Contacts of the helix formed by residues 277 - 299 (chain B) in PDB entry 3KTC
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 ASN 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU* 1.3 73.0 - - - +
278B HIS* 1.3 59.7 + - - +
279B VAL* 3.1 12.7 + - - +
280B GLU* 2.8 59.1 + - + +
281B ALA* 3.0 28.6 + - - +
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Residues in contact with HIS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 3.0 34.7 + - - +
16B PHE* 3.9 14.5 - - + +
17B ALA 2.8 31.8 + - - -
18B ASN* 3.6 18.1 + - - -
19B TYR* 3.6 13.1 - + - -
40B ALA* 6.4 0.4 - - + -
273B PRO* 2.9 34.4 + - + -
274B PHE 4.0 9.4 - - - -
276B GLU 2.9 21.7 + - - -
277B ASN* 1.3 73.6 + - - +
279B VAL* 1.3 63.8 + - + +
281B ALA* 3.4 3.5 + - - +
282B ALA* 3.2 18.4 + - - +
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 4.3 10.1 - - + -
40B ALA* 3.5 32.5 - - + +
43B GLU* 3.9 47.3 - - + +
44B VAL* 4.0 4.0 - - - +
277B ASN* 3.1 8.4 + - - +
278B HIS* 1.3 78.4 - - + +
280B GLU* 1.3 64.3 + - + +
282B ALA* 3.2 5.0 + - - +
283B GLN* 3.0 36.2 + - - +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ASN* 2.8 43.2 + - + +
279B VAL* 1.3 71.7 - - + +
281B ALA* 1.3 65.8 + - - +
283B GLN* 3.6 19.4 - - - +
284B LEU* 2.9 25.3 + - - +
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 4.1 2.7 - - + -
242B VAL* 3.9 21.4 - - + +
273B PRO* 3.7 27.4 - - + -
276B GLU* 4.8 6.1 - - + -
277B ASN 3.0 17.6 + - - +
278B HIS 3.5 6.5 - - - +
279B VAL 3.2 0.2 - - - -
280B GLU* 1.3 77.6 - - - +
282B ALA* 1.3 59.5 + - - +
284B LEU* 3.4 5.7 + - - +
285B SER* 2.8 27.9 + - - -
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 3.6 24.1 - - + +
16B PHE* 4.0 8.1 - - + -
44B VAL* 3.7 26.7 - - + -
47B LEU* 5.2 1.3 - - + -
269B LEU* 4.1 9.6 - - + +
278B HIS 3.2 6.6 + - - +
279B VAL 3.2 7.6 + - - +
281B ALA* 1.3 77.5 - - - +
283B GLN* 1.3 62.3 + - - +
285B SER* 3.2 5.9 + - - -
286B ILE* 3.0 27.1 + - + +
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU 3.6 13.1 + - - -
44B VAL* 3.0 36.9 + - + +
279B VAL* 3.0 19.6 + - - +
280B GLU* 3.6 27.8 - - - +
281B ALA 3.3 0.2 - - - -
282B ALA* 1.3 76.8 - - - +
284B LEU* 1.3 61.7 + - - +
286B ILE* 3.3 6.3 + - - +
287B ARG* 3.0 23.0 + - - +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B VAL* 4.3 19.7 - - + +
245B THR* 5.1 8.7 - - + -
280B GLU 2.9 16.1 + - - +
281B ALA* 3.8 5.6 - - - +
283B GLN* 1.3 77.3 - - - +
285B SER* 1.3 62.2 + - - +
287B ARG* 3.3 34.0 + - - +
288B PHE* 3.1 21.7 + - + +
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Residues in contact with SER 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B VAL* 3.4 13.8 - - - +
243B VAL* 3.8 12.0 - - - +
269B LEU* 3.7 25.6 - - - -
271B GLN* 2.8 25.2 + - - -
