Contacts of the helix formed by residues 273 - 288 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ARG* 4.8 1.6 - - - +
271B THR 3.2 0.6 + - - -
272B THR* 1.3 76.9 - - - +
274B ALA* 1.3 63.7 + - - +
275B GLY 3.3 2.2 - - - -
276B ASP* 3.3 23.3 + - - -
277B LEU* 2.9 30.3 + - - +
306B VAL* 3.8 4.0 - - - -
312B PRO* 4.3 12.3 - - - -
401B ADN 3.6 10.2 + - - -
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B THR* 3.1 19.2 + - + +
272B THR 3.5 1.0 + - - -
273B GLY* 1.3 76.2 - - - +
275B GLY* 1.3 60.0 + - - +
277B LEU 3.9 0.2 - - - -
278B PHE* 3.0 25.3 + - - +
303B ALA* 3.4 17.5 - - + +
306B VAL* 3.8 11.2 - - - +
307B ILE* 3.6 18.6 - - + -
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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
----------------------------------------------------------
152B TYR* 5.1 1.3 + - - -
211B PHE* 5.7 0.9 - - - -
243B THR* 5.5 7.6 - - - -
273B GLY 3.3 0.2 - - - -
274B ALA* 1.3 76.0 - - - +
276B ASP* 1.3 66.0 + - - +
278B PHE* 3.2 9.8 + - - +
279B ALA* 3.1 21.7 + - - +
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Residues in contact with ASP 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 2.2 40.3 + - - +
61B ASN* 3.0 32.4 + - + -
62B THR* 2.7 28.1 + - - +
152B TYR* 5.0 2.6 + - - -
273B GLY* 3.3 9.2 + - - +
275B GLY* 1.3 75.8 - - - +
277B LEU* 1.3 58.2 + - + +
279B ALA* 3.2 5.3 + - - +
280B SER* 3.0 18.7 + - - -
401B ADN 2.7 26.7 + - - -
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASN* 4.1 12.3 - - + +
65B GLY* 3.8 15.7 - - - -
273B GLY 2.9 18.8 + - - +
274B ALA 4.1 0.2 - - - +
276B ASP* 1.3 82.4 - - + +
278B PHE* 1.3 67.1 + - - +
279B ALA 3.2 0.4 - - - -
280B SER* 3.3 16.4 - - - +
281B GLY 3.1 18.5 + - - -
302B ALA* 3.3 28.5 - - + +
303B ALA 4.0 1.3 - - - +
306B VAL* 4.0 10.1 - - + -
312B PRO 3.4 25.1 - - - +
314B PRO* 3.7 30.5 - - + -
318B LEU* 3.9 10.1 - - + -
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Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 3.8 17.7 - + - -
241B ALA* 3.8 23.6 - - + -
243B THR* 3.5 30.7 - - + -
249B ALA* 3.7 28.7 - - + -
251B ILE* 4.0 16.2 - - + -
274B ALA 3.0 14.6 + - - +
275B GLY* 3.2 11.0 + - - +
277B LEU* 1.3 75.0 - - - +
279B ALA* 1.3 58.7 + - - +
282B PHE* 2.9 35.7 + + + +
296B GLY* 3.8 17.3 - - - -
299B GLY* 3.3 31.7 - - - +
300B CYS* 3.7 7.4 - - - -
303B ALA* 4.0 6.3 - - + +
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B THR* 3.9 6.7 - - + -
152B TYR* 3.6 34.5 - - + +
211B PHE* 3.8 25.6 - - + -
275B GLY 3.1 10.5 + - - +
276B ASP 3.3 10.1 - - - +
277B LEU 3.2 0.2 - - - -
278B PHE* 1.3 73.1 - - - +
280B SER* 1.3 59.9 + - - +
283B LEU* 2.8 37.0 + - + +
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Residues in contact with SER 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASN 3.7 1.0 + - - -
62B THR* 2.7 32.7 + - - +
65B GLY* 3.3 28.8 - - - -
66B VAL* 3.6 13.7 - - - +
69B LEU* 3.6 4.9 - - - +
276B ASP 3.0 8.3 + - - -
277B LEU* 3.1 17.2 + - - +
279B ALA* 1.3 76.8 - - - +
281B GLY* 1.3 57.1 + - - +
284B TYR* 2.9 31.4 + - - +
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Residues in contact with GLY 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.6 16.4 - - - -
277B LEU 3.1 10.3 + - - -
