Contacts of the helix formed by residues 272 - 286 (chain B) in PDB entry 4A69
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 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ASP* 2.7 30.8 + - - -
261B LEU* 3.5 2.6 - - - +
270B ASN 3.8 1.8 + - - -
271B LEU* 1.3 77.3 - - - +
273B ILE* 1.3 58.8 + - - +
274B ARG* 3.5 8.4 + - - +
275B GLY 3.0 10.7 + - - -
276B HIS* 3.0 28.1 + - - +
342B VAL* 3.9 13.0 - - - -
343B SER* 6.1 1.1 - - - -
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Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 3.8 21.3 - - + +
272B SER* 1.3 72.3 - - - +
274B ARG* 1.3 57.6 + - - +
276B HIS* 3.4 2.5 + - - +
277B GLY* 2.8 26.2 + - - -
302B ASN* 4.3 6.5 - - - +
305B ARG* 4.1 15.9 - - + +
306B CYS* 3.8 26.5 - - + +
309B TYR* 3.7 26.3 - - + -
310B GLU* 4.6 0.9 - - - +
338B LEU 3.6 20.4 - - - +
339B HIS* 3.9 16.4 - - + +
340B PRO* 3.8 24.6 + - + +
342B VAL* 4.5 10.5 - - + +
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASP* 5.4 0.4 - - - +
272B SER* 3.3 7.2 + - - +
273B ILE* 1.3 75.8 - - - +
275B GLY* 1.3 64.4 + - - +
277B GLY* 3.4 1.4 + - - -
278B GLU* 3.0 34.7 + - + +
309B TYR* 3.7 27.8 + - - +
321B GLU* 3.9 9.9 + - - -
339B HIS* 3.6 46.1 + - + +
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Residues in contact with GLY 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASP* 3.3 32.7 + - - -
232B TYR* 5.9 0.2 - - - -
271B LEU* 5.1 4.5 - - - -
272B SER* 3.0 10.9 + - - -
274B ARG* 1.3 74.7 - - - +
276B HIS* 1.3 63.3 + - - +
278B GLU* 3.3 27.3 + - - +
279B CYS* 3.7 10.4 + - - -
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Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 3.5 22.4 - - + +
256B CYS* 3.4 18.2 + - - +
257B GLY 3.0 25.6 - - - -
258B ALA* 3.9 7.2 - - - -
260B SER* 3.2 20.2 + - - -
261B LEU* 3.9 13.8 - - + +
271B LEU* 4.2 14.5 - - + +
272B SER 3.0 17.1 + - - +
273B ILE 3.6 4.5 - - - +
275B GLY* 1.3 74.5 - - - +
277B GLY* 1.3 61.5 + - - +
279B CYS* 3.2 24.5 + - - +
280B VAL* 3.7 2.9 + - - +
306B CYS* 3.5 12.8 - - - -
310B GLU* 2.5 39.7 + - - +
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Residues in contact with GLY 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE 2.8 16.9 + - - -
274B ARG 3.4 2.2 + - - -
275B GLY 3.3 0.2 - - - -
276B HIS* 1.3 77.4 - - - +
278B GLU* 1.3 54.9 + - - +
280B VAL* 3.0 6.5 + - - +
281B GLU 2.9 24.6 + - - -
309B TYR* 4.1 3.1 - - - -
310B GLU* 3.3 23.5 + - - -
313B LEU* 3.4 19.8 - - - +
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASP* 5.5 3.2 - - - +
233B LYS* 3.3 39.8 + - + +
237B GLN* 4.4 9.9 - - - +
274B ARG* 3.0 30.5 + - - +
275B GLY* 3.5 13.9 - - - +
276B HIS 3.3 0.8 - - - -
277B GLY* 1.3 71.8 - - - +
279B CYS* 1.3 61.1 + - - +
281B GLU* 3.8 16.9 - - - +
282B TYR* 2.9 30.8 + - - +
309B TYR* 6.1 0.4 - - - +
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Residues in contact with CYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 4.1 17.0 - - + -
232B TYR* 3.6 36.6 - - - -
233B LYS* 6.1 1.8 - - - -
236B PHE* 3.6 32.9 - - + -
254B LEU* 5.0 2.0 - - + -
271B LEU* 5.5 0.9 - - - -
275B GLY 3.9 10.1 - - - -
276B HIS* 3.2 15.4 + - - +