281B ALA 2.8 12.3 + - - -
282B ALA 3.3 8.1 - - - -
284B LEU* 1.3 78.0 - - - +
286B ILE* 1.3 57.2 + - - +
288B PHE* 3.2 5.2 + - - +
289B LEU* 2.9 31.9 + - - +
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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
----------------------------------------------------------
9B PHE* 3.8 30.1 - - + -
44B VAL* 3.8 28.5 - - + -
46B GLU* 3.9 22.0 - - + +
47B LEU* 4.0 18.6 - - + -
269B LEU* 4.5 10.8 - - + -
282B ALA 3.0 11.9 + - - +
283B GLN* 3.3 4.9 + - - +
285B SER* 1.3 73.0 - - - +
287B ARG* 1.3 67.0 + - - +
289B LEU* 3.2 6.9 + - + +
290B LYS* 2.9 48.8 + - - +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLN 3.0 14.2 + - - +
284B LEU* 3.5 31.4 + - - +
286B ILE* 1.3 78.5 - - - +
288B PHE* 1.3 62.2 + - - +
290B LYS* 3.4 9.7 + - - +
291B HIS* 3.1 21.0 + - - +
294B ARG* 4.7 3.0 + - - +
328B ILE* 3.8 46.4 + - + +
329B THR* 4.7 10.3 - - - +
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B VAL* 3.9 23.8 - - + +
244B GLY* 3.5 30.7 - - - -
248B MSE 3.8 35.9 - - + -
251B ILE* 3.7 16.2 - - + -
284B LEU* 3.1 13.4 + - + +
285B SER 3.2 7.2 + - - +
287B ARG* 1.3 75.6 - - - +
289B LEU* 1.3 63.5 + - + +
291B HIS* 3.0 19.3 + + - +
292B ILE* 2.9 53.2 + - + +
324B LEU* 5.1 1.3 - - + -
328B ILE* 4.5 15.0 - - + +
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.9 31.6 - - + -
230B VAL* 4.4 7.0 - - + -
243B VAL* 4.2 22.2 - - + -
255B PHE* 3.7 32.5 - - + -
267B TRP* 3.4 26.5 - - + +
269B LEU* 3.9 26.0 - - + -
285B SER 2.9 19.2 + - - +
286B ILE* 3.2 4.7 + - + +
288B PHE* 1.3 80.3 - - + +
290B LYS* 1.3 56.8 + - - +
292B ILE* 3.1 7.3 + - + +
293B TYR* 2.9 24.1 + - - +
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 3.7 37.0 - - + +
9B PHE* 3.9 20.4 - - + -
46B GLU* 2.5 43.0 + - - -
286B ILE* 2.9 32.7 + - + +
287B ARG* 3.7 7.6 - - - +
289B LEU* 1.3 76.2 - - - +
291B HIS* 1.3 56.4 + - - +
293B TYR* 3.2 3.7 + - - +
294B ARG* 3.0 47.5 + - - +
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Residues in contact with HIS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B MSE 6.2 0.9 - - + +
287B ARG 3.1 6.7 + - - +
288B PHE* 3.0 22.8 + + - +
290B LYS* 1.3 77.4 - - - +
292B ILE* 1.3 52.5 + - - +
294B ARG* 3.2 16.1 + - + +
295B ALA* 2.7 34.9 + - + +
324B LEU* 2.8 38.2 + - + +
326B SER* 3.1 39.9 - - - -
327B SER 4.0 5.3 + - - -
328B ILE* 3.7 42.7 - - + -
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Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ILE* 4.5 0.9 - - + -
252B PHE* 3.8 37.6 - - + +
255B PHE* 3.8 39.0 - - + -
267B TRP* 4.2 4.3 - - + -
288B PHE* 2.9 51.4 + - + +
289B LEU* 3.1 15.0 + - + +
291B HIS* 1.3 75.7 - - + +
293B TYR* 1.3 58.2 + - - +
295B ALA* 3.2 4.3 + - - +
296B LEU* 2.8 32.6 + - + +
