Contacts of the helix formed by residues 275 - 294 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLN* 5.8 7.9 - - - +
238A ASP* 6.0 0.2 + - - -
274A PRO* 1.3 75.1 - - - +
276A PRO* 1.3 75.0 - - + +
277A SER* 4.0 9.0 - - - +
278A THR* 3.0 43.2 + - + -
279A LEU* 3.1 8.0 + - - +
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Residues in contact with PRO 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A PRO 3.6 5.1 - - - +
275A LYS* 1.3 85.9 - - + +
277A SER* 1.3 62.7 + - - +
279A LEU* 3.5 8.5 + - + -
280A ALA* 3.2 19.8 + - - +
309A LEU* 3.6 26.4 - - + +
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LYS* 4.0 8.9 - - - +
276A PRO* 1.3 82.6 - - - +
278A THR* 1.3 80.8 + - - +
280A ALA* 3.2 7.8 + - - +
281A ASN* 3.1 21.3 + - - +
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Residues in contact with THR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ASP* 5.7 6.5 - - - +
241A PHE* 4.3 21.1 - - - -
274A PRO* 4.2 8.5 - - - +
275A LYS* 3.0 41.2 + - + -
277A SER* 1.3 91.7 + - - +
279A LEU* 1.3 56.7 + - - +
281A ASN* 3.7 8.4 - - - +
282A TYR* 2.9 26.7 + - - +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PHE* 3.5 32.8 - - + -
267A MET* 4.4 13.5 - - + -
274A PRO* 3.9 26.7 - - + +
275A LYS 3.1 14.3 + - - +
276A PRO* 3.8 7.4 - - + +
277A SER 3.1 0.6 - - - -
278A THR* 1.3 76.3 + - - +
280A ALA* 1.3 59.9 + - - +
281A ASN 3.1 1.8 - - - -
282A TYR* 3.1 9.4 + - + +
283A TYR* 2.8 54.6 + - + +
309A LEU* 3.8 17.3 - - + -
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PRO 3.2 14.5 + - - +
277A SER* 3.5 10.3 - - - +
279A LEU* 1.3 76.4 - - - +
281A ASN* 1.3 58.7 + - - +
283A TYR* 4.1 1.5 - - - -
284A GLU* 3.1 30.8 + - - +
306A PHE* 3.4 25.1 - - + +
309A LEU* 3.4 20.3 - - + +
310A TYR* 5.8 3.4 - - + +
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Residues in contact with ASN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PHE 5.5 1.2 - - - +
245A ASP* 3.7 20.2 + - - +
277A SER 3.1 12.2 + - - +
278A THR* 3.7 11.7 - - - +
280A ALA* 1.3 74.8 - - - +
282A TYR* 1.3 66.8 + - - +
284A GLU* 3.1 12.6 + - - +
285A ASN* 2.9 40.8 + - - +
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Residues in contact with TYR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PHE* 3.3 31.2 - + + -
244A VAL* 4.3 17.7 - - + -
260A ILE* 3.2 30.5 + - + +
263A VAL* 3.5 29.7 - - + +
264A PHE* 3.3 28.1 - + - -
267A MET* 4.9 2.0 - - - -
278A THR 2.9 19.2 + - - +
279A LEU* 3.1 10.7 + - + +
281A ASN* 1.3 77.8 + - - +
283A TYR* 1.3 74.2 + + - +
285A ASN* 3.0 10.5 + - - +
286A LEU* 2.9 57.1 + - + +
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Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PHE* 5.2 7.8 - + - -
267A MET* 5.1 6.6 - - + +
279A LEU* 2.8 46.5 + - + +
280A ALA 4.2 1.3 - - - +
282A TYR* 1.3 96.6 - + - +
284A GLU* 1.3 63.3 + - - +
286A LEU* 3.0 26.8 + - + +
287A VAL* 3.1 19.1 + - - +
302A ALA* 3.9 14.8 - - - +
305A LYS* 3.4 65.4 - - + -
306A PHE* 4.0 10.1 - - + -
309A LEU* 4.1 14.4 - - + -
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ALA* 3.1 19.1 + - - +
281A ASN* 3.1 12.1 + - - +
283A TYR* 1.3 77.5 - - - +
285A ASN* 1.3 60.2 + - - +
287A VAL* 3.1 30.6 - - + +
288A LYS* 3.7 21.6 + - - +
303A TRP* 6.3 2.7 - - + -
306A PHE* 3.5 38.2 - - + -
324A TYR* 4.8 6.4 + - - -
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PHE 5.1 0.8 + - - -
244A VAL* 3.9 15.8 - - + +
245A ASP* 2.8 48.4 + - - +
248A VAL* 4.0 21.2 - - + +
249A LYS* 6.0 0.2 - - - +
281A ASN* 2.9 24.1 + - - +
282A TYR* 3.0 10.1 + - - +
284A GLU* 1.3 77.1 - - - +
