Contacts of the strand formed by residues 232 - 245 (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 232 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52o VAL* 3.4 5.2 - - - +
53o LYS* 2.9 81.6 + - + +
55o GLU* 4.7 2.4 + - - +
65o PHE* 3.6 7.4 - - + -
218o GLU* 4.5 10.9 - - - +
219o GLN 3.8 4.5 - - - +
220o LEU* 4.0 17.5 - - + -
230o PRO 5.9 0.2 - - - +
231o HIS* 1.3 72.9 - - - +
233o VAL* 1.3 59.4 + - - +
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Residues in contact with VAL 233 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50o PHE* 4.6 6.3 - - + -
51o LEU 3.4 12.1 - - - +
52o VAL* 4.3 15.7 - - + -
65o PHE* 3.9 3.0 - - - -
116o ILE* 4.8 1.1 - - + -
118o LEU* 4.0 25.6 - - + -
217o SER 3.7 0.3 - - - +
218o GLU* 3.3 7.4 - - - +
219o GLN 2.7 41.2 + - - +
220o LEU 4.5 0.2 - - - -
221o SER* 3.8 30.7 - - - +
231o HIS 3.9 1.1 - - - +
232o GLU* 1.3 78.5 - - - +
234o LYS* 1.3 64.5 + - - +
235o ILE* 3.8 26.3 - - + +
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Residues in contact with LYS 234 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49o THR 3.9 0.9 - - - +
50o PHE* 3.8 0.9 - - - -
51o LEU* 2.8 51.4 + - + +
65o PHE* 3.7 45.1 - - + +
216o GLU* 3.4 38.2 + - + +
217o SER 3.3 4.7 - - - +
218o GLU* 4.1 17.4 + - + +
233o VAL* 1.3 73.2 - - - +
235o ILE* 1.3 62.6 + - - +
236o GLN* 4.1 21.0 + - + +
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Residues in contact with ILE 235 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47o PRO* 3.6 30.1 - - + -
49o THR 3.6 4.0 - - - +
50o PHE* 3.6 26.7 - - + -
118o LEU* 4.1 2.7 - - + -
120o PHE* 3.7 26.0 - - + -
215o PHE* 3.7 9.6 - - + -
216o GLU* 3.3 4.2 - - - +
217o SER* 2.8 48.3 + - - +
219o GLN* 3.7 37.0 - - + +
233o VAL* 3.8 14.8 - - + +
234o LYS* 1.3 73.6 - - - +
236o GLN* 1.3 64.9 + - - +
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Residues in contact with GLN 236 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47o PRO* 3.5 2.6 - - - +
48o THR* 2.7 30.8 + - - +
49o THR* 3.0 31.6 + - - +
51o LEU* 3.7 28.6 - - + +
215o PHE* 3.4 11.9 - - - +
216o GLU* 3.2 34.2 + - + +
234o LYS* 4.1 10.3 + - + +
235o ILE* 1.3 78.8 - - - +
237o GLY* 1.3 52.4 + - - +
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Residues in contact with GLY 237 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46o GLN 3.2 13.0 - - - -
48o THR* 3.5 15.7 + - - -
214o THR* 3.2 10.9 - - - +
215o PHE* 2.9 33.8 + - - +
236o GLN* 1.3 77.3 - - - +
238o VAL* 1.3 64.7 - - - +
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Residues in contact with VAL 238 (chain o).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19o CYS* 4.4 6.9 - - + +
21o THR* 6.1 4.5 - - + -
46o GLN* 2.9 63.4 + - + +
48o THR* 5.0 8.7 - - + -
213o GLY 3.2 11.2 - - - +
214o THR* 4.4 12.3 - - + -
215o PHE* 3.4 7.9 - - - -
237o GLY* 1.3 79.2 - - - +
239o PHE* 1.3 63.2 + - - +