324B LEU* 3.8 14.6 - - + -
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Residues in contact with TYR 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 4.0 24.0 - + + -
5B ASN* 3.1 29.7 + - - +
6B TYR* 3.6 24.2 - + + -
7B PRO* 3.6 29.2 - - + -
259B LYS* 6.4 0.2 - - - -
267B TRP* 3.9 17.9 - + + -
289B LEU 2.9 12.7 + - - +
290B LYS 3.2 7.4 + - - +
292B ILE* 1.3 77.0 - - - +
294B ARG* 1.3 64.2 + - - +
296B LEU* 3.3 12.0 + - + +
297B ASP* 3.2 20.6 + - + +
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Residues in contact with ARG 294 (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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4B TYR* 3.5 43.9 - - + +
6B TYR* 2.9 30.9 + - + +
287B ARG* 4.7 3.4 + - - +
290B LYS* 3.0 36.0 + - - +
291B HIS* 3.6 31.0 + - - +
293B TYR* 1.3 76.0 - - - +
295B ALA* 1.3 63.8 + - - +
297B ASP* 3.1 14.3 + - - +
298B LYS* 3.1 28.0 + - - +
327B SER 5.0 0.8 + - - -
328B ILE* 3.4 27.5 + - - +
330B VAL 3.9 6.5 + - - -
331B SER* 3.6 31.0 - - - +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PHE* 3.6 18.4 - - + -
291B HIS* 2.7 25.9 + - - +
292B ILE* 3.6 6.5 - - - +
294B ARG* 1.3 73.4 - - - +
296B LEU* 1.3 56.3 + - - +
298B LYS* 3.1 4.9 + - - +
299B LEU* 2.9 29.1 + - - +
323B ALA* 3.4 30.2 - - - +
324B LEU* 4.1 7.4 - - + -
326B SER* 4.4 5.8 + - - +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PHE* 3.5 21.5 - - + -
255B PHE* 3.9 27.8 - - + +
256B TYR* 3.8 31.0 - - + +
259B LYS* 4.0 40.3 - - + +
267B TRP* 4.4 14.6 - - + -
292B ILE* 2.8 23.4 + - + +
293B TYR* 3.5 11.4 - - + +
295B ALA* 1.3 75.7 - - - +
297B ASP* 1.3 60.7 + - - +
299B LEU* 3.5 23.5 + - + +
301B ILE* 4.6 1.7 - - - +
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 3.9 26.5 + - + -
259B LYS* 5.4 5.9 + - - +
293B TYR* 3.2 11.2 + - + +
294B ARG 3.1 11.0 + - - +
296B LEU* 1.3 79.7 - - - +
298B LYS* 1.3 61.0 + - + +
299B LEU 3.4 2.8 - - - +
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 3.7 20.4 + - - +
294B ARG* 3.1 24.9 + - - +
295B ALA* 3.1 8.2 + - - +
297B ASP* 1.3 78.0 - - + +
299B LEU* 1.3 66.7 + - - +
300B ASP* 3.4 3.6 + - - +
322B ASP 5.7 0.7 - - - +
323B ALA* 4.3 10.6 - - + +
326B SER* 3.8 34.2 + - - +
327B SER 5.6 2.0 + - - -
330B VAL 5.3 5.5 + - - -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 4.9 1.1 - - + -
252B PHE* 4.1 17.9 - - + -
256B TYR* 3.7 31.0 - - + -
295B ALA 2.9 15.3 + - - +
296B LEU* 3.6 18.2 - - + +
297B ASP 3.4 3.6 - - - +
298B LYS* 1.3 77.4 - - - +
300B ASP* 1.3 64.8 + - - +
301B ILE* 3.0 25.8 + - + +
304B LEU* 4.1 9.6 - - + -
319B ILE* 3.9 23.3 - - + +
320B VAL* 4.0 15.0 - - + -
323B ALA* 3.7 21.8 - - + -
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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