
180O ASN* 2.7 39.3 + - - +
182O THR* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O THR 3.2 7.2 + - - +
100O MET* 3.4 25.8 - - - +
101O GLY 2.8 19.0 + - - -
154O VAL* 1.3 73.2 - - - +
156O SER* 1.3 73.5 + - - +
174O ALA* 3.1 16.5 - - - +
175O ILE 3.4 8.0 + - - -
177O GLY 4.3 1.0 + - - -
178O ARG 2.9 25.6 + - - -
179O LEU* 4.5 9.9 - - - -
68U TRP* 3.9 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 156 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O MET* 3.8 3.4 - - - +
101O GLY 3.4 13.7 + - - +
155O SER* 1.3 84.3 + - - +
157O GLU* 1.3 68.9 + - - +
158O ASP* 2.9 11.1 + - - -
159O VAL 2.6 28.0 + - - -
161O HIS* 4.1 2.9 - - - -
174O ALA* 3.4 21.5 - - - -
175O ILE 3.8 3.2 + - - -
176O PRO* 3.4 21.9 - - - +
177O GLY 4.4 1.4 + - - -
68U TRP* 5.4 1.4 + - - -
----------------------------------------------------------
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