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Residues in contact with PHE 239 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19o CYS* 4.8 4.3 - - - -
20o PRO 4.9 0.7 - - - +
43o LEU* 4.2 6.3 - - + -
44o CYS 3.1 14.8 - - - +
45o LEU* 4.3 11.9 - - + -
142o PHE* 5.7 2.0 - + - -
199o LEU* 3.8 36.3 - - + -
200o ASN 3.5 16.6 - - - -
201o VAL* 4.2 17.0 - - + -
211o ILE* 4.1 25.1 - - + -
212o ALA* 3.3 11.9 - - - +
213o GLY 2.7 60.1 + - - +
214o THR 3.4 25.1 - - - -
215o PHE* 4.4 2.2 - - + -
238o VAL* 1.3 77.3 - - - +
240o TYR* 1.3 70.7 + - - +
241o ALA* 4.6 1.8 - - + -
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Residues in contact with TYR 240 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19o CYS* 4.2 4.0 - - + -
20o PRO* 3.3 61.2 - - + +
21o THR 5.2 0.2 - - - -
22o LEU* 4.5 12.8 - - + -
42o ARG* 4.1 28.3 - - - -
43o LEU* 3.4 4.3 - - - +
44o CYS* 2.8 34.4 + - + +
210o GLU* 2.7 49.7 + - + +
211o ILE 3.4 11.4 - - - -
212o ALA* 4.4 0.9 - - + +
239o PHE* 1.3 77.3 - - - +
241o ALA* 1.3 65.2 + - - +
242o SER* 3.6 22.9 - - - -
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Residues in contact with ALA 241 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40o ILE* 4.4 17.9 - - + -
42o ARG 3.1 8.5 - - - +
43o LEU* 4.0 15.5 - - + -
209o GLY 3.9 0.3 - - - +
210o GLU* 3.4 2.9 - - - +
211o ILE* 2.7 65.3 + - + +
239o PHE* 4.6 2.9 - - + -
240o TYR* 1.3 81.3 - - - +
242o SER* 1.3 60.0 + - - +
243o ILE* 5.3 0.7 - - + -
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Residues in contact with SER 242 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40o ILE* 3.6 3.9 - - - -
41o ALA* 2.9 32.3 + - - +
42o ARG* 3.0 26.4 + - - +
208o THR 5.9 0.9 - - - -
209o GLY 3.5 4.3 - - - -
210o GLU* 4.2 8.3 - - - +
240o TYR* 3.6 22.8 - - - -
241o ALA* 1.3 73.7 - - - +
243o ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 243 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30o TYR* 3.9 31.7 + - + -
38o TYR* 4.0 13.9 - - + -
39o ARG 3.4 10.5 - - - +
40o ILE* 4.1 19.1 - - + -
85o LEU* 3.8 21.1 - - + -
136o ILE* 3.6 28.7 - - + -
142o PHE* 5.8 1.3 - - + -
208o THR 4.2 4.9 - - - +
209o GLY* 2.7 30.1 + - - +
211o ILE* 4.1 30.1 - - + -
241o ALA* 5.1 0.7 - - + +
242o SER* 1.3 75.8 - - - +
244o GLU* 1.3 64.8 + - - +
245o PRO* 4.3 0.7 - - - +
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Residues in contact with GLU 244 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38o TYR* 3.7 3.9 - - - -
39o ARG* 3.0 46.8 + - + +
41o ALA* 3.6 28.5 - - + +
242o SER 4.0 0.4 + - - -
243o ILE* 1.3 75.2 - - - +
245o PRO* 1.3 72.5 - - + +
246o ALA* 3.1 5.9 + - - +
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Residues in contact with PRO 245 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30o TYR* 3.4 20.4 - - - +
36o GLN* 3.4 32.6 + - - +
37o THR 3.5 6.5 - - - +
38o TYR* 3.8 13.0 - - + -
243o ILE 4.3 0.7 - - - +
244o GLU* 1.3 84.0 - - + +
246o ALA* 1.3 68.3 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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