Contacts of the helix formed by residues 245 - 257 (chain D) 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 SER 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459C ILE* 4.2 3.1 - - - -
464C GLU* 2.4 31.4 + - - -
221D THR* 2.9 20.9 + - - -
223D PHE* 3.5 23.5 - - - -
242D GLU* 3.9 1.9 + - - -
244D TYR* 1.3 72.7 - - - +
246D MET* 1.3 57.1 + - - +
247D VAL* 3.4 4.7 + - - +
248D THR* 3.0 19.1 + - - -
249D ALA* 3.0 27.4 + - - +
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Residues in contact with MET 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A TYR* 3.2 25.1 - - - +
239A PHE* 4.2 11.2 - - + -
240A GLY* 5.0 3.8 - - - +
242D GLU* 3.8 15.8 + - - +
244D TYR* 3.5 9.7 + - - -
245D SER* 1.3 69.6 - - - +
247D VAL* 1.3 60.4 + - - +
249D ALA* 3.7 2.8 - - - +
250D ASN* 2.8 32.4 + - - +
261D PHE* 3.8 13.9 - - + +
262D SER 3.7 25.4 - - - +
263D ASN 4.0 2.2 - - - +
264D LYS* 3.8 31.0 - - + +
267D LEU* 4.5 1.8 - - + -
407D PL9 3.7 44.0 - - + -
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Residues in contact with VAL 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PHE* 3.8 20.4 - - + -
240A GLY* 3.6 31.0 - - - +
464C GLU* 4.2 4.0 - - - +
466C VAL* 3.8 19.5 - - + -
467C LEU* 3.9 20.6 - - + -
242D GLU* 5.3 1.9 + - - +
245D SER* 3.3 6.3 + - - +
246D MET* 1.3 77.8 - - - +
248D THR* 1.3 62.6 + - - +
250D ASN* 3.7 2.3 - - - +
251D ARG* 3.1 21.3 + - - +
29T ILE* 4.0 21.8 - - + -
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Residues in contact with THR 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 4.4 6.0 + - + +
139A MET* 3.4 35.0 - - + -
459C ILE* 3.9 11.1 - - + +
464C GLU* 2.5 31.4 + - - +
465C PRO* 5.7 0.5 - - - +
466C VAL* 3.7 25.6 - - + +
221D THR* 4.3 2.2 - - + -
245D SER* 3.0 18.3 + - - -
247D VAL* 1.3 73.2 - - - +
249D ALA* 1.3 67.1 + - - +
251D ARG* 3.2 2.6 + - - +
252D PHE* 3.0 23.0 + - - +
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Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D THR* 3.7 27.1 - - + -
221D THR* 3.8 15.1 - - + +
244D TYR* 5.0 0.9 - - + -
245D SER 3.0 18.2 + - - +
246D MET* 3.7 5.8 - - - +
248D THR* 1.3 77.4 - - - +
250D ASN* 1.3 61.6 + - - +
252D PHE* 3.4 3.7 + - - +
253D TRP* 3.2 29.5 + - - -
407D PL9 3.9 19.1 - - + -
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Residues in contact with ASN 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PHE* 3.5 22.6 - - + -
472C LEU* 6.1 0.2 - - - +
246D MET 2.8 19.5 + - - +
247D VAL 3.7 2.4 - - - +
249D ALA* 1.3 76.5 - - - +
251D ARG* 1.3 62.0 + - - +
254D SER* 2.7 39.9 + - - -
260D ALA* 3.3 18.4 + - - +
261D PHE 2.7 28.6 + - - +
262D SER* 3.7 13.5 - - - -
407D PL9 3.8 3.5 - - - +
24T ARG* 4.9 2.0 + - - +
27T PRO* 3.8 20.2 - - - +
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Residues in contact with ARG 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR 2.9 21.6 + - - -
25A ASP* 3.6 14.1 + - - +
137A LEU* 3.9 6.5 - - + +
466C VAL* 3.7 36.3 + - + +
469C MET* 3.8 19.6 + - - +
470C PRO 3.1 29.9 + - - -
