Contacts of the helix formed by residues 267 - 281 (chain B) in PDB entry 6UZA
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 PHE 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A CYS 3.7 19.7 - - - -
337A ARG 3.3 20.6 - - - -
338A ASN 3.5 16.2 - - - +
339A THR* 4.5 6.5 - - - -
342A VAL* 4.1 10.1 - - + -
382A ASN* 3.3 36.6 - - - -
385A GLN* 4.1 33.4 - - + +
265B ASP* 3.3 12.0 + - - +
266B SER* 1.3 78.3 + - - +
268B SER* 1.3 61.0 + - - +
269B HIS 3.2 1.5 + - - -
270B SER* 3.3 5.8 + - - -
271B ARG* 3.0 40.3 + - + +
314B PHE* 5.4 11.4 - + - -
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ARG* 3.8 17.9 - - - -
338A ASN* 4.6 6.7 + - - -
218B HIS* 4.3 23.6 + - - -
265B ASP* 3.4 27.5 + - - +
267B PHE* 1.3 77.6 - - - +
269B HIS* 1.3 61.4 + - - +
271B ARG* 3.8 7.1 - - - +
272B SER* 2.9 31.2 + - - -
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Residues in contact with HIS 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B CYS* 4.3 16.8 + - + +
261B LYS* 3.8 39.9 - - + +
262B GLN* 4.5 21.7 + - + -
265B ASP 3.5 17.3 + - - +
266B SER* 4.4 7.0 - - - +
267B PHE 3.2 0.8 - - - -
268B SER* 1.3 79.1 + - - +
270B SER* 1.3 65.8 + - - +
272B SER* 2.6 23.7 + - - -
273B ARG* 3.0 34.9 + - + +
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B TYR* 5.9 1.0 - - - -
266B SER 3.3 14.2 + - - -
267B PHE* 3.3 8.3 + - - -
269B HIS* 1.3 80.0 - - - +
271B ARG* 1.3 61.5 + - - +
273B ARG* 3.4 10.9 + - - +
274B ILE* 3.0 29.7 + - - +
311B GLU* 4.1 13.8 + - - -
314B PHE* 3.8 29.1 - - - -
318B TYR* 5.2 0.3 + - - -
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Residues in contact with ARG 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ASP* 4.0 14.3 + - - -
335A LEU 5.5 0.6 + - - -
336A CYS 3.0 27.6 + - - -
337A ARG* 4.1 38.0 - - - +
382A ASN* 5.2 3.4 + - - +
217B SER* 4.9 7.0 + - - -
219B ASP* 6.2 0.2 - - - -
267B PHE* 3.0 31.8 + - + +
268B SER* 3.8 7.2 - - - +
270B SER* 1.3 77.9 - - - +
272B SER* 1.3 56.0 + - - +
274B ILE* 3.3 10.2 - - + +
275B ASN* 2.9 50.9 + - - +
314B PHE* 4.9 6.9 - - + -
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B HIS* 5.6 5.6 - - - -
219B ASP* 3.2 34.1 - - - +
261B LYS* 5.9 1.4 - - - +
268B SER 2.9 16.1 + - - -
269B HIS* 2.6 30.0 + - - -
271B ARG* 1.3 74.0 - - - +
273B ARG* 1.3 59.7 + - - +
275B ASN* 3.3 1.4 + - - +
276B ALA* 3.0 29.3 + - - +
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Residues in contact with ARG 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PRO* 4.2 15.5 - - + +
249B HIS* 3.1 34.5 + - - +
250B ASP 3.3 17.1 + - - -
251B TYR* 3.9 19.2 - - - +
269B HIS* 3.0 34.6 + - + +
270B SER* 3.7 8.7 - - - +
271B ARG 3.4 0.2 - - - -
272B SER* 1.3 78.0 + - - +
274B ILE* 1.3 56.8 + - - +
276B ALA* 3.4 2.8 + - - +
277B TYR* 3.0 42.0 + - + -
307B LEU* 3.7 22.8 - - - +
311B GLU* 3.7 17.9 + - - -
318B TYR* 3.4 23.1 - - - +
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B SER 3.0 15.8 + - - +
271B ARG* 3.3 18.4 - - + +
273B ARG* 1.3 76.1 - - - +
275B ASN* 1.3 69.8 + - - +
277B TYR* 3.8 2.6 - - - +
278B LYS* 2.9 39.6 + - - +
314B PHE* 3.7 36.1 - - + +
317B ASP* 3.7 31.6 - - + +
318B TYR* 4.1 24.7 - - + +
321B LEU* 4.6 9.2 - - + -
