Contacts of the strand formed by residues 210 - 220 (chain o) in PDB entry 4IL6
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 210 (chain o).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22o LEU* 3.6 26.9 - - + +
204o VAL* 4.2 0.2 - - - +
205o ASP* 2.8 32.6 + - + +
208o THR* 2.8 34.3 + - - +
209o GLY* 1.3 82.2 - - - +
211o ILE* 1.3 64.5 + - - +
240o TYR* 2.7 37.5 + - + +
241o ALA 3.4 5.4 - - - +
242o SER* 4.2 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22o LEU* 3.8 1.8 - - - -
30o TYR* 5.6 1.3 - - + -
40o ILE* 5.9 1.8 - - + -
136o ILE* 3.9 23.8 - - + -
142o PHE* 4.3 16.4 - - + -
201o VAL* 4.1 19.5 - - + -
203o LYS 3.3 6.3 - - - +
204o VAL* 4.0 17.7 - - + -
209o GLY 5.2 0.7 - - - -
210o GLU* 1.3 81.6 - - - +
212o ALA* 1.3 62.2 + - - +
239o PHE* 4.1 15.0 - - + -
240o TYR* 3.4 5.7 - - - -
241o ALA* 2.7 59.7 + - + +
243o ILE* 4.1 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20o PRO 5.0 5.6 - - - +
21o THR* 5.2 1.1 - - - -
22o LEU* 3.8 27.6 - - + +
201o VAL* 3.7 2.1 - - - -
202o ALA* 2.8 20.5 + - - -
203o LYS* 2.9 25.6 + - + +
211o ILE* 1.3 76.7 - - - +
213o GLY* 1.3 59.5 + - - +
239o PHE* 3.3 22.0 - - - +
240o TYR* 4.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 213 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200o ASN 3.3 12.8 - - - -
202o ALA* 3.7 13.9 - - - -
212o ALA* 1.3 77.5 - - - +
214o THR* 1.3 61.3 + - - -
238o VAL* 3.2 9.3 - - - +
239o PHE* 2.7 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200o ASN* 3.0 43.5 + - - +
202o ALA* 5.0 5.5 - - + +
213o GLY* 1.3 77.5 - - - +
215o PHE* 1.3 63.1 + - - +
237o GLY 3.2 12.8 - - - +
238o VAL* 4.4 10.8 - - + -
239o PHE* 3.4 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45o LEU* 3.9 15.9 - - + -
46o GLN 3.7 9.2 - - - -
47o PRO* 4.1 4.9 - - + -
120o PHE* 3.8 28.3 - + - -
197o ILE* 3.9 15.9 - - + -
198o SER 3.2 13.0 - - - +
199o LEU* 4.2 16.2 - - + -
214o THR* 1.3 76.6 - - - +
216o GLU* 1.3 68.0 + - - +
217o SER* 4.4 4.0 - - - -
235o ILE* 3.7 30.1 - - + -
236o GLN* 3.4 5.5 - - - +
237o GLY* 2.9 51.0 + - - +
238o VAL 3.4 29.6 - - - -
239o PHE* 4.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196o GLN 4.2 0.2 - - - +
197o ILE* 3.3 3.3 - - - -
198o SER* 2.9 37.6 + - - +
215o PHE* 1.3 74.8 - - - +
217o SER* 1.3 64.5 + - - +
218o GLU* 4.5 7.9 - - + +
234o LYS* 3.4 40.0 + - + +
235o ILE 3.3 4.0 - - - -
236o GLN* 3.2 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 217 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120o PHE* 4.9 4.4 - - - -
121o THR 4.8 1.2 + - - -
146o PHE* 3.2 30.3 - - - -
196o GLN 3.2 6.8 + - - -
197o ILE* 3.8 16.3 - - - +
215o PHE* 4.1 8.0 - - - -
216o GLU* 1.3 76.7 - - - +
218o GLU* 1.3 65.9 + - - +
219o GLN* 4.7 1.0 + - - -
233o VAL 3.7 0.2 - - - +
234o LYS* 3.3 5.5 - - - +
235o ILE* 2.8 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53o LYS* 5.7 0.2 + - - -
65o PHE* 3.8 24.5 - - - -
146o PHE* 4.0 0.7 - - - -
194o LYS 4.7 0.2 - - - +
195o GLY* 3.2 5.4 - - - -
196o GLN* 2.8 48.6 + - + +
216o GLU* 4.5 7.0 - - + +
217o SER* 1.3 77.1 + - - +
219o GLN* 1.3 62.1 + - - +
232o GLU* 4.5 9.0 - - - +
233o VAL 3.3 8.4 - - - +
234o LYS* 4.1 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 219 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118o LEU* 4.2 5.3 - - - +
119o LEU 2.9 26.8 + - - +
120o PHE* 3.5 14.5 - - - -
121o THR 3.3 27.4 + - - +
146o PHE* 4.2 8.3 - - + -
148o VAL* 3.8 27.7 - - + +
194o LYS 4.7 3.1 - - - -
195o GLY* 4.4 4.0 - - - -
217o SER* 4.7 0.3 + - - -
218o GLU* 1.3 75.2 - - - +
220o LEU* 1.3 76.6 + - - +
232o GLU* 3.7 1.8 - - - -
233o VAL* 2.7 37.5 + - + +
235o ILE* 3.7 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118o LEU* 4.6 0.9 - - - +
119o LEU 5.2 0.9 + - - -
148o VAL* 4.0 10.5 - - + +
193o THR* 3.7 41.6 + - + +
194o LYS 5.1 3.9 + - - +
219o GLN* 1.3 96.3 + - - +
221o SER* 1.3 68.1 + - - +
230o PRO* 4.0 25.6 - - + +
231o HIS 3.4 13.5 - - - +
232o GLU* 4.0 21.8 - - + -
233o VAL* 4.5 1.3 - - - -
----------------------------------------------------------
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