278B GLU* 1.3 76.8 - - - +
280B VAL* 1.3 56.9 + - - +
282B TYR* 3.3 2.4 + - - +
283B VAL* 2.9 34.3 + - - +
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 5.0 3.8 - - + -
254B LEU* 3.9 14.9 - - + +
256B CYS* 3.8 25.1 - - + -
276B HIS 4.1 3.1 - - - +
277B GLY* 3.0 8.9 + - - +
279B CYS* 1.3 76.1 - - - +
281B GLU* 1.3 56.8 + - - +
283B VAL* 3.2 2.6 + - - +
284B LYS* 3.0 29.1 + - - +
290B LEU* 5.2 0.9 - - + +
292B VAL* 5.3 0.9 - - + -
310B GLU* 3.7 39.0 - - + +
313B LEU* 5.1 3.8 - - + -
314B LEU* 3.9 37.8 - - + +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLY 2.9 13.3 + - - +
278B GLU* 3.8 18.9 - - - +
280B VAL* 1.3 76.9 - - - +
282B TYR* 1.3 61.9 + - - +
284B LYS* 3.6 14.3 + - + +
285B SER* 3.1 22.3 + - - -
309B TYR* 5.1 2.1 + - - -
313B LEU* 4.0 33.7 - - + +
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Residues in contact with TYR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B PHE* 4.4 10.8 - + + -
237B GLN* 3.4 62.8 + - + +
240B ILE* 4.2 8.7 - - + -
241B ASN* 3.1 31.0 + - - +
278B GLU 2.9 19.6 + - - +
279B CYS* 3.6 5.8 - - - +
281B GLU* 1.3 74.3 - - - +
283B VAL* 1.3 65.4 + - - +
285B SER* 2.7 32.6 + - - -
286B PHE* 3.4 29.1 - + - -
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 3.8 21.3 - - + -
236B PHE* 3.9 18.2 - - + -
240B ILE* 4.6 5.6 - - + -
252B ILE* 3.8 36.9 - - + +
254B LEU* 4.1 18.4 - - + -
279B CYS 2.9 20.6 + - - +
280B VAL 3.2 4.4 + - - +
282B TYR* 1.3 76.1 - - - +
284B LYS* 1.3 64.0 + - - +
285B SER 3.3 0.7 + - - -
286B PHE* 3.3 22.6 + - - +
287B ASN 4.7 0.2 + - - -
288B ILE 5.6 1.7 + - - +
290B LEU* 3.8 16.4 - - + +
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Residues in contact with LYS 284 (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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3B LYS* 3.7 23.8 + - - +
125B ILE* 4.2 17.3 - - + -
280B VAL 3.0 16.5 + - - +
281B GLU* 3.6 13.7 - - + +
282B TYR 3.3 0.2 - - - -
283B VAL* 1.3 77.9 - - - +
285B SER* 1.3 62.1 + - - +
286B PHE 3.0 2.1 + - - -
287B ASN* 3.0 19.1 + - - +
288B ILE 4.9 1.7 + - - +
290B LEU* 4.0 17.4 - - + +
313B LEU 3.5 19.3 - - - +
314B LEU* 3.3 35.0 + - + +
316B GLU* 2.9 33.7 + - - +
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Residues in contact with SER 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLU 3.1 13.5 + - - -
282B TYR* 2.7 33.4 + - - -
284B LYS* 1.3 75.3 - - - +
286B PHE* 1.3 65.1 + - - +
287B ASN* 3.1 18.3 + - - -
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Residues in contact with PHE 286 (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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240B ILE* 3.9 12.3 - - + -
241B ASN* 3.8 35.4 - - - -
244B VAL* 3.5 35.0 - - + -
252B ILE* 4.8 4.7 - - + -
282B TYR* 3.4 46.9 - + - -
283B VAL* 3.3 15.0 + - - +
284B LYS 3.0 1.8 + - - -
285B SER* 1.3 79.5 + - - +
287B ASN* 1.3 68.8 + - - +
288B ILE* 3.2 24.5 + - + +
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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
------------------------------------------------------------
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