Contacts of the helix formed by residues 267 - 281 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A ASP* 3.3 12.0 + - - +
266A SER* 1.3 78.1 + - - +
268A SER* 1.3 60.4 + - - +
269A HIS 3.2 1.3 + - - -
270A SER* 3.3 6.3 + - - -
271A ARG* 3.0 40.1 + - + +
314A PHE* 5.4 11.6 - + - -
336D CYS 3.7 20.2 - - - -
337D ARG 3.3 21.1 - - - -
338D ASN 3.5 16.4 - - - +
339D THR* 4.5 7.2 - - - -
342D VAL* 4.1 11.0 - - + -
382D ASN* 3.3 35.9 - - - -
385D GLN* 4.1 33.0 - - + +
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A HIS* 4.3 23.1 + - - -
265A ASP* 3.4 27.6 + - - +
267A PHE* 1.3 77.8 - - - +
269A HIS* 1.3 61.6 + - - +
271A ARG* 3.8 7.5 - - - +
272A SER* 2.9 29.5 + - - -
337D ARG 3.8 17.9 - - - -
338D ASN* 4.6 7.2 - - - -
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Residues in contact with HIS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A CYS* 4.3 16.8 + - + +
261A LYS* 3.8 40.6 - - + +
262A GLN* 4.5 21.2 + - + -
265A ASP 3.5 17.5 + - - +
266A SER* 4.4 6.5 - - - +
267A PHE 3.2 0.6 - - - -
268A SER* 1.3 78.3 + - - +
270A SER* 1.3 63.5 + - - +
272A SER* 2.6 24.4 + - - -
273A ARG* 3.0 35.6 + - + +
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A TYR* 5.9 1.0 - - - -
266A SER 3.3 14.7 + - - -
267A PHE* 3.3 8.5 + - - -
269A HIS* 1.3 79.6 - - - +
271A ARG* 1.3 60.8 + - - +
273A ARG* 3.4 10.8 + - - +
274A ILE* 3.0 29.6 + - - +
311A GLU* 4.1 14.5 + - - -
314A PHE* 3.8 30.9 - - - -
318A TYR* 5.2 0.2 + - - -
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Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A SER* 4.9 7.5 + - - -
219A ASP* 6.2 0.2 - - - -
267A PHE* 3.0 32.6 + - + +
268A SER* 3.8 7.6 - - - +
270A SER* 1.3 79.1 - - - +
272A SER* 1.3 55.2 + - - +
274A ILE* 3.3 10.6 - - + +
275A ASN* 2.9 49.6 + - - +
314A PHE* 4.9 7.3 - - + -
334D ASP* 4.0 13.9 + - - -
335D LEU 5.1 1.0 + - - -
336D CYS 3.0 26.8 + - - -
337D ARG* 4.1 37.4 - - - +
382D ASN* 5.2 2.8 - - - +
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A HIS* 5.6 4.9 - - - -
219A ASP* 3.2 33.0 - - - +
261A LYS* 5.9 1.6 - - - +
268A SER 2.9 17.3 + - - -
269A HIS* 2.6 30.1 + - - -
271A ARG* 1.3 74.3 - - - +
273A ARG* 1.3 60.1 + - - +
275A ASN* 3.3 1.6 + - - +
276A ALA* 3.0 30.0 + - - +
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Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PRO* 4.4 14.9 - - + +
249A HIS* 3.1 34.1 + - - +
250A ASP 3.3 15.6 + - - -
251A TYR* 3.9 19.5 - - - +
269A HIS* 3.0 36.5 + - + +
270A SER* 3.7 8.0 - - - +
272A SER* 1.3 78.0 + - - +
274A ILE* 1.3 56.9 + - - +
276A ALA* 3.4 2.8 + - - +
277A TYR* 3.0 41.3 + - + -
307A LEU* 3.7 22.8 - - - +
311A GLU* 3.7 19.5 + - - -
318A TYR* 3.4 22.7 - - - +
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A SER 3.0 16.4 + - - +
271A ARG* 3.3 18.4 - - + +
273A ARG* 1.3 75.2 - - - +
275A ASN* 1.3 70.3 + - - +
277A TYR* 4.0 2.2 - - - +
278A LYS* 2.9 40.1 + - - +
