Contacts of the helix formed by residues 240 - 255 (chain B) in PDB entry 1ESQ
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 GLY 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B LEU* 4.9 6.5 - - - +
236B THR* 3.7 7.7 - - - +
237B ALA 4.9 1.0 + - - -
238B ASP 3.5 2.7 - - - -
239B LYS* 1.3 80.9 - - - +
241B PRO* 1.3 73.7 - - - +
243B SER 3.4 0.5 + - - -
244B PHE* 3.1 21.8 + - - +
250C ASN* 3.0 13.3 - - - +
253C SER* 4.5 3.1 - - - -
254C THR* 5.1 2.0 - - - -
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Residues in contact with PRO 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.7 10.7 - - + -
192B LYS* 3.9 49.8 - - + +
193B VAL* 4.0 5.8 - - + +
240B GLY* 1.3 83.7 - - - +
242B GLY* 1.3 57.4 + - - +
244B PHE* 3.2 8.0 + - + +
245B GLN* 2.9 30.0 + - - +
34C ASN 5.7 0.7 - - - +
38C ALA* 4.4 13.2 - - + -
249C LEU* 4.3 0.9 - - + +
250C ASN* 4.1 6.1 - - - +
253C SER* 3.2 27.8 - - - +
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Residues in contact with GLY 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PRO* 1.3 80.1 - - - +
243B SER* 1.3 61.9 + - - +
245B GLN* 3.2 14.9 + - - +
246B ILE* 3.3 18.2 + - - +
246C ILE* 3.4 16.0 - - - +
249C LEU* 4.0 28.4 - - - +
250C ASN* 3.1 8.2 + - - -
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B THR* 4.1 6.7 - - - -
239B LYS* 3.8 35.5 - - - +
240B GLY 3.4 2.2 + - - -
242B GLY* 1.3 75.1 - - - +
244B PHE* 1.3 58.1 + - - +
246B ILE* 3.3 6.4 + - - +
247B GLU* 2.8 31.7 + - - +
246C ILE* 3.6 10.5 - - - +
247C GLU* 4.3 3.8 + - - -
250C ASN* 2.7 30.9 + - - -
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Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B HIS* 4.9 2.9 - - + -
189B LEU* 3.4 36.8 - - + -
190B LEU* 3.5 50.9 - - + -
193B VAL* 3.6 19.3 - - + -
229B ALA* 3.4 28.5 - - + -
232B ALA* 3.9 7.9 - - + -
233B ALA* 3.8 15.7 - - + -
236B THR* 3.5 17.7 + - + -
240B GLY 3.1 13.7 + - - +
241B PRO* 3.4 8.1 - - + +
243B SER* 1.3 75.3 - - - +
245B GLN* 1.3 56.1 + - - +
247B GLU 3.1 0.5 + - - -
248B LEU* 2.7 39.8 + - + +
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Residues in contact with GLN 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLN* 5.8 0.3 - - - +
31B PHE* 3.7 30.1 - - + -
193B VAL* 4.0 20.4 - - + +
241B PRO 2.9 13.0 + - - +
242B GLY* 3.5 8.6 + - - +
244B PHE* 1.3 76.8 - - - +
246B ILE* 1.3 78.0 + - + +
248B LEU* 3.4 7.5 - - - +
249B LEU* 3.3 23.6 + - + +
30C ASN* 4.7 5.3 + - - +
34C ASN* 3.3 29.0 + - - +
245C GLN* 5.6 1.6 - - - +
246C ILE* 4.9 4.5 - - - +
249C LEU* 4.0 18.2 - - - +
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLY 3.4 27.1 - - - +
243A SER* 3.5 14.8 - - - +
245A GLN* 5.1 4.7 - - - +
246A ILE* 3.6 24.9 - - + -
242B GLY 3.3 14.1 + - - +
243B SER* 3.6 8.3 - - - +
244B PHE 3.1 0.2 - - - -
245B GLN* 1.3 88.4 - - + +
247B GLU* 1.3 66.0 + - - +
249B LEU* 3.0 25.5 + - + +
250B ASN* 3.1 13.0 + - - +
246C ILE* 3.6 28.5 - - + -
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LYS* 5.0 4.9 - - - +
243A SER* 4.3 2.8 + - - -
232B ALA* 3.5 12.7 - - + +
235B GLN* 3.0 30.7 + - + +
236B THR* 3.6 22.9 - - - +
239B LYS* 5.4 4.3 - - - +
243B SER* 2.8 20.9 + - - +
244B PHE 3.7 1.1 - - - +
246B ILE* 1.3 73.7 - - - +
248B LEU* 1.3 57.4 + - - +
250B ASN* 2.8 31.3 + - - +
251B LYS* 2.8 66.5 + - - +
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 4.0 25.6 - - + -
190B LEU* 4.4 16.8 - - + -
193B VAL* 6.5 0.2 - - + -
