Contacts of the helix formed by residues 232 - 247 (chain O) in PDB entry 5A31
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 THR 232 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A HIS* 4.1 23.4 - - + +
230O ALA 4.0 0.4 + - - -
231O LEU* 1.3 72.5 - - - +
233O PRO* 1.3 77.7 - - - +
234O ALA* 3.6 8.3 + - - +
235O SER* 2.7 40.2 + - - +
236O LEU* 3.0 9.0 + - - +
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Residues in contact with PRO 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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30A HIS* 3.6 20.4 - - + +
32A PRO* 3.8 19.5 - - + -
232O THR* 1.3 88.6 - - - +
234O ALA* 1.3 64.4 + - - +
236O LEU* 3.1 8.3 + - - +
237O GLN* 3.1 12.6 + - - +
260O ASN* 3.5 16.0 + - - +
263O ARG* 3.0 33.8 - - + +
264O VAL* 4.6 15.7 - - + -
500O ASN* 6.2 2.7 - - - +
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Residues in contact with ALA 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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29A LYS 4.7 3.8 - - - +
30A HIS* 3.1 27.4 + - + +
31A HIS 3.4 16.8 + - - +
32A PRO* 4.2 7.2 - - - +
232O THR* 3.9 6.7 - - - +
233O PRO* 1.3 80.4 - - - +
235O SER* 1.3 62.0 + - - +
237O GLN* 3.6 3.6 + - - +
238O LYS* 3.3 38.3 + - - +
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Residues in contact with SER 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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231O LEU* 3.6 13.4 - - - +
232O THR* 2.7 43.9 + - - +
234O ALA* 1.3 77.0 - - - +
236O LEU* 1.3 63.3 + - - +
238O LYS* 3.4 12.7 + - - +
239O GLU* 3.0 22.3 + - - +
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Residues in contact with LEU 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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215O PHE* 4.5 9.4 - - + -
219O GLN* 4.1 27.8 - - + +
223O LEU* 3.8 26.0 - - + -
231O LEU* 3.9 18.8 - - + +
232O THR 3.0 11.9 + - - +
233O PRO 3.1 7.8 + - - +
235O SER* 1.3 73.1 + - - +
237O GLN* 1.3 63.3 + - - +
239O GLU* 3.0 4.0 + - - +
240O LEU* 2.8 50.3 + - + +
256O LEU* 4.8 4.0 - - + +
260O ASN* 3.3 28.3 - - + +
263O ARG* 4.1 5.6 - - - +
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Residues in contact with GLN 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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32A PRO* 2.8 45.1 + - + +
34A ALA* 2.8 44.5 + - - +
233O PRO 3.1 10.9 + - - +
234O ALA 3.9 3.7 + - - +
236O LEU* 1.3 81.9 - - - +
238O LYS* 1.3 62.3 + - - +
240O LEU* 2.9 12.0 + - - +
241O ASN* 2.9 54.0 + - - +
257O SER* 4.7 12.3 - - - +
260O ASN* 4.1 10.3 - - - +
261O ASN* 4.8 3.8 + - - +
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Residues in contact with LYS 238 (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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32A PRO 5.9 2.7 - - - -
234O ALA* 3.3 29.3 + - - +
235O SER* 3.5 12.1 - - - +
236O LEU 3.2 0.4 - - - -
237O GLN* 1.3 83.5 - - - +
239O GLU* 1.3 59.5 + - - +
241O ASN* 3.4 10.7 + - - +
242O ASN* 3.3 30.3 + - - +
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Residues in contact with GLU 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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207O LEU* 4.5 16.6 - - - +
215O PHE* 3.4 36.9 - - + -
231O LEU* 4.4 8.5 - - + -
235O SER 3.0 12.4 + - - +
236O LEU 3.0 9.9 + - - +
238O LYS* 1.3 74.9 - - - +
240O LEU* 1.3 65.8 + - - +
242O ASN* 3.6 14.6 + - - +
243O LEU* 3.3 21.8 + - - +
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Residues in contact with LEU 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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215O PHE* 4.7 4.3 - - + -
216O LEU* 3.6 30.5 - - + -
236O LEU* 2.8 37.7 + - + +