286A LEU* 1.3 65.3 + - - +
287A VAL 3.2 0.2 - - - -
288A LYS* 3.1 19.6 + - - +
289A VAL* 3.0 25.4 + - - +
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL* 4.9 2.2 - - + -
260A ILE* 3.5 35.7 - - + -
264A PHE* 4.3 15.0 - - + -
282A TYR* 2.9 54.8 + - + +
283A TYR* 3.0 18.6 + - + +
285A ASN* 1.3 78.8 - - - +
287A VAL* 1.3 57.5 + - - +
289A VAL* 4.4 3.8 - - - -
290A PHE* 2.9 51.4 + - + -
302A ALA* 3.7 12.3 - - + -
355A LEU* 4.4 10.1 - - + -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TYR 3.1 14.5 + - - +
284A GLU* 3.1 28.7 - - + +
285A ASN 3.2 0.4 - - - -
286A LEU* 1.3 77.2 - - - +
288A LYS* 1.3 66.1 + - + +
291A PHE* 3.4 9.5 + - - +
299A HIS* 3.0 29.5 + - + +
302A ALA* 3.6 7.2 - - + +
303A TRP* 3.4 68.6 - - + +
306A PHE* 5.4 1.6 - - + -
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Residues in contact with LYS 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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248A VAL* 4.0 25.3 - - + +
253A TRP* 4.0 9.4 - - + -
284A GLU* 3.7 24.8 + - - +
285A ASN* 3.1 20.7 + - - +
287A VAL* 1.3 81.4 - - + +
289A VAL* 1.3 68.0 + - - +
291A PHE* 3.4 5.3 + - - +
292A VAL* 3.3 25.5 + - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL* 5.6 0.2 - - + -
248A VAL* 3.6 29.8 - - + -
253A TRP* 3.9 16.9 - - + +
256A ALA* 3.7 17.7 - - + -
257A TYR* 4.7 15.5 - - + +
260A ILE* 3.7 28.3 - - + -
285A ASN 3.0 14.2 + - - +
286A LEU 3.8 3.1 - - - +
288A LYS* 1.3 78.2 - - - +
290A PHE* 1.3 70.5 + - + +
292A VAL* 3.3 4.5 + - - +
293A SER* 2.9 29.4 + - - -
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Residues in contact with PHE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TYR* 3.9 25.4 - + - -
260A ILE* 5.0 5.6 - - + -
286A LEU* 2.9 43.4 + - + +
289A VAL* 1.3 81.1 - - + +
291A PHE* 1.3 63.2 + - - +
293A SER* 3.5 4.5 - - - -
294A GLY* 3.4 1.9 + - - -
295A ASP* 3.2 40.7 + - - +
298A LEU* 3.4 49.4 - - + -
299A HIS* 3.7 20.9 - - - +
302A ALA* 4.5 0.4 - - + -
351A MET* 3.4 32.3 - - + -
355A LEU* 4.7 6.1 - - + -
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Residues in contact with PHE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL 3.4 18.9 + - - +
288A LYS* 3.7 6.3 - - - +
289A VAL 3.3 0.4 - - - -
290A PHE* 1.3 74.4 - - - +
292A VAL* 1.3 71.6 + - + +
293A SER 3.3 0.5 + - - -
294A GLY* 3.5 9.7 + - - -
299A HIS* 3.8 31.8 + + + +
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Residues in contact with VAL 292 (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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253A TRP* 3.5 60.1 - - + +
288A LYS 3.5 12.6 - - - +
289A VAL 3.3 7.3 + - - +
291A PHE* 1.3 83.4 - - + +
293A SER* 1.3 61.4 + - - +
294A GLY* 3.4 1.4 + - - -
271B LYS* 4.1 8.5 - - - -
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Residues in contact with SER 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A TRP* 6.5 0.2 - - - -
257A TYR* 5.7 0.4 - - - -
289A VAL* 2.9 20.8 + - - -
290A PHE* 3.5 17.1 - - - -
291A PHE 3.1 0.2 - - - -
292A VAL* 1.3 79.1 - - - +
294A GLY* 1.3 58.8 + - - +
295A ASP* 2.2 34.2 + - - +
348A HIS* 3.2 15.8 + - - -
271B LYS* 3.2 30.5 - - - +
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Residues in contact with GLY 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PHE 3.4 4.0 + - - -
291A PHE 3.5 6.0 + - - -
292A VAL 3.3 4.8 - - - -
293A SER* 1.3 79.4 - - - +
295A ASP* 1.3 62.9 + - - +
296A PRO* 3.6 11.7 - - - +
271B LYS* 5.2 2.2 - - - -
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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