278B PHE 3.8 0.4 - - - -
280B SER* 1.3 73.5 - - - +
282B PHE* 1.3 60.4 + - - +
284B TYR* 3.4 1.7 + - - +
285B GLY* 2.9 25.3 + - - -
298B LEU* 3.5 31.7 - - - +
299B GLY* 3.7 7.6 - - - -
302B ALA* 4.5 0.9 - - - +
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Residues in contact with PHE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ILE* 4.5 10.5 - - + -
211B PHE* 3.7 28.5 - + + -
239B ILE* 4.4 8.1 - - + -
241B ALA* 4.1 11.9 - - + -
251B ILE* 3.7 40.2 - - + -
278B PHE* 2.9 23.1 + + + +
281B GLY* 1.3 76.6 - - - +
283B LEU* 1.3 56.4 + - + +
285B GLY 3.3 0.9 + - - -
286B TYR* 2.7 54.1 + + + +
292B LEU* 3.9 23.3 - - + -
295B CYS* 3.5 37.4 + - + +
296B GLY 3.9 1.3 - - - -
299B GLY* 3.8 0.4 - - - -
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 3.9 27.6 - - + -
62B THR* 4.5 3.4 - - + -
66B VAL* 4.8 1.8 - - + -
150B VAL* 4.2 24.5 - - + -
152B TYR* 3.7 44.2 - - + -
182B SER* 4.4 3.4 - - - +
209B ILE* 5.0 6.3 - - + -
211B PHE* 3.9 22.9 - - + -
279B ALA 2.8 27.3 + - - +
280B SER 4.3 1.3 - - - +
282B PHE* 1.3 78.2 - - + +
284B TYR* 1.3 61.7 + - - +
286B TYR* 3.7 5.1 - - + +
287B THR* 2.8 32.3 + - - +
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Residues in contact with TYR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 4.3 9.7 - - - +
69B LEU* 3.5 53.6 + - + -
70B GLY* 3.9 3.6 - - - -
71B GLY* 3.6 31.2 - - - -
280B SER 2.9 19.7 + - - +
281B GLY 3.6 2.9 - - - +
283B LEU* 1.3 76.9 - - - +
285B GLY* 1.3 65.6 + - - +
287B THR* 3.2 7.4 + - - -
288B GLN* 3.2 51.7 + - + +
290B ARG* 5.8 3.1 - - - -
298B LEU* 4.2 20.2 - - + -
322B ALA* 5.8 0.7 - - + -
328B ILE 4.2 21.1 + - - -
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLY 2.9 11.7 + - - -
282B PHE 3.7 2.7 - - - -
284B TYR* 1.3 78.9 - - - +
286B TYR* 1.3 63.2 + - - +
288B GLN* 3.1 7.6 + - - -
290B ARG* 3.0 31.8 + - - +
295B CYS* 3.4 12.6 - - - -
298B LEU* 3.6 24.2 - - - -
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Residues in contact with TYR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B VAL* 4.2 18.6 - - + -
180B GLU* 2.9 39.6 + - - -
209B ILE* 3.6 20.1 - - + +
239B ILE* 3.7 28.4 - - + +
282B PHE* 2.7 40.8 + + + +
283B LEU* 3.7 9.6 - - + +
284B TYR 3.2 0.2 - - - -
285B GLY* 1.3 72.7 - - - +
287B THR* 1.3 62.3 + - + +
289B GLY* 3.3 13.5 + - - -
290B ARG 4.9 3.7 - - - +
292B LEU* 4.2 12.8 - - + -
295B CYS* 3.2 9.9 - - - -
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Residues in contact with THR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP* 3.6 38.9 - - - +
4B VAL* 4.2 2.4 - - + +
66B VAL* 5.9 0.2 - - - +
71B GLY* 6.1 0.2 - - - -
149B LYS* 3.0 43.2 + - + +
150B VAL* 3.5 32.3 - - + -
283B LEU 2.8 23.0 + - - +
284B TYR* 3.2 9.7 + - - -
286B TYR* 1.3 79.0 - - + +
288B GLN* 1.3 62.0 + - - +
289B GLY 3.3 2.0 - - - -
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Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP* 4.1 17.5 - - - +
71B GLY* 5.2 1.4 - - - -
149B LYS* 4.9 2.1 + - - -
284B TYR* 3.2 48.3 + - + +
285B GLY* 3.1 6.4 + - - +
287B THR* 1.3 86.4 + - - +
289B GLY* 1.3 61.1 + - - +
290B ARG* 3.4 17.1 - - + +
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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