471C SER* 4.3 4.8 - - - +
472C LEU* 3.3 32.8 - - + +
247D VAL 3.1 17.1 + - - +
248D THR 3.2 4.4 + - - +
250D ASN* 1.3 77.1 + - - +
252D PHE* 1.3 68.8 + - - +
254D SER* 3.3 4.7 + - - -
255D GLN* 3.0 45.0 + - - +
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Residues in contact with PHE 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLN* 3.4 36.6 - - + -
133A LEU* 3.4 19.7 - - + +
134A SER* 3.7 14.6 - - - -
137A LEU* 3.7 9.1 - - + +
139A MET* 3.6 28.0 - - + -
143A ILE* 3.7 27.6 - - + -
217D THR* 6.0 0.2 - - + -
248D THR 3.0 16.4 + - - +
249D ALA* 3.4 5.1 + - - +
251D ARG* 1.3 77.5 - - - +
253D TRP* 1.3 93.9 + + - +
255D GLN 3.3 0.2 + - - -
256D ILE* 2.9 52.9 + - + +
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Residues in contact with TRP 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLN* 3.5 14.6 - - - -
143A ILE* 3.6 20.8 - - + +
1007A PHO 3.2 49.1 - - - -
213D ILE* 3.4 22.0 - - + -
217D THR* 2.8 29.3 + - + +
249D ALA 3.2 18.0 + - - +
252D PHE* 1.3 90.1 - + - +
254D SER* 1.3 60.1 + - - +
256D ILE* 4.0 16.4 - - + -
257D PHE* 2.7 40.1 + - + +
258D GLY 3.3 3.6 + - - -
259D ILE 3.4 9.7 - - - +
260D ALA* 3.5 8.3 - - + -
407D PL9 3.2 46.5 - + + +
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Residues in contact with SER 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG* 2.8 25.7 + - - -
28A LEU* 3.7 1.6 - - - +
472C LEU* 4.0 11.7 - - - -
250D ASN* 2.7 29.6 + - - -
251D ARG* 3.6 4.3 - - - -
253D TRP* 1.3 76.4 - - - +
255D GLN* 1.3 56.4 + - - +
258D GLY* 3.1 26.8 + - - -
260D ALA* 3.3 10.7 - - - +
24T ARG* 2.8 31.0 + - - -
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Residues in contact with GLN 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A SER 4.5 0.4 + - - -
24A THR* 2.9 28.8 + - - +
26A ASN 2.8 26.5 + - - +
27A ARG 3.6 6.3 - - - +
28A LEU* 3.5 6.7 - - - +
29A TYR* 3.0 24.6 + - - +
129A ARG* 2.8 27.4 + - - -
133A LEU* 3.6 28.2 - - + +
137A LEU* 4.1 2.6 - - - +
472C LEU* 3.6 21.7 - - + +
251D ARG* 3.0 38.4 + - - +
254D SER* 1.3 77.2 - - - +
256D ILE* 1.3 52.2 + - - +
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Residues in contact with ILE 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 5.3 0.2 - - - -
29A TYR* 5.1 1.1 - - + -
126A TYR* 3.5 26.7 + - + +
129A ARG* 3.0 65.2 + - + +
130A GLN* 4.1 16.4 - - + -
133A LEU* 3.6 20.6 - - + -
252D PHE* 2.9 34.6 + - + +
253D TRP* 4.0 21.3 - - + +
255D GLN* 1.3 78.1 - - - +
257D PHE* 1.3 58.1 + - - +
258D GLY 3.7 0.2 - - - -
410D LHG 3.7 13.4 - - - +
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Residues in contact with PHE 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.9 0.4 - - - -
126A TYR* 3.5 18.8 - - - +
1005A CLA 3.9 25.6 - - + -
1007A PHO 3.5 46.7 - - + -
253D TRP* 2.7 24.2 + - + +
256D ILE* 1.3 74.5 - - - +
258D GLY* 1.3 54.9 + - - +
259D ILE* 3.3 33.4 + - + +
407D PL9 4.1 25.6 - - + -
410D LHG 3.4 65.0 - - + +
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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