314A PHE* 3.7 35.7 - - + -
317A ASP* 3.7 31.9 - - + +
318A TYR* 4.1 24.0 - - + +
321A LEU* 4.6 8.3 - - + -
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Residues in contact with ASN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER* 3.3 19.4 + - - -
219A ASP* 2.9 29.5 + - - +
220A VAL* 4.2 4.7 - - + +
224A ILE* 3.8 10.1 - - + +
228A HIS* 3.0 24.4 + - + -
271A ARG* 2.9 29.4 + - - +
272A SER 3.8 0.2 - - - +
274A ILE* 1.3 78.1 - - - +
276A ALA* 1.3 59.6 + - - +
278A LYS* 3.3 22.5 + - - -
279A GLY 3.0 23.0 + - - -
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ILE* 4.5 16.5 - - + +
245A ILE* 4.0 7.1 - - + +
246A GLU 4.4 9.4 - - - +
248A PRO* 3.7 26.5 - - + -
272A SER 3.0 17.2 + - - +
273A ARG* 3.8 0.9 - - - +
275A ASN* 1.3 77.6 - - - +
277A TYR* 1.3 56.8 + - - +
279A GLY* 3.3 1.7 + - - -
280A LEU* 2.9 33.0 + - - +
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Residues in contact with TYR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 4.4 5.7 - - - +
248A PRO* 3.9 31.7 + - + +
249A HIS 4.7 2.3 + - - -
273A ARG* 3.0 41.4 + - + +
274A ILE 4.0 3.1 - - - +
276A ALA* 1.3 74.1 - - - +
278A LYS* 1.3 59.7 + - - +
280A LEU* 3.8 10.9 - - + +
281A ALA* 2.9 33.8 + - - +
300A LEU* 4.3 14.1 - - + -
303A GLU* 2.6 37.9 + - + +
304A LEU* 3.8 25.6 - - + -
307A LEU* 3.7 26.6 - - + +
318A TYR* 4.1 15.9 - + + -
321A LEU* 4.1 7.2 - - + -
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A HIS* 3.6 32.7 - - + +
274A ILE* 2.9 32.1 + - - +
275A ASN* 3.6 16.3 + - - +
277A TYR* 1.3 76.3 - - - +
279A GLY* 1.3 60.0 + - - +
281A ALA 3.9 6.6 + - - -
282A SER* 4.1 12.1 + - - -
317A ASP* 6.3 3.1 - - - -
321A LEU* 3.9 27.7 - - + +
324A GLN* 4.6 3.9 + - - +
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ILE* 4.6 2.9 - - - -
227A ALA* 3.6 9.0 - - - +
228A HIS* 3.3 16.8 + - - -
245A ILE* 3.5 25.2 - - - +
275A ASN 3.0 12.2 + - - -
276A ALA 3.8 2.7 - - - -
278A LYS* 1.3 77.0 - - - +
280A LEU* 1.3 62.1 + - - +
282A SER* 3.5 16.5 + - - -
285A TYR* 3.8 4.3 - - - +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ILE* 3.9 22.7 - - + +
247A ARG* 3.9 53.4 - - + +
248A PRO* 4.1 10.1 - - + -
276A ALA 2.9 19.9 + - - +
277A TYR* 3.3 15.2 + - + +
279A GLY* 1.3 76.6 - - - +
281A ALA* 1.3 57.6 + - - +
282A SER 3.3 4.6 + - - -
285A TYR* 3.7 34.1 - - + -
286A LEU* 3.8 13.3 - - - +
300A LEU* 3.4 18.5 - - + +
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Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A TYR 2.9 17.7 + - - +
278A LYS 3.9 1.5 + - - +
279A GLY 3.3 1.0 - - - -
280A LEU* 1.3 75.6 - - - +
282A SER* 1.3 52.3 + - - +
283A PRO* 4.4 0.3 - - - +
286A LEU* 4.5 6.3 - - - +
300A LEU* 3.8 8.5 - - + -
304A LEU* 4.0 15.7 - - + -
321A LEU* 4.2 9.4 - - + +
324A GLN* 2.4 41.9 + - - +
325A CYS* 3.6 22.0 - - - -
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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