Contacts of the helix formed by residues 275 - 290 (chain B) in PDB entry 6T2C
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 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLY* 1.3 71.1 - - - -
276B ASN* 1.3 61.2 + - - -
277B GLU 3.3 0.4 + - - -
278B LYS* 3.9 8.7 + - - +
279B LYS* 3.8 18.6 - - - +
495B PHE* 4.3 12.2 - - - -
504B ASN* 5.3 2.1 + - - -
536B ASN* 4.2 36.2 - - - +
538B ASP* 5.8 0.2 - - - -
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Residues in contact with ASN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLY 3.6 0.8 + - - -
275B GLY* 1.3 70.1 - - - -
277B GLU* 1.3 61.8 + - + +
278B LYS 3.2 6.1 + - - -
279B LYS* 3.9 24.5 + - - +
280B ALA* 3.9 16.9 + - - +
535B ILE 5.4 7.2 + - - +
536B ASN 5.0 0.4 + - - -
237C GLY 4.8 9.2 - - - +
238C THR* 6.0 0.7 - - - -
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Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 3.8 29.7 - - + +
274B GLY 3.5 13.4 + - - +
275B GLY 3.3 1.4 - - - -
276B ASN* 1.3 79.5 - - + +
278B LYS* 1.3 57.9 + - - +
280B ALA* 4.5 9.2 - - - +
281B LYS* 3.8 13.9 + - - +
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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
----------------------------------------------------------
270B GLY* 4.0 23.3 + - - +
271B LEU* 5.6 2.2 - - - +
273B VAL* 4.6 10.9 + - + +
274B GLY* 4.3 12.9 + - - -
275B GLY 3.9 9.1 + - - +
276B ASN 3.2 0.4 - - - -
277B GLU* 1.3 79.1 - - - +
279B LYS* 1.3 64.4 + - - +
280B ALA 3.2 2.0 - - - -
281B LYS* 3.2 18.1 + - + +
282B LEU* 3.3 20.3 - - + +
441B LEU* 6.3 0.2 - - + -
443B SER* 4.7 4.9 + - - -
492B PHE* 3.6 27.8 - - + -
493B THR* 2.9 27.7 + - - +
495B PHE* 3.8 30.4 - - + -
506B SER* 6.0 0.2 - - - -
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLY 3.8 18.8 - - - +
276B ASN* 3.9 24.9 + - - +
278B LYS* 1.3 73.4 - - - +
280B ALA* 1.3 60.9 + - - +
282B LEU* 3.3 6.7 + - - +
283B ALA* 3.0 29.9 + - - +
495B PHE* 4.2 11.4 - - + -
501B PHE* 5.9 0.8 - - - -
502B VAL* 3.5 52.9 + - + +
504B ASN* 4.5 1.1 - - - +
536B ASN 5.6 0.2 - - - -
538B ASP* 2.5 40.9 + - - -
238C THR* 4.9 12.9 + - - +
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ASN* 3.9 15.4 + - - +
277B GLU* 4.8 8.3 - - - +
278B LYS 3.2 0.6 - - - -
279B LYS* 1.3 77.7 - - - +
281B LYS* 1.3 56.8 + - + +
283B ALA* 3.8 5.2 - - - +
284B ASN* 2.8 43.8 + - - +
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Residues in contact with LYS 281 (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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263B CYS 5.2 1.8 + - - -
264B GLU* 5.7 3.6 + - - +
266B LEU 4.3 10.3 + - - -
267B GLU* 4.1 33.7 + - - +
269B SER* 2.4 38.4 + - - +
270B GLY* 4.8 4.9 - - - -
271B LEU 4.7 2.4 + - - -
273B VAL* 4.0 30.1 - - + +
277B GLU 3.8 14.4 - - - +
278B LYS* 3.2 11.6 + - + +
279B LYS 3.2 0.4 - - - -
280B ALA* 1.3 75.0 - - + +
282B LEU* 1.3 59.3 + - + +
284B ASN* 3.3 4.7 + - - +
285B VAL* 3.0 35.8 + - - +
441B LEU* 4.4 16.6 - - + -
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LYS* 3.3 29.2 - - + +
279B LYS* 3.3 9.5 + - - +
281B LYS* 1.3 80.0 - - - +
283B ALA* 1.3 62.4 + - - +
285B VAL* 3.3 8.7 - - - +
286B ILE* 3.1 30.8 + - - +
441B LEU* 3.9 18.6 - - + -
490B PHE* 3.7 34.5 - - + -
492B PHE* 4.2 15.5 - - + -
495B PHE* 4.3 27.1 - - + +
497B TYR* 4.1 21.5 - - + -
