Contacts of the helix formed by residues 273 - 288 (chain A) in PDB entry 4K8T
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 GLY 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ARG* 4.9 1.4 - - - +
271A THR 3.1 0.8 + - - -
272A THR* 1.3 77.8 - - - +
274A ALA* 1.3 58.3 + - - +
275A GLY 3.4 1.8 - - - -
276A ASP* 3.2 23.3 + - - -
277A LEU* 2.9 35.3 + - - +
306A VAL* 3.7 4.3 - - - -
312A PRO* 4.2 13.5 - - - -
401A ADN 3.7 9.2 + - - -
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 3.1 19.3 + - - +
272A THR 3.5 0.8 + - - -
273A GLY* 1.3 77.1 - - - +
275A GLY* 1.3 57.6 + - - +
277A LEU 3.8 0.2 - - - -
278A PHE* 2.9 25.7 + - - +
303A ALA* 3.4 18.7 - - + +
306A VAL* 3.8 11.6 - - - +
307A ILE* 3.6 18.2 - - + -
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TYR* 5.0 1.8 + - - -
211A PHE* 5.6 0.7 - - - +
243A THR* 5.5 7.9 - - - -
274A ALA* 1.3 76.7 - - - +
276A ASP* 1.3 67.8 + - - +
278A PHE* 3.4 9.6 + - - +
279A ALA* 3.2 21.5 + - - +
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Residues in contact with ASP 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER* 2.4 36.2 + - - +
61A ASN* 2.9 34.1 + - + -
62A THR* 2.8 26.9 + - - +
152A TYR* 5.0 2.6 + - - -
273A GLY* 3.2 9.5 + - - +
275A GLY* 1.3 78.9 - - - +
277A LEU* 1.3 57.3 + - + +
279A ALA* 3.3 2.8 + - - +
280A SER* 3.1 19.0 + - - -
401A ADN 2.7 27.6 + - - -
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Residues in contact with LEU 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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61A ASN* 4.3 11.2 - - + +
65A GLY* 3.9 24.5 - - - -
273A GLY 2.9 18.8 + - - +
274A ALA 4.1 0.2 - - - +
276A ASP* 1.3 82.1 - - + +
278A PHE* 1.3 67.6 + - - +
279A ALA 3.2 0.2 - - - -
280A SER* 3.1 5.9 + - - +
281A GLY 3.0 18.2 + - - -
302A ALA* 3.2 31.1 - - + +
303A ALA 4.0 0.9 - - - +
306A VAL* 3.9 11.4 - - + -
312A PRO 3.3 26.2 - - - +
313A ARG* 4.9 0.2 - - - -
314A PRO* 3.6 31.0 - - + -
318A LEU* 4.0 9.6 - - + -
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Residues in contact with PHE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PHE* 3.8 17.3 - + - -
241A ALA* 3.8 22.4 - - + -
243A THR* 3.4 31.9 - - + -
249A ALA* 3.7 28.3 - - + -
251A ILE* 4.1 15.7 - - + -
274A ALA 2.9 17.9 + - - +
275A GLY* 3.5 7.6 - - - +
277A LEU* 1.3 75.6 - - - +
279A ALA* 1.3 53.2 + - - +
282A PHE* 2.8 41.7 + + - +
296A GLY* 3.8 17.3 - - - -
299A GLY* 3.2 32.2 - - - +
300A CYS* 3.7 7.6 - - - -
303A ALA* 4.0 7.0 - - + +
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR* 4.0 5.6 - - + -
152A TYR* 3.6 33.2 - - + +
211A PHE* 3.8 27.4 - - + -
275A GLY 3.2 7.9 + - - +
276A ASP 3.5 9.9 - - - +
278A PHE* 1.3 76.5 - - - +
280A SER* 1.3 66.6 + - - +
283A LEU* 2.9 30.5 + - + +
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN 3.8 1.2 + - - -
62A THR* 2.6 34.0 + - - +
65A GLY* 3.4 28.7 - - - -
66A VAL* 3.7 13.5 - - - +
69A LEU* 3.8 4.4 - - - +
276A ASP 3.1 6.7 + - - -
277A LEU* 3.1 18.4 + - - -
279A ALA* 1.3 76.5 - - - +
281A GLY* 1.3 62.0 + - - +
284A TYR* 3.0 26.5 + - - +
302A ALA* 5.0 0.2 - - - -
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Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.7 15.0 - - - -
277A LEU 3.0 11.4 + - - -
278A PHE 3.7 0.4 - - - -
280A SER* 1.3 76.3 - - - +
282A PHE* 1.3 64.8 + - - +
284A TYR* 3.5 1.6 - - - +
285A GLY* 3.0 19.9 + - - -
298A LEU* 3.5 18.4 - - - +
299A GLY* 3.6 20.9 - - - -
302A ALA* 4.3 1.1 - - - +
