Contacts of the helix formed by residues 268 - 285 (chain A) in PDB entry 4ACR
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 CYS 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PRO* 1.3 73.1 - - - +
269A PRO* 1.3 67.5 - - + +
270A ASP* 4.5 1.1 - - + +
271A TYR* 3.4 10.9 - - + +
272A CYS* 2.9 29.0 + - - +
415A CYS* 2.0 48.5 - - - -
416A TRP 3.0 20.4 + - - -
417A ASN 4.0 1.3 - - - -
422A GLY 3.6 9.2 - - - -
424A TYR* 3.7 31.4 - - + -
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Residues in contact with PRO 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PRO 4.0 4.3 - - - +
268A CYS* 1.3 87.8 - - + +
270A ASP* 1.3 66.3 + - - +
272A CYS* 3.4 6.2 + - + +
273A ARG* 2.9 56.6 + - - +
401A CYS* 4.1 9.1 - - + +
415A CYS* 4.8 6.5 - - + -
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Residues in contact with ASP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A CYS* 3.4 0.8 - - + +
269A PRO* 1.3 77.9 - - - +
271A TYR* 1.3 59.7 + - - +
273A ARG* 3.3 21.0 + - - +
274A ASN* 2.9 33.3 + - - +
424A TYR* 3.5 25.5 - - + +
426A PRO 4.4 5.8 - - - +
427A GLU* 5.1 1.2 - - - -
428A VAL* 3.4 30.5 + - + +
472B ASN* 6.0 0.2 - - - -
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Residues in contact with TYR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA 4.3 1.9 + - - -
252A LYS* 3.3 39.0 + - - +
253A LEU* 3.5 37.9 + - + -
268A CYS* 3.3 14.5 + - + +
269A PRO 3.3 0.2 - - - -
270A ASP* 1.3 76.5 - - - +
272A CYS* 1.3 63.5 + - - +
274A ASN* 3.2 3.1 + - - +
275A VAL* 3.0 33.5 + - + +
416A TRP* 3.5 20.9 - - - -
417A ASN 3.8 20.4 - - - -
418A GLY* 3.8 6.6 - - - -
424A TYR* 3.5 39.8 - + + -
441A GLU* 3.2 31.1 - - + +
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Residues in contact with CYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.8 30.9 - - + +
267A PRO* 5.2 5.2 - - + +
268A CYS 2.9 17.4 + - - +
269A PRO* 3.6 2.2 - - + +
271A TYR* 1.3 75.7 - - - +
273A ARG* 1.3 56.8 + - - +
275A VAL* 3.3 1.7 + - - +
276A LEU* 2.9 45.5 + - - +
400A LEU 4.8 1.6 - - - -
401A CYS* 2.0 48.7 - - + -
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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
----------------------------------------------------------
269A PRO* 2.9 36.8 + - - +
270A ASP* 3.3 26.9 + - - +
272A CYS* 1.3 77.6 - - - +
274A ASN* 1.3 57.4 + - - +
276A LEU* 4.1 0.3 - - - +
277A LYS* 2.9 42.5 + - - +
397A PRO* 4.4 15.7 - - + +
398A GLY* 4.6 10.2 + - - +
401A CYS* 4.0 21.0 - - - +
402A SER* 5.1 8.3 + - - -
428A VAL* 4.1 20.8 - - + +
472B ASN* 3.2 52.6 + - - +
474B ASN* 4.8 8.5 - - - +
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Residues in contact with ASN 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 ASP 2.9 14.7 + - - +
271A TYR 3.7 3.8 - - - +
273A ARG* 1.3 72.7 - - - +
275A VAL* 1.3 60.7 + - - +
277A LYS* 4.5 2.0 - - - +
278A GLY* 2.9 24.3 + - - -
424A TYR* 2.9 35.6 + - - +
426A PRO* 4.4 0.2 - - - +
427A GLU 3.2 21.0 + - - -
428A VAL* 3.4 4.2 - - - +
429A MET* 2.7 40.1 + - - +
439A ASN* 3.0 20.0 + - - +
440A PRO* 4.3 7.8 - - + +
441A GLU* 4.0 8.1 - - + -
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA* 4.1 20.6 - - + +
250A VAL* 4.0 26.9 - - + -
253A LEU* 4.1 24.5 - - + -
271A TYR* 3.0 33.5 + - + +
272A CYS 3.6 6.7 - - - +
274A ASN* 1.3 76.5 - - - +
276A LEU* 1.3 59.9 + - + +
278A GLY* 3.1 3.3 + - - -
279A CYS* 2.9 29.3 + - - -
441A GLU* 3.8 19.7 - - + -
442A VAL* 3.7 8.1 - - - +
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Residues in contact with LEU 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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85A LEU* 4.0 36.6 - - + -
250A VAL* 5.1 1.6 - - + -
253A LEU* 5.2 4.0 - - + -
272A CYS* 2.9 21.5 + - - +
273A ARG 4.1 0.2 - - - +
275A VAL* 1.3 82.7 - - + +
277A LYS* 1.3 60.8 + - - +
279A CYS* 4.4 4.3 - - + +
280A LEU* 2.9 40.9 + - + +
397A PRO* 3.6 43.1 - - + +
400A LEU* 3.7 26.0 - - + -
401A CYS* 3.7 11.9 - - - -
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Residues in contact with LYS 277 (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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273A ARG* 2.9 28.6 + - - +
274A ASN* 4.0 4.3 - - - +
276A LEU* 1.3 73.5 - - - +