502B VAL* 4.5 8.3 - - + -
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LYS 3.0 16.5 + - - +
280B ALA* 4.2 4.7 - - - +
282B LEU* 1.3 76.7 - - - +
284B ASN* 1.3 56.3 + - - +
286B ILE* 4.0 1.5 - - - +
287B LYS* 2.8 54.2 + - - +
497B TYR* 4.4 19.0 - - + +
500B GLY* 5.8 3.8 - - - +
502B VAL* 5.6 2.0 - - + +
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Residues in contact with ASN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLU* 4.9 13.7 - - - +
280B ALA* 2.8 32.0 + - - +
281B LYS* 3.6 6.9 - - - +
282B LEU 3.2 0.2 - - - -
283B ALA* 1.3 76.1 - - - +
285B VAL* 1.3 61.7 + - + +
287B LYS* 3.7 11.2 - - - +
288B LYS* 2.9 30.0 + - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLU* 5.2 9.0 - - + +
268B GLN* 5.7 2.7 - - + -
281B LYS 3.0 19.9 + - - +
282B LEU* 3.3 15.9 - - - +
284B ASN* 1.3 78.2 - - + +
286B ILE* 1.3 62.2 + - + +
288B LYS* 4.4 7.2 - - + -
289B MET* 3.0 37.3 + - + +
439B ASP* 5.1 8.5 - - - +
440B GLY* 4.7 13.0 - - - +
441B LEU* 3.8 30.7 - - + -
450B ILE* 4.5 18.3 - - + +
490B PHE* 5.3 2.9 - - + -
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Residues in contact with ILE 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU 3.1 17.6 + - - +
283B ALA 4.1 1.3 - - - +
285B VAL* 1.3 79.7 - - + +
287B LYS* 1.3 63.1 + - + +
289B MET* 5.2 0.7 - - + -
290B MET* 3.2 30.8 + - + +
450B ILE* 4.1 20.0 - - + -
487B THR* 3.7 31.9 - - + -
488B GLY* 5.3 3.1 - - - +
490B PHE* 3.6 32.8 - - + -
497B TYR* 3.4 32.1 - - + +
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Residues in contact with LYS 287 (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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283B ALA* 2.8 42.0 + - - +
284B ASN* 3.8 13.9 - - - +
286B ILE* 1.3 78.9 - - + +
288B LYS* 1.3 60.2 + - - +
290B MET 4.2 0.6 - - - -
291B ALA* 3.3 23.2 + - - +
497B TYR* 5.9 1.1 - - - +
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Residues in contact with LYS 288 (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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284B ASN 2.9 17.8 + - - +
285B VAL* 3.9 8.3 - - + +
287B LYS* 1.3 77.3 - - - +
289B MET* 1.3 72.1 + - + +
290B MET 3.2 1.4 + - - -
291B ALA* 3.3 17.1 + - - +
292B LYS 5.0 0.2 + - - -
439B ASP* 4.2 21.1 + - - +
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Residues in contact with MET 289 (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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285B VAL* 3.0 23.4 + - + +
286B ILE* 4.8 1.3 - - + +
288B LYS* 1.3 89.2 - - + +
290B MET* 1.3 59.4 + - + +
291B ALA 3.5 1.0 + - - -
297B GLU* 5.0 0.2 - - - +
437B TRP* 3.7 30.5 - - + +
438B TRP* 4.2 2.9 - - - +
439B ASP* 3.7 36.3 - - + +
450B ILE* 3.7 37.2 - - + +
452B ASN* 2.6 51.1 + - - +
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Residues in contact with MET 290 (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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286B ILE* 3.2 22.1 + - + +
287B LYS* 4.2 3.1 - - - -
289B MET* 1.3 79.6 - - + +
291B ALA* 1.3 63.7 + - - +
292B LYS 3.8 0.4 - - - -
293B SER* 3.9 23.3 + - - -
299B SER* 3.7 35.0 - - - +
452B ASN* 4.9 0.7 - - - +
487B THR* 3.8 39.7 - - + +
488B GLY* 5.5 1.3 - - - -
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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