Contacts of the strand formed by residues 141 - 150 (chain B) in PDB entry 5JES
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 LEU 141 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TYR* 3.6 7.1 - - - -
121B THR* 4.3 9.4 - - + -
122B HIS 3.2 15.3 - - - +
123B TRP* 3.6 16.8 - - + -
131B PHE* 3.7 22.9 - - + -
134B ALA* 4.4 1.8 - - + -
135B VAL* 3.9 15.5 - - + -
139B ASP 4.6 0.5 - - - -
140B GLY* 1.3 86.6 + - - +
142B ALA* 1.3 63.8 + - - +
143B VAL* 4.7 1.6 - - + -
198B LEU* 3.4 32.3 - - + -
206B CYS* 2.8 20.8 + - - +
207B VAL* 4.1 9.9 - - + -
208B THR* 2.9 27.2 + - - -
302B EVF 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 4.0 11.0 - - + -
84B LEU* 3.9 27.1 - - + -
88B TYR* 3.6 25.3 - - + -
122B HIS* 2.9 37.6 + - - -
141B LEU* 1.3 73.9 - - - +
143B VAL* 1.3 62.1 + - - +
144B LEU 4.1 0.2 - - - -
208B THR 3.3 7.4 - - - +
210B ILE* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 5.4 0.4 - - - -
119B HIS* 3.7 22.7 - - + -
120B LEU 3.4 10.5 - - - +
121B THR* 4.3 17.7 - - + +
141B LEU* 4.7 2.7 - - + -
142B ALA* 1.3 76.7 - - - +
144B LEU* 1.3 64.0 + - - +
207B VAL* 3.6 24.2 - - + -
208B THR 3.2 6.7 + - - +
209B TRP* 3.3 38.4 - - + -
210B ILE* 3.0 28.2 + - - +
302B EVF 3.8 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.0 7.0 - - + -
49B VAL* 4.4 17.7 - - + -
51B TYR* 4.2 11.4 - - - +
79B LEU* 4.6 10.5 - - + +
118B LEU 3.4 4.3 - - - +
119B HIS* 3.5 0.7 - - - -
120B LEU* 2.9 61.2 + - + +
122B HIS* 4.2 6.7 + - + -
142B ALA 4.1 1.0 - - - -
143B VAL* 1.3 71.6 - - - +
145B GLY* 1.3 59.1 + - - +
146B ILE* 4.4 5.8 - - + -
185B LEU* 4.4 15.5 - - + -
189B LEU* 6.0 0.4 - - + -
210B ILE* 3.3 26.5 - - + +
212B LEU* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLU* 4.5 7.2 - - - -
118B LEU 3.2 6.7 - - - -
119B HIS* 4.0 12.6 - - - -
143B VAL 3.7 2.4 + - - -
144B LEU* 1.3 71.4 - - - +
146B ILE* 1.3 66.5 + - - +
209B TRP* 4.6 4.4 - - - -
210B ILE 2.8 13.4 + - - +
211B VAL* 3.5 10.7 - - - +
212B LEU* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLU* 3.3 4.1 - - - +
118B LEU* 2.8 44.5 + - + +
120B LEU* 3.8 19.3 - - + -
144B LEU* 4.4 5.4 - - + -
145B GLY* 1.3 80.9 - - - +
147B PHE* 1.3 74.1 - - - +
148B LEU* 3.5 2.1 - - - +
184B LEU 3.9 11.0 - - - +
185B LEU* 3.7 30.5 - - + -
186B PRO* 4.0 7.4 - - + -
212B LEU* 3.7 23.1 - - + +
214B GLU 4.5 4.9 - - - +
216B ILE* 3.9 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.7 0.4 - - + -
105B SER* 4.0 10.5 - - - -
107B HIS* 3.4 33.2 - - + -
109B VAL* 3.5 30.3 - - + -
114B TYR* 3.5 40.8 - + + -
116B ALA 3.7 1.8 - - - -
117B GLU* 3.6 17.3 - - + -
146B ILE* 1.3 76.2 - - - +
148B LEU* 1.3 60.4 + - - +
192B TRP* 4.5 2.9 - + - -
211B VAL* 3.6 30.5 - - + -
212B LEU 3.7 16.0 + - - -
213B LYS 4.8 6.3 - - - -
214B GLU 5.0 0.2 + - - -
215B PRO* 3.2 9.5 - - + +
216B ILE* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 3.9 20.0 - - + -
114B TYR* 3.4 6.1 - - - +
115B ALA* 3.1 26.8 + - + +
116B ALA* 2.9 34.1 + - + +
117B GLU* 4.3 0.9 - - - -
118B LEU* 3.9 20.0 - - + +
146B ILE 3.5 16.8 - - - +
147B PHE* 1.3 76.5 - - - +
149B LYS* 1.3 60.5 + - - +
157B LEU* 4.9 2.2 - - + -
216B ILE* 3.3 28.9 - - + +
218B VAL* 3.7 31.2 - - + -
223B VAL* 6.3 1.1 - - + -
226B PHE* 4.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS* 6.2 0.7 - - - -
114B TYR* 4.2 15.9 - - + -
115B ALA* 4.6 3.6 - - - +
147B PHE 4.2 0.2 - - - -
148B LEU* 1.3 75.2 - - - +
150B VAL* 1.3 65.8 + - - +
151B GLY* 6.1 0.9 - - - -
215B PRO* 4.3 22.3 - - + +
216B ILE 2.9 15.3 + - - +
217B SER* 3.3 18.4 - - - +
218B VAL* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASP* 3.6 38.8 - - + +
115B ALA* 3.9 16.7 - - + +
149B LYS* 1.3 80.4 - - - +
151B GLY* 1.3 60.9 + - - +
217B SER* 4.3 0.4 - - - -
218B VAL* 3.2 9.2 - - + +
220B SER* 3.5 33.7 - - - +
223B VAL* 4.1 14.4 - - + -
----------------------------------------------------------
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