199B LEU* 4.0 5.6 - - + -
225B TYR* 4.4 10.3 - - + +
228B ALA* 4.4 2.9 - - + -
229B ALA* 3.8 37.2 - - + +
232B ALA* 3.5 8.9 - - + +
244B PHE* 2.7 27.5 + - + +
245B GLN* 3.4 7.9 - - - +
247B GLU* 1.3 73.7 - - - +
249B LEU* 1.3 63.0 + - + +
251B LYS* 3.4 0.9 + - - -
252B LEU* 3.1 57.0 + - + +
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PRO* 4.2 1.4 - - + +
242A GLY* 3.7 18.8 - - - +
245A GLN* 4.0 23.6 - - - +
31B PHE* 4.1 23.8 - - + -
34B ASN* 3.8 15.9 - - + +
35B GLY* 3.5 37.0 - - - +
38B ALA* 3.2 26.8 - - + +
245B GLN* 3.3 16.4 + - + +
246B ILE* 3.0 17.8 + - + +
248B LEU* 1.3 75.5 - - - +
250B ASN* 1.3 65.8 + - - +
252B LEU* 3.4 9.5 + - + +
253B SER* 4.0 0.5 - - - -
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Residues in contact with ASN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LYS* 3.2 22.1 - - - +
240A GLY* 2.8 15.7 - - - -
241A PRO* 4.0 4.8 - - - +
242A GLY 2.7 33.9 - - - +
243A SER* 2.7 28.2 + - - +
246B ILE 3.1 12.2 + - - +
247B GLU* 2.8 28.9 + - - +
249B LEU* 1.3 76.3 - - - +
251B LYS* 1.3 61.9 + - + +
253B SER* 2.8 11.6 + - - -
254B THR* 2.8 26.0 + - - -
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Residues in contact with LYS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LYS 5.3 2.6 + - - -
228B ALA* 3.5 32.5 - - + +
231B LEU* 3.6 37.0 - - + -
232B ALA* 3.7 4.7 - - + +
235B GLN* 4.3 12.1 - - - +
247B GLU* 2.8 47.8 + - - +
248B LEU 3.8 3.8 - - - +
250B ASN* 1.3 73.9 - - + +
252B LEU* 1.3 57.7 + - - +
253B SER 2.9 5.6 - - - -
254B THR* 3.5 21.9 + - - +
255B VAL* 2.7 32.9 + - - +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 2.8 19.8 + - - -
35B GLY* 3.9 18.4 - - - +
38B ALA* 3.2 16.3 - - + +
39B LEU* 3.3 26.7 - - + +
199B LEU* 3.9 20.0 - - + -
203B VAL* 5.4 2.9 - - + -
224B SER 5.2 0.7 - - - +
225B TYR* 3.9 26.0 - - + -
228B ALA* 3.7 22.0 - - + -
248B LEU* 3.1 40.5 + - + +
249B LEU* 3.8 8.1 - - - +
250B ASN 3.3 0.6 - - - -
251B LYS* 1.3 76.1 - - - +
253B SER* 1.3 57.3 + - - +
255B VAL* 4.4 3.1 - - + -
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Residues in contact with SER 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 4.8 6.1 + - - -
240A GLY* 5.1 0.7 - - - -
241A PRO* 3.4 33.4 - - - +
14B ARG* 3.6 14.2 + - - +
38B ALA* 3.0 19.1 + - - -
249B LEU 3.7 0.2 + - - -
250B ASN 2.8 11.8 + - - -
252B LEU* 1.3 81.7 - - - +
254B THR* 1.3 60.2 + - - +
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Residues in contact with THR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ASP 4.9 3.6 + - - -
239A LYS 3.8 16.5 + - - -
240A GLY* 5.1 1.2 - - - -
231B LEU* 5.7 2.7 - - + -
250B ASN 2.8 15.4 + - - -
251B LYS* 3.9 27.5 + - + +
253B SER* 1.3 76.0 + - - +
255B VAL* 1.3 70.7 + - - +
256B THR* 3.4 14.4 + - - +
259B ASP* 4.5 2.3 - - - +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 4.2 10.5 - - + -
14B ARG* 2.6 48.6 + - - +
39B LEU* 5.8 2.0 - - + -
224B SER* 4.8 6.1 - - - +
227B VAL* 4.2 12.3 - - + -
228B ALA* 4.3 16.8 - - + +
231B LEU* 4.1 15.0 - - + -
251B LYS* 2.7 24.8 + - - +
252B LEU* 4.1 4.3 - - + +
254B THR* 1.3 76.1 - - - +
256B THR* 1.3 58.9 + - - +
259B ASP* 3.7 25.1 - - + -
260B VAL* 4.4 7.9 - - + -
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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
------------------------------------------------------------
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