Contacts of the strand formed by residues 134 - 140 (chain D) in PDB entry 4JRY
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 ALA 134 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ASP 3.9 5.6 - - - +
133D PRO* 1.3 75.4 - - - +
135D VAL* 1.3 64.6 + - - +
136D TYR* 3.5 36.8 - - + +
150D LEU 3.5 1.3 - - - +
151D PHE* 3.3 6.6 - - - -
152D THR* 3.0 32.1 + - - +
212D THR* 4.2 2.6 - - - -
213D PHE* 3.2 24.9 - - + +
149E HIS* 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ALA* 1.3 75.3 - - - +
136D TYR* 1.3 66.8 + - - +
149D CYS* 4.4 2.0 - - + -
150D LEU 3.3 6.3 - - - +
151D PHE* 3.8 15.5 - - + -
199D CYS* 3.5 37.2 - - + +
203D PHE* 3.7 35.0 - - + -
208D ILE* 5.3 0.7 - - + -
212D THR* 4.7 1.1 - - - +
213D PHE 3.1 6.7 + - - +
214D PHE* 3.8 33.1 - - + -
215D PRO* 3.2 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ASP 5.0 1.4 + - - -
134D ALA* 3.5 19.1 - - + +
135D VAL* 1.3 73.7 - - - +
137D GLN* 1.3 60.1 + - - +
138D LEU* 3.9 8.0 - - + +
149D CYS* 3.3 4.3 - - - -
150D LEU* 2.8 42.5 + - + +
152D THR* 3.5 32.7 - - + +
153D ASP* 5.7 0.2 - - - -
199D CYS* 3.7 5.4 - - - -
213D PHE* 4.1 4.9 - + - -
215D PRO* 3.7 25.1 - - + -
143E SER* 3.5 26.5 - - - +
145E ALA* 3.9 5.2 - - + -
146E GLU* 3.4 38.0 - - + +
149E HIS* 3.3 22.3 + - - -
150E THR* 3.3 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D TYR* 1.3 73.6 - - - +
138D LEU* 1.3 66.2 + - - +
139D ARG* 3.9 29.3 + - - +
147D SER* 3.3 24.9 + - - +
148D VAL 3.7 2.2 - - - +
149D CYS* 4.7 0.7 - - - -
199D CYS* 3.4 24.0 - - + +
143E SER* 3.2 22.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D TYR* 3.9 11.4 - - + +
137D GLN* 1.3 79.0 - - - +
139D ARG* 1.3 63.3 + - - +
147D SER* 3.4 8.8 + - - -
148D VAL* 2.9 42.3 + - + +
150D LEU* 3.6 35.4 - - + -
140E PHE* 3.8 17.4 - - + +
141E GLU 2.9 26.7 - - - +
142E PRO* 3.5 5.8 - - + -
143E SER 3.8 5.6 - - - +
146E GLU* 4.9 2.2 - - - +
154E THR 3.3 25.8 - - - +
156E VAL* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D GLN* 3.9 30.4 + - - +
138D LEU* 1.3 79.2 - - - +
140D ASP* 1.4 67.8 + - - +
141D SER 3.3 0.5 + - - -
143D SER 5.0 4.9 - - - +
144D SER* 5.0 15.4 + - - +
145D ASP 4.1 6.5 - - - -
147D SER* 5.0 2.9 - - - -
140E PHE* 3.8 3.6 - - - -
141E GLU* 2.8 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ARG* 1.4 73.0 - - - +
141D SER* 1.4 67.4 + - - +
142D LYS* 3.4 22.7 + - - +
143D SER* 2.8 36.6 + - - +
145D ASP* 3.0 42.6 + - + +
138E ALA* 4.0 15.5 - - - +
139E VAL 3.1 16.3 + - - +
140E PHE* 3.3 20.5 - - + -
----------------------------------------------------------
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