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Residues in contact with ASN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B SER* 3.3 19.4 + - - -
219B ASP* 2.9 30.2 + - - +
220B VAL* 4.2 5.3 - - + +
224B ILE* 3.8 10.1 - - + +
228B HIS* 3.0 23.8 + - + -
271B ARG* 2.9 28.8 + - - +
272B SER 3.8 0.2 - - - +
273B ARG 3.3 0.2 - - - -
274B ILE* 1.3 78.3 - - - +
276B ALA* 1.3 60.2 + - - +
278B LYS* 3.3 21.9 + - - -
279B GLY 3.0 22.9 + - - -
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ILE* 4.5 16.3 - - + +
245B ILE* 4.0 6.3 - - + +
246B GLU 4.4 9.2 - - - +
248B PRO* 3.7 26.0 - - + -
272B SER 3.0 17.2 + - - +
273B ARG* 3.8 0.7 - - - +
274B ILE 3.4 0.2 - - - -
275B ASN* 1.3 77.4 - - - +
277B TYR* 1.3 57.8 + - - +
279B GLY* 3.3 1.6 + - - -
280B LEU* 2.9 32.5 + - - +
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Residues in contact with TYR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 4.4 5.4 - - - +
248B PRO* 3.9 29.8 + - + +
249B HIS 4.7 2.1 + - - -
273B ARG* 3.0 40.7 + - + +
274B ILE 4.0 3.6 - - - +
276B ALA* 1.3 74.3 - - - +
278B LYS* 1.3 60.2 + - - +
280B LEU* 3.3 11.2 + - + +
281B ALA* 2.9 34.1 + - - +
300B LEU* 4.3 14.1 - - + -
303B GLU* 2.6 37.7 + - + +
304B LEU* 3.8 25.1 - - + -
307B LEU* 3.7 26.4 - - + +
318B TYR* 4.1 16.6 - + + -
321B LEU* 4.1 7.4 - - + -
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Residues in contact with LYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ALA 4.9 0.2 - - - +
228B HIS* 3.6 32.8 - - + +
274B ILE* 2.9 30.8 + - - +
275B ASN* 3.6 16.5 + - - +
276B ALA 3.3 0.2 - - - -
277B TYR* 1.3 75.9 - - - +
279B GLY* 1.3 61.2 + - - +
281B ALA 3.9 6.1 + - - -
282B SER* 4.1 12.3 + - - -
317B ASP* 6.3 2.7 - - - -
321B LEU* 3.9 27.1 - - + +
324B GLN* 4.6 4.5 + - - +
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Residues in contact with GLY 279 (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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224B ILE* 4.6 2.7 - - - -
227B ALA* 3.6 8.4 - - - +
228B HIS* 3.3 17.2 + - - -
245B ILE* 3.5 24.3 - - - +
275B ASN 3.0 12.6 + - - -
276B ALA 3.8 2.9 - - - -
277B TYR 3.2 0.2 - - - -
278B LYS* 1.3 76.6 - - - +
280B LEU* 1.3 62.8 + - - +
282B SER* 3.5 16.5 + - - -
285B TYR* 3.8 4.3 - - - +
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Residues in contact with LEU 280 (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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245B ILE* 3.9 22.4 - - + +
247B ARG* 3.9 54.1 - - + +
248B PRO* 4.1 10.1 - - + -
276B ALA 2.9 19.2 + - - +
277B TYR* 3.8 15.3 - - + +
279B GLY* 1.3 76.4 - - - +
281B ALA* 1.3 57.4 + - - +
282B SER 3.3 4.2 + - - -
285B TYR* 3.7 33.9 - - + +
286B LEU* 3.8 13.5 - - - +
300B LEU* 3.4 19.0 - - + +
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B TYR 2.9 17.7 + - - +
278B LYS 3.9 1.3 + - - -
279B GLY 3.3 0.6 - - - -
280B LEU* 1.3 75.5 - - - +
282B SER* 1.3 52.4 + - - +
283B PRO* 4.4 0.3 - - - +
286B LEU* 4.5 6.4 - - - +
300B LEU* 3.8 8.7 - - + -
304B LEU* 4.0 15.5 - - + -
321B LEU* 4.2 11.0 - - + +
324B GLN* 2.4 42.7 + - - +
325B CYS* 3.6 21.4 + - - -
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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