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Residues in contact with PHE 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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209A ILE* 4.7 10.5 - - + -
211A PHE* 3.7 29.2 - + + -
239A ILE* 4.3 7.9 - - + -
241A ALA* 4.1 10.8 - - + -
251A ILE* 3.6 46.9 - - + -
278A PHE* 2.8 22.8 + + + +
279A ALA 4.0 0.2 - - - +
281A GLY* 1.3 77.5 - - - +
283A LEU* 1.3 63.3 + - + +
285A GLY 3.5 0.3 + - - -
286A TYR* 2.8 46.2 + + + +
292A LEU* 4.0 12.6 - - + -
295A CYS* 3.4 39.4 - - + +
296A GLY 3.9 1.3 - - - -
299A GLY 3.7 2.0 - - - +
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 3.9 33.1 - - + +
62A THR* 4.6 4.5 - - + -
66A VAL* 4.8 1.8 - - + -
150A VAL* 4.2 21.5 - - + -
152A TYR* 3.7 38.8 - - + -
182A SER* 4.5 3.6 - - - +
209A ILE* 5.0 4.7 - - + -
211A PHE* 3.8 22.2 - - + -
279A ALA 2.9 24.3 + - - +
280A SER 4.3 1.1 - - - +
282A PHE* 1.3 78.6 - - + +
284A TYR* 1.3 53.8 + - - +
286A TYR* 4.0 8.5 - - + -
287A THR* 2.7 41.3 + - - +
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Residues in contact with TYR 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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66A VAL* 4.5 10.5 - - + +
69A LEU* 3.4 54.7 + - + -
70A GLY* 4.0 3.3 - - - -
71A GLY* 3.7 28.5 - - - -
280A SER 3.0 19.1 + - - +
281A GLY 3.5 2.7 - - - +
283A LEU* 1.3 73.2 - - - +
285A GLY* 1.3 68.2 + - - +
287A THR* 3.0 13.8 + - - -
288A GLN* 3.0 49.1 + - + +
290A ARG* 5.8 2.7 - - + -
298A LEU* 4.0 21.8 - - + -
322A ALA* 5.8 0.9 - - + -
328A ILE 4.5 17.9 + - - -
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Residues in contact with GLY 285 (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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281A GLY 3.0 9.2 + - - -
282A PHE 3.8 2.2 - - - -
284A TYR* 1.3 82.1 - - - +
286A TYR* 1.3 56.2 + - - +
288A GLN* 2.8 19.2 + - - -
290A ARG* 3.1 28.1 + - - +
295A CYS* 3.5 11.9 - - - -
298A LEU* 3.6 23.3 - - - -
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Residues in contact with TYR 286 (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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150A VAL* 4.1 21.1 - - + -
180A GLU* 2.8 39.1 + - - -
209A ILE* 3.6 19.5 - - + +
239A ILE* 3.7 29.3 - - + +
282A PHE* 2.8 40.8 + + + +
283A LEU* 3.7 10.5 - - + +
284A TYR 3.2 0.2 - - - -
285A GLY* 1.3 70.5 - - - +
287A THR* 1.3 63.9 + - + +
288A GLN 3.3 1.0 + - - -
289A GLY* 3.3 12.3 + - - -
290A ARG 4.8 4.4 - - - +
292A LEU* 4.3 13.2 - - + -
295A CYS* 3.1 10.1 - - - -
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Residues in contact with THR 287 (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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3A ASP* 3.6 47.0 - - - +
4A VAL* 4.2 3.0 - - + +
149A LYS* 2.9 41.4 + - + +
150A VAL* 3.8 22.9 - - + -
283A LEU 2.7 24.8 + - - +
284A TYR* 3.0 11.4 + - - -
286A TYR* 1.3 77.6 - - + +
288A GLN* 1.3 61.6 + - - +
289A GLY 3.3 1.8 - - - -
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Residues in contact with GLN 288 (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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3A ASP* 4.1 18.5 - - - +
70A GLY 5.3 1.0 - - - +
71A GLY* 4.8 1.7 - - - -
149A LYS* 5.2 1.0 + - - -
284A TYR* 3.0 58.4 + - + +
285A GLY* 2.8 7.1 + - - +
287A THR* 1.3 82.2 + - - +
289A GLY* 1.3 61.8 + - - +
290A ARG* 3.3 16.9 + - + +
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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