Contacts of the strand formed by residues 137 - 141 (chain O) in PDB entry 3DXA
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 GLU 137 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142N SER* 5.8 0.2 + - - -
135O PRO* 5.2 5.2 - - + +
136O PRO* 1.3 77.4 - - - +
138O VAL* 1.3 62.8 + - - +
139O ALA* 5.5 0.2 - - - +
159O LEU 3.8 2.4 - - - +
160O ALA* 3.8 0.7 - - - -
161O THR* 2.7 43.7 + - - +
162O GLY 4.7 4.1 + - - +
200O ARG* 4.7 12.0 + - - +
248O VAL* 4.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141N SER* 5.5 0.5 + - - -
136O PRO* 4.6 2.5 - - + -
137O GLU* 1.3 76.1 - - - +
139O ALA* 1.3 65.0 + - - +
158O CYS* 3.8 24.2 - - - -
159O LEU 4.0 3.6 - - - +
160O ALA* 3.8 8.5 - - + -
223O CYS* 3.8 7.6 - - - +
225O VAL* 3.3 32.5 - - + -
248O VAL* 3.3 31.0 - - + +
249O SER 4.2 6.7 - - - +
250O ALA* 3.5 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139N SER* 3.3 26.0 - - - +
141N SER* 4.3 9.4 - - - +
142N SER* 3.5 17.9 - - - +
137O GLU 4.0 0.6 + - - +
138O VAL* 1.3 77.8 - - - +
140O VAL* 1.3 60.3 + - - +
141O PHE* 3.9 8.7 - - + -
158O CYS* 3.7 3.3 - - - -
159O LEU 3.2 31.3 + - - +
250O ALA* 3.6 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138N ASP* 3.3 19.0 - - - +
139N SER* 3.3 10.0 + - - +
139O ALA* 1.3 76.8 - - - +
141O PHE* 1.3 68.8 + - - +
156O LEU* 4.7 6.5 - - + -
157O VAL 3.1 22.9 - - - +
158O CYS* 4.5 0.9 - - - +
172O TRP* 4.1 20.0 - - + -
221O PHE* 5.4 0.9 - - + +
223O CYS* 4.7 9.0 - - + +
250O ALA* 3.8 12.0 - - + +
251O GLU 3.2 30.5 - - - +
252O ALA* 3.6 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136N LEU* 3.9 23.6 - - + +
137N ARG 3.8 1.1 - - - -
138N ASP* 3.4 15.0 - - - +
139N SER* 3.9 22.0 - - - -
142N SER* 4.6 12.6 - - - -
144N LYS* 2.8 33.9 - - - -
146N VAL* 3.1 33.4 - - + -
189N TRP* 6.0 0.9 - + - -
139O ALA* 3.9 16.8 - - + -
140O VAL* 1.3 79.7 - - - +
142O GLU* 1.3 66.4 + - - +
143O PRO 3.7 0.5 - - - -
156O LEU* 4.0 3.5 - - - +
157O VAL 3.0 36.7 + - - +
159O LEU* 3.7 21.8 - - + -
----------------------------------------------------------
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