Contacts of the strand formed by residues 37 - 45 (chain A) in PDB entry 5I2S
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 37 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP 3.9 13.0 - - - +
36A LEU* 1.3 73.8 - - - +
38A GLY* 1.3 70.5 + - - +
39A THR* 4.8 2.2 - - + -
188A PHE 3.5 1.9 - - - +
189A PHE* 3.2 3.2 - - - -
190A SER* 2.8 38.3 + - - +
191A GLU* 3.2 24.2 - - - +
192A ASP 5.4 0.2 - - - -
193A GLY* 3.6 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU 4.1 0.6 + - - -
37A ILE* 1.3 80.4 - - - +
39A THR* 1.3 67.7 + - - +
187A THR* 3.8 19.3 - - - -
188A PHE 3.5 5.2 - - - -
189A PHE* 3.8 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 4.8 2.2 - - + -
38A GLY* 1.3 78.9 - - - +
40A ALA* 1.3 63.6 + - - +
187A THR* 3.3 8.8 - - - +
188A PHE* 2.9 37.9 + - - -
193A GLY* 3.3 35.2 + - - +
194A GLU* 5.2 0.7 - - - -
195A LEU* 3.7 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 1.3 77.9 + - - +
41A LEU* 1.3 62.4 + - - +
42A GLN* 6.0 0.9 - - + -
185A ASP* 4.4 20.9 - - + +
186A ILE 3.6 6.3 - - - +
187A THR* 4.8 0.2 - - - +
195A LEU* 4.0 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 1.3 74.6 - - - +
42A GLN* 1.3 68.4 + - - +
43A VAL* 3.4 20.5 + - + -
185A ASP* 3.4 3.3 - - - -
186A ILE* 2.8 48.4 + - + +
188A PHE* 4.4 11.2 - - + -
195A LEU* 3.8 29.6 - - + -
198A LEU* 4.3 10.8 - - + -
205A PHE* 3.8 29.2 - - + -
237A PHE* 4.3 5.4 - - + -
239A MET* 3.9 27.4 - - + -
241A ASP* 6.4 0.2 - - + -
244A LEU* 4.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 6.0 1.1 - - + -
41A LEU* 1.3 76.6 - - - +
43A VAL* 1.3 64.0 + - - +
183A SER* 6.6 0.4 - - - -
184A MET 3.7 1.6 - - - +
185A ASP* 3.3 19.1 - - - +
239A MET* 3.9 1.4 - - - +
240A ALA* 3.0 43.6 + - + +
241A ASP* 4.6 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.8 18.4 - - + +
42A GLN* 1.3 80.7 - - - +
44A LYS* 1.3 64.9 + - - +
45A MET* 4.4 3.6 - - + -
183A SER* 3.3 6.1 - - - -
184A MET* 2.9 48.7 + - + +
186A ILE* 3.6 35.4 - - + -
237A PHE* 3.5 36.6 - - + -
238A GLU 3.1 12.8 - - - +
239A MET* 4.4 2.7 - - - -
240A ALA* 4.2 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 1.3 79.6 - - - +
45A MET* 1.3 64.3 + - - +
181A LEU* 3.7 30.5 - - + +
182A ILE 3.2 7.0 - - - +
183A SER* 3.8 19.8 + - - +
236A TRP* 4.2 3.1 - - - -
237A PHE* 3.5 0.7 - - - -
238A GLU* 2.8 52.5 + - + +
240A ALA* 4.6 15.9 - - - +
242A LYS* 4.2 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 4.4 3.8 - - + -
44A LYS* 1.3 80.8 - - - +
46A PRO* 1.3 77.7 - - + +
47A LYS 3.5 1.0 + - - -
50A LYS* 5.7 8.3 - - - +
139A TYR* 3.1 24.9 - - - +
181A LEU* 3.9 4.9 - - - -
182A ILE* 2.9 30.4 + - - +
184A MET* 4.1 28.4 - - + +
186A ILE* 4.4 10.1 - - - -
207A SER* 5.5 1.1 - - - -
209A TYR* 6.4 2.2 - - + -
210A PHE* 4.0 22.0 - - + -
235A VAL* 3.7 20.4 - - + -
236A TRP 3.3 7.2 - - - +
237A PHE* 3.4 19.3 - - + -
262A PRO* 6.2 1.8 - - + -
----------------------------------------------------------
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