Contacts of the strand formed by residues 153 - 161 (chain B) in PDB entry 4OA5
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 153 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 5.2 0.7 - - + -
129B PRO* 4.5 1.1 - - - -
130B PHE* 3.4 27.6 - - + +
131B ASP 4.0 3.8 - - - +
132B MET 3.7 24.9 - - - +
133B ILE* 3.8 14.1 - - + +
148B TRP* 4.3 9.2 - - + -
149B ALA* 2.9 35.0 + - + +
150B LYS 4.5 0.3 - - - +
151B MET 4.6 1.9 - - - +
152B TYR* 1.3 80.3 + - - +
154B ARG* 1.3 70.2 + - - +
157B GLY* 3.8 21.8 - - - -
158B LEU 4.1 6.7 - - - +
159B ILE* 4.9 1.6 - - + -
216B LYS* 2.8 34.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA* 4.4 14.6 + - - +
56B GLY 5.2 3.4 + - - -
57B ILE* 4.6 5.5 - - - +
129B PRO* 3.9 15.2 - - + +
130B PHE 3.0 20.2 + - - +
131B ASP* 2.8 34.1 + - - +
153B ILE* 1.3 79.2 - - - +
155B LYS* 1.3 81.1 + - - +
156B GLY* 3.4 22.4 + - - -
157B GLY* 2.9 28.6 + - - +
216B LYS* 3.7 5.7 - - - +
306B IOD 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE 3.7 0.8 + - - -
154B ARG* 1.3 94.8 + - - +
156B GLY* 1.3 61.2 + - - +
216B LYS* 4.0 3.2 - - - +
217B LEU 3.6 19.7 + - - +
218B THR* 3.4 36.0 - - - +
303B IOD 4.6 0.2 - - + -
306B IOD 3.5 17.3 - - + +
315B IOD 3.9 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA* 5.9 2.3 - - - +
57B ILE* 5.9 0.5 - - - +
154B ARG* 3.4 16.5 + - - -
155B LYS* 1.3 72.4 - - - +
157B GLY* 1.3 61.5 + - - +
158B LEU* 4.8 4.2 - - - +
215B ILE* 3.9 10.8 - - - +
216B LYS 2.7 21.3 + - - -
303B IOD 3.7 21.5 - - - -
315B IOD 3.9 2.9 - - - -
316B IOD 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 5.5 0.4 - - - -
131B ASP 3.2 15.0 - - - -
153B ILE* 3.8 9.0 - - - -
154B ARG* 2.9 26.5 + - - -
155B LYS 3.2 1.6 + - - -
156B GLY* 1.3 80.6 - - - +
158B LEU* 1.3 61.9 + - - -
215B ILE* 3.5 2.8 - - - -
216B LYS* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.2 11.7 - - + +
55B ALA* 3.9 15.0 - - + -
57B ILE* 4.1 19.3 - - + -
131B ASP 2.9 7.5 + - - -
132B MET* 3.2 22.3 - - + -
133B ILE* 3.0 26.0 + - - +
153B ILE* 4.1 2.5 - - - +
156B GLY 4.8 3.1 - - - +
157B GLY* 1.3 74.4 - - - +
159B ILE* 1.3 64.2 + - - +
160B VAL* 4.0 11.0 - - + -
213B VAL* 5.0 3.8 - - + -
214B SER 3.3 12.8 - - - +
215B ILE* 3.8 22.4 - - + -
54C MET* 3.9 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE* 3.8 22.0 - - + -
135B ILE* 4.5 13.0 - - + -
146B LEU* 3.9 31.4 - - + -
149B ALA* 4.2 12.8 - - + -
150B LYS* 5.4 0.4 - - + +
153B ILE* 4.9 4.3 - - + -
157B GLY 4.1 0.2 + - - -
158B LEU* 1.3 76.6 - - - +
160B VAL* 1.3 61.4 + - - +
190B PHE* 4.6 4.7 - - + -
194B LEU* 4.2 15.9 - - + -
200B TYR* 4.1 22.0 - - + -
212B MET* 3.8 2.9 - - + +
213B VAL* 3.7 1.9 + - - -
214B SER* 2.8 45.9 + - - +
216B LYS* 4.3 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.9 18.8 - - + -
51B LEU* 4.4 13.2 - - + -
132B MET* 3.8 21.1 - - + -
133B ILE 2.9 11.2 + - - +
134B PHE* 3.2 21.0 - - + -
135B ILE* 2.8 32.2 + - - +
158B LEU* 4.3 14.4 - - + -
159B ILE* 1.3 79.1 - - - +
161B ALA* 1.3 59.5 + - - +
211B MET* 3.9 12.1 - - + -
212B MET* 3.2 13.0 - - - +
213B VAL* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 4.5 1.3 - - - -
135B ILE* 3.2 18.8 - - + +
142B TYR* 3.8 13.2 - - + -
160B VAL* 1.3 77.4 - - - +
162B ASP* 1.3 62.9 + - - +
164B THR* 3.6 6.8 - - + +
190B PHE* 3.7 30.5 - - + -
211B MET* 3.5 5.5 - - - -
212B MET* 2.8 38.9 + - + -
----------------------------------------------------------
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