Contacts of the helix formed by residues 275 - 294 (chain B) in PDB entry 4U1D
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 LYS 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLN* 4.7 3.8 - - - +
274B PRO* 1.3 74.6 - - - +
276B PRO* 1.3 75.6 - - + +
277B SER* 3.1 25.7 + - - +
278B THR* 3.1 25.4 + - + +
279B LEU* 3.0 19.8 + - - +
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Residues in contact with PRO 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ILE* 3.7 25.1 - - + -
274B PRO 3.3 7.4 - - - +
275B LYS* 1.3 89.8 - - + +
277B SER* 1.3 62.2 + - - +
279B LEU* 4.0 8.7 - - + -
280B ALA* 3.0 27.2 + - - +
309B LEU* 4.0 23.6 - - + +
312B THR* 5.8 2.5 - - - +
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Residues in contact with SER 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LYS* 3.1 22.2 - - - +
276B PRO* 1.3 85.2 - - - +
278B THR* 1.3 65.2 + - - +
280B ALA* 3.4 3.7 + - - +
281B ASN* 3.3 19.3 + - - +
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Residues in contact with THR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLN* 5.7 0.9 + - - -
238B ASP* 5.2 13.1 - - - +
241B PHE* 4.5 21.0 - - - +
274B PRO* 4.3 6.1 - - - +
275B LYS* 3.1 46.0 + - + +
277B SER* 1.3 78.5 - - - +
279B LEU* 1.3 60.3 + - - +
281B ASN* 3.7 8.3 + - - +
282B TYR* 3.3 19.1 + - - +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ILE* 4.3 18.4 - - + -
344A GLY 4.7 4.9 - - - +
345A TYR* 4.3 20.2 - - + -
241B PHE* 4.0 26.2 - - + -
267B MET* 4.7 7.4 - - + -
274B PRO* 4.2 17.3 - - + +
275B LYS 3.0 15.7 + - - +
276B PRO* 3.8 6.5 - - + +
277B SER 3.1 0.2 - - - -
278B THR* 1.3 78.1 + - - +
280B ALA* 1.3 64.9 + - - +
281B ASN 3.2 0.2 - - - -
282B TYR* 3.1 22.3 + - + +
283B TYR* 3.1 32.4 + - + +
309B LEU* 3.8 16.8 - - + -
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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 PRO 3.0 18.3 + - - +
277B SER* 3.8 4.3 - - - +
279B LEU* 1.3 73.9 - - - +
281B ASN* 1.3 65.5 + - - +
283B TYR* 3.4 2.3 + - - +
284B GLU* 3.0 19.3 + - - +
306B PHE* 3.2 32.7 - - + -
309B LEU* 3.4 24.3 - - + +
310B TYR* 5.6 2.7 - - + +
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Residues in contact with ASN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ASP* 3.5 18.2 + - - +
277B SER 3.3 11.8 + - - +
278B THR* 3.8 11.4 - - - +
279B LEU 3.2 0.6 - - - -
280B ALA* 1.3 76.4 - - - +
282B TYR* 1.3 64.9 + - - +
284B GLU* 3.1 14.7 + - - +
285B ASN* 3.0 36.9 + - - +
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Residues in contact with TYR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PHE* 3.4 35.0 - + + -
244B VAL* 4.1 19.7 - - + -
260B ILE* 3.3 27.0 + - - +
263B VAL* 3.5 37.1 - - + +
264B PHE* 4.7 2.4 + - - +
267B MET* 4.7 7.7 - - - -
278B THR 3.3 8.6 + - - +
279B LEU* 3.1 14.1 + - + +
281B ASN* 1.3 78.8 + - - +
283B TYR* 1.3 79.0 + + - +
285B ASN* 3.0 25.6 + - - +
286B LEU* 3.1 42.6 + - + +
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Residues in contact with TYR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLY 5.5 4.8 + - - -
345A TYR* 5.8 0.9 - - - -
267B MET* 4.2 18.5 - - - +
279B LEU* 3.1 34.9 + - + +
280B ALA 3.9 5.2 - - - +
281B ASN 3.3 0.4 - - - -
282B TYR* 1.3 100.4 - + - +
284B GLU* 1.3 61.5 - - - +
286B LEU* 3.1 27.4 + - + +
287B VAL* 3.2 19.3 + - - +
302B ALA* 3.9 16.1 - - - +
305B LYS* 3.6 53.9 + - + +
306B PHE* 4.0 9.6 - - + -
309B LEU* 4.0 16.4 - - + -
355B LEU* 5.9 1.3 - - + -
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Residues in contact with GLU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA 3.0 14.9 + - - +
281B ASN* 3.4 15.4 + - - +
283B TYR* 1.3 78.2 - - - +
285B ASN* 1.3 57.8 + - - +
287B VAL* 3.1 31.4 - - + +
288B LYS* 3.7 20.4 + - - +
303B TRP* 6.4 2.2 - - + -