278A GLY* 1.3 60.1 + - - +
280A LEU* 4.5 1.8 - - - +
281A ALA* 2.9 33.4 + - - +
394A ILE 5.5 1.8 - - - -
397A PRO* 3.9 22.4 - - + -
428A VAL* 3.4 20.5 - - + +
429A MET* 2.8 32.1 + - + +
430A GLY* 3.8 8.2 - - - +
431A ASP* 3.6 29.2 + - - +
436A GLN* 3.7 16.5 + - - +
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Residues in contact with GLY 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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274A ASN 2.9 16.1 + - - -
275A VAL 3.1 4.7 + - - -
277A LYS* 1.3 77.9 - - - +
279A CYS* 1.3 60.6 + - - +
281A ALA* 4.0 6.4 + - - +
436A GLN* 3.6 16.7 - - - +
439A ASN* 4.1 1.1 - - - -
442A VAL* 4.1 22.4 - - - +
444A VAL* 3.6 17.0 - - - +
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Residues in contact with CYS 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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85A LEU* 4.8 5.2 - - + -
242A LEU* 4.4 10.4 - - + +
246A CYS* 2.0 58.7 - - - +
250A VAL* 4.1 12.6 - - - -
275A VAL* 2.9 23.9 + - - +
276A LEU* 3.4 6.7 + - - +
278A GLY* 1.3 79.1 - - - +
280A LEU* 1.3 67.8 + - + +
281A ALA 3.7 0.5 + - - -
282A ASN* 4.9 2.4 + - - +
283A GLN* 3.9 6.6 + - - +
442A VAL* 4.7 2.7 - - - -
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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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85A LEU* 5.8 2.5 - - + -
89A LEU* 4.0 35.9 - - + -
242A LEU* 4.4 7.9 - - + -
276A LEU* 2.9 30.5 + - + +
277A LYS* 3.8 2.5 - - - -
279A CYS* 1.3 81.1 - - + +
281A ALA* 1.3 65.1 + - - +
282A ASN 3.3 0.2 - - - -
283A GLN* 2.9 34.4 + - + +
284A ALA* 2.9 20.8 + - + +
393A TRP 5.3 4.4 - - - +
396A LEU* 3.9 31.4 - - + -
397A PRO* 4.4 12.6 - - + -
400A LEU* 5.4 2.2 - - + -
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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 LYS 2.9 19.6 + - - +
278A GLY 4.2 5.6 - - - +
279A CYS 3.4 2.4 - - - -
280A LEU* 1.3 74.4 - - - +
282A ASN* 1.3 59.6 + - - +
284A ALA* 2.9 24.7 + - - +
285A ASP* 3.0 10.6 + - - -
432A GLY 3.4 25.6 - - - +
433A LEU* 3.7 22.8 + - + -
436A GLN* 3.8 11.7 - - + +
444A VAL* 5.3 1.1 - - + -
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Residues in contact with ASN 282 (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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240A VAL* 6.0 2.4 - - + +
279A CYS 4.9 2.3 + - - +
280A LEU 3.3 0.6 - - - -
281A ALA* 1.3 77.3 - - - +
283A GLN* 1.3 70.7 + - - +
285A ASP* 3.2 19.8 + - - +
433A LEU* 3.6 30.4 - - - +
448A LYS 4.4 5.7 + - - -
449A PRO* 3.9 1.4 - - - +
450A ASP* 3.5 34.8 + - + +
453A ILE* 3.2 35.6 - - + +
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Residues in contact with GLN 283 (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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89A LEU* 5.9 1.2 - - - +
237A VAL* 4.0 22.7 + - + +
240A VAL* 4.2 30.5 + - - +
241A PRO 5.5 1.0 + - - -
242A LEU* 5.2 5.5 - - - +
279A CYS 3.9 4.8 + - - +
280A LEU* 3.0 43.0 - - + +
282A ASN* 1.3 82.4 + - - +
284A ALA* 1.3 62.0 + - - +
286A LEU* 3.2 29.4 + - - +
393A TRP* 3.5 26.6 - - + +
396A LEU* 6.4 2.5 - - + -
453A ILE* 4.6 4.9 - - + -
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Residues in contact with ALA 284 (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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280A LEU* 2.9 11.4 + - + +
281A ALA* 2.9 14.5 + - - +
283A GLN* 1.3 72.4 - - - +
285A ASP* 1.3 65.0 + - - +
286A LEU 3.1 2.8 + - - -
287A ASP* 3.3 21.0 + - - +
393A TRP* 4.0 19.2 + - - +
394A ILE* 4.6 4.4 - - + +
431A ASP* 4.6 11.6 - - + +
432A GLY* 3.7 22.9 + - - +
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Residues in contact with ASP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ALA 3.0 10.6 + - - +
282A ASN* 3.3 20.1 - - - +
283A GLN 3.2 0.6 - - - -
284A ALA* 1.3 78.6 - - - +
286A LEU* 1.3 57.3 + - - +
287A ASP* 3.1 2.4 + - - +
288A ALA* 4.3 7.6 + - - +
289A GLU* 5.2 1.2 + - - +
432A GLY* 3.7 5.1 - - - -
433A LEU* 3.3 39.7 + - - +
434A ALA 5.0 0.3 + - - -
449A PRO* 5.7 1.9 - - - +
453A ILE* 4.6 2.5 - - + +
457A ILE* 4.1 22.2 - - + +
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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