237O GLN* 2.9 11.6 + - - +
239O GLU* 1.3 72.9 - - - +
241O ASN* 1.3 61.9 + - - +
243O LEU* 3.1 10.5 + - + +
244O LEU* 2.9 32.8 + - + +
253O ALA* 3.9 22.9 - - + +
256O LEU* 3.6 14.4 - - + -
257O SER* 3.5 39.9 - - - +
260O ASN* 5.2 0.7 - - + -
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Residues in contact with ASN 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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34A ALA* 5.3 3.0 - - - +
36A ASN* 3.4 42.2 + - - +
237O GLN* 2.9 38.3 + - - +
238O LYS* 3.6 11.5 - - - +
239O GLU 3.2 0.2 - - - -
240O LEU* 1.3 79.0 - - - +
242O ASN* 1.3 67.2 + - - +
244O LEU* 3.0 7.5 + - - +
245O LYS* 2.8 38.6 + - + +
257O SER* 5.2 2.6 + - - -
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Residues in contact with ASN 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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206O PRO* 4.9 9.2 - - + -
238O LYS* 3.3 18.6 + - - +
239O GLU* 3.6 17.2 + - - +
241O ASN* 1.3 80.8 - - - +
243O LEU* 1.3 60.0 + - - +
245O LYS* 4.6 18.3 - - - +
246O PHE* 3.6 30.6 + - + +
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Residues in contact with LEU 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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207O LEU* 5.4 19.1 - - + +
212O ALA* 3.8 22.4 - - + -
215O PHE* 5.2 6.1 - - + -
216O LEU* 4.2 17.0 - - + -
239O GLU* 3.3 15.8 + - - +
240O LEU* 3.1 12.4 + - + +
241O ASN 3.0 0.8 - - - -
242O ASN* 1.3 75.5 - - - +
244O LEU* 1.3 64.2 - - - +
246O PHE* 3.5 3.3 + - - +
247O ASN* 3.3 29.4 + - - +
250O PHE* 3.6 46.9 - - + -
253O ALA* 4.4 6.5 - - + -
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Residues in contact with LEU 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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36A ASN* 4.5 22.2 - - - +
39A LEU* 4.5 9.2 - - + -
240O LEU* 2.9 16.9 + - + +
241O ASN* 3.0 8.3 + - - +
243O LEU* 1.3 74.3 - - - +
245O LYS* 1.3 67.7 + - - +
246O PHE 3.1 0.9 + - - -
247O ASN 3.1 19.9 - - - +
248O PRO* 3.2 30.1 - - + +
250O PHE* 3.6 24.0 - - + +
253O ALA* 3.8 20.9 - - + +
254O HIS* 3.5 39.5 - - + +
257O SER* 5.8 3.4 - - - +
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Residues in contact with LYS 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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36A ASN* 5.4 6.7 + - - +
39A LEU* 5.1 11.9 - - + +
41A GLN* 4.3 22.4 + - - +
140C PRO* 4.7 6.6 - - - +
145C GLN* 4.2 21.6 - - - +
241O ASN* 2.8 26.1 + - + +
242O ASN* 4.1 15.7 - - - +
244O LEU* 1.3 73.8 - - - +
246O PHE* 1.3 81.2 + - + +
247O ASN 3.5 0.2 + - - -
248O PRO* 4.1 10.8 - - - +
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Residues in contact with PHE 246 (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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138C LEU 5.4 0.9 - - - +
139C GLY* 4.9 3.5 - - - -
140C PRO* 3.9 14.6 - - - +
145C GLN* 4.1 35.3 - - + +
206O PRO* 3.0 54.1 - - + -
207O LEU 5.1 3.4 - - - +
242O ASN* 3.6 21.1 + - + +
243O LEU* 3.5 4.0 + - - +
244O LEU 3.2 1.0 - - - -
245O LYS* 1.3 97.0 - - + +
247O ASN* 1.3 65.5 + - - +
248O PRO* 4.5 0.2 - - - -
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Residues in contact with ASN 247 (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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138C LEU 6.0 2.2 - - - +
139C GLY 6.0 0.4 - - - -
140C PRO* 5.0 4.5 - - + -
207O LEU 4.4 11.8 - - - +
209O GLN* 4.1 24.3 - - - +
243O LEU* 3.3 22.7 + - - +
244O LEU* 3.1 7.6 + - - +
246O PHE* 1.3 82.3 - - - +
248O PRO* 1.3 66.0 - - + +
249O ASP* 3.2 14.1 - - + +
250O PHE* 3.5 32.7 + - - +
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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