306B PHE* 3.2 40.1 - - + -
324B TYR* 5.3 4.0 + - - -
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Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PHE 5.1 1.0 + - - -
244B VAL* 4.1 10.6 - - + +
245B ASP* 2.9 46.5 + - - +
248B VAL* 4.1 23.6 - - + +
281B ASN* 3.0 23.3 + - - +
282B TYR* 3.0 13.4 + - - +
284B GLU* 1.3 75.6 - - - +
286B LEU* 1.3 64.8 + - - +
287B VAL 3.1 1.8 - - - -
288B LYS* 3.1 24.0 + - - +
289B VAL* 3.0 25.4 + - - +
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL* 4.8 3.1 - - + -
260B ILE* 3.5 40.2 - - + -
282B TYR* 3.1 53.6 + - + +
283B TYR* 3.1 21.5 + - + +
285B ASN* 1.3 78.4 - - - +
287B VAL* 1.3 61.8 + - - +
289B VAL* 3.8 4.2 - - + +
290B PHE* 3.0 48.6 + - + -
302B ALA* 3.7 12.6 - - + -
355B LEU* 4.8 14.6 - - + -
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B TYR 3.2 14.1 + - - +
284B GLU* 3.1 29.8 - - + +
285B ASN 3.1 0.8 - - - -
286B LEU* 1.3 78.1 - - - +
288B LYS* 1.3 67.1 + - + +
291B PHE* 3.2 9.5 + - - +
299B HIS* 2.8 38.3 + - + +
302B ALA* 3.5 7.2 - - + +
303B TRP* 3.4 58.3 - - + +
306B PHE* 5.4 1.8 - - + -
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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
----------------------------------------------------------
248B VAL* 3.9 24.8 - - + +
253B TRP* 4.3 8.7 - - + -
284B GLU* 3.7 23.8 + - - +
285B ASN* 3.1 22.6 + - - +
287B VAL* 1.3 81.6 - - + +
289B VAL* 1.3 66.0 + - - +
291B PHE* 3.1 7.3 + - - +
292B VAL* 3.0 27.6 + - + +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL* 5.6 0.9 - - + -
248B VAL* 3.7 22.9 - - + -
253B TRP* 3.9 17.0 - - + +
256B ALA* 3.8 20.6 - - + -
257B TYR* 4.7 8.7 - - + +
260B ILE* 3.8 29.4 - - + -
285B ASN 3.0 19.2 + - - +
286B LEU* 3.8 4.0 - - + +
288B LYS* 1.3 78.4 - - - +
290B PHE* 1.3 60.8 + - + +
292B VAL* 3.2 4.7 + - - +
293B SER* 2.8 44.7 + - - +
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Residues in contact with PHE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TYR* 4.0 22.9 - + - -
260B ILE* 4.5 9.9 - - + -
286B LEU* 3.0 46.9 + - + +
289B VAL* 1.3 82.3 - - + +
291B PHE* 1.3 63.4 + - - +
293B SER* 3.6 12.8 - - - -
294B GLY* 3.2 15.9 + - - -
295B ASP* 3.2 19.8 + - - +
296B PRO* 5.0 0.3 - - - +
298B LEU* 3.5 45.1 - - + -
299B HIS* 3.7 20.9 - - - +
351B MET* 3.6 28.0 - - + -
355B LEU* 4.6 7.6 - - + -
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Residues in contact with PHE 291 (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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287B VAL 3.2 18.5 + - - +
288B LYS* 3.1 7.9 + - - +
290B PHE* 1.3 76.5 - - - +
292B VAL* 1.3 68.6 + - + +
293B SER 3.4 0.2 + - - -
294B GLY* 3.4 10.9 + - - -
299B HIS* 3.8 26.4 + + + +
419B GLN* 3.2 42.2 - - + -
420B TYR* 4.0 21.5 - + - -
423B PRO* 6.0 4.7 - - + -
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TRP* 3.7 57.7 - - + +
288B LYS* 3.0 13.9 + - + +
289B VAL 3.5 7.4 - - - +
291B PHE* 1.3 83.9 - - + +
293B SER* 1.3 59.6 + - - +
294B GLY* 3.4 0.9 + - - -
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Residues in contact with SER 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TRP* 6.1 1.2 - - - +
257B TYR* 4.5 4.3 - - - -
289B VAL* 2.8 30.7 + - - +
290B PHE* 3.7 13.5 - - - -
291B PHE 3.2 0.2 - - - -
292B VAL* 1.3 77.4 - - - +
294B GLY* 1.3 60.6 + - - +
295B ASP* 3.3 25.7 + - - +
348B HIS* 4.3 16.9 - - - -
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Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE 3.2 5.7 + - - -
291B PHE 3.4 7.3 + - - -
292B VAL 3.2 4.0 - - - -
293B SER* 1.3 80.2 - - - +
295B ASP* 1.3 64.4 + - - +
296B PRO* 3.3 13.8 - - - +
336B GLN* 5.6 2.1 - - - +
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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