Contacts of the helix formed by residues 314 - 329 (chain A) in PDB entry 5U03
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 TYR 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 3.3 5.2 - - - -
303A LEU* 3.6 29.8 - - + -
305A GLY* 4.7 0.5 - - - -
306A LYS 4.5 1.7 + - - -
307A TYR* 3.4 34.6 + - + +
308A THR* 3.0 37.3 + - - -
311A SER* 4.6 7.1 + - - +
312A ASP* 2.9 1.0 - - - -
313A SER* 1.3 92.1 - - - +
315A ALA* 1.3 52.5 + - - +
316A SER 3.3 0.4 - - - -
317A VAL* 3.1 23.4 + - + -
318A ILE* 2.8 45.4 + - + +
336A TYR* 5.4 3.6 - + + -
370A PRO* 3.6 30.5 - - + +
371A GLY 4.9 6.2 + - - -
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 3.1 5.2 + - - +
69A LEU* 4.3 10.5 - - + -
312A ASP* 3.0 29.6 + - + +
314A TYR* 1.3 76.8 - - - +
316A SER* 1.3 57.5 + - - +
318A ILE* 4.0 7.2 - - - +
319A LYS* 3.0 28.2 + - - +
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Residues in contact with SER 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 2.6 34.3 + - - +
69A LEU* 3.9 25.0 - - - +
76A ARG* 4.2 14.2 + - - +
315A ALA* 1.3 72.6 - - - +
317A VAL* 1.3 58.2 + - - +
319A LYS* 3.6 8.0 - - - +
320A ALA* 2.8 27.7 + - - +
528A GLU* 4.0 26.7 - - - +
529A PHE* 4.5 5.3 - - - -
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 4.4 4.7 - - + +
303A LEU* 5.6 1.1 - - + -
313A SER 5.3 0.4 - - - +
314A TYR* 3.1 33.8 + - + +
316A SER* 1.3 76.7 - - - +
318A ILE* 1.3 67.1 + - + +
320A ALA* 3.1 5.4 + - - +
321A LEU* 3.0 24.6 + - + +
368A LEU* 3.8 28.9 - - + -
370A PRO* 6.0 4.3 - - + -
528A GLU* 4.0 29.6 - - + +
540A TYR* 4.2 14.3 - - + +
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 5.8 1.1 - - + -
314A TYR* 2.8 33.5 + - + +
315A ALA* 4.1 5.8 - - - +
317A VAL* 1.3 72.1 - - + +
319A LYS* 1.3 57.8 + - - +
321A LEU* 2.9 13.3 + - + +
322A GLU* 2.8 45.5 + - + +
332A LEU* 4.7 2.0 - - + -
334A ILE* 3.9 38.1 - - + -
336A TYR* 3.2 31.9 - - + +
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Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 3.6 28.3 - - - +
249A SER* 4.7 10.3 + - - -
250A ILE* 5.4 12.5 - - - +
292A TYR* 5.9 0.8 + - - +
315A ALA 3.0 21.1 + - - +
316A SER* 3.6 9.0 - - - +
318A ILE* 1.3 77.6 - - - +
320A ALA* 1.3 62.4 + - - +
322A GLU* 2.8 37.0 + - + +
323A HIS* 2.9 49.9 + - + +
533A PRO* 6.1 0.2 - - + -
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A SER 2.8 14.4 + - - +
317A VAL 3.1 9.6 + - - +
319A LYS* 1.3 75.4 - - - +
321A LEU* 1.3 62.8 + - - +
323A HIS* 3.0 30.4 + - - +
324A SER* 3.3 9.4 + - - -
528A GLU* 4.0 9.0 - - + +
531A SER* 4.0 14.5 + - - +
540A TYR* 3.7 32.6 - - + +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 4.1 30.1 - - + -
317A VAL* 3.0 24.8 + - + +
318A ILE* 2.9 15.5 + - + +
320A ALA* 1.3 75.1 - - - +
322A GLU* 1.3 55.6 + - - +
324A SER* 3.0 9.3 + - - -
325A ALA* 2.8 27.0 + - - +
332A LEU* 3.6 17.4 - - + +
334A ILE* 3.7 26.2 - - + -
368A LEU* 5.0 3.1 - - + -
540A TYR* 3.7 38.8 - - + +
543A LEU* 5.0 2.5 - - + -
544A LEU* 4.9 4.1 - - + +
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Residues in contact with GLU 322 (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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249A SER* 5.2 3.1 + - - -
292A TYR* 5.4 13.9 + - + +
318A ILE* 2.8 34.1 + - + +
319A LYS* 2.8 45.7 + - + +
321A LEU* 1.3 73.4 - - - +
323A HIS* 1.3 68.5 + - + +
325A ALA* 3.1 8.7 + - + +
326A LEU* 2.8 25.8 + - - +
332A LEU* 4.4 8.3 - - + -
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Residues in contact with HIS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 3.7 14.2 + - - -
292A TYR* 5.7 4.5 - - - -
316A SER 5.7 0.2 - - - -
319A LYS* 2.9 45.3 + - + +
320A ALA* 3.2 11.0 - - - +
322A GLU* 1.3 79.1 - - + +
324A SER* 1.3 61.3 + - - +
326A LEU* 3.4 6.7 + - - +
327A ALA* 3.1 20.6 + - - +
528A GLU 5.8 0.9 - - - -
531A SER* 3.0 39.6 + - - +
532A ARG* 3.3 19.3 - - - +
533A PRO* 3.4 40.3 - - + +
536A PRO* 3.9 13.9 - - + +
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Residues in contact with SER 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ALA 3.3 8.4 + - - -
321A LEU* 3.0 11.2 + - - -
323A HIS* 1.3 76.0 - - - +
325A ALA* 1.3 64.8 + - - +
327A ALA* 3.0 13.5 + - - +
328A ILE* 3.0 12.1 + - - +
536A PRO* 4.2 6.8 - - - +
537A SER 4.3 0.5 + - - -
540A TYR* 3.6 7.1 - - - +
541A PHE* 3.1 46.6 + - - +
544A LEU* 3.4 22.2 - - - +
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Residues in contact with ALA 325 (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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295A LEU* 5.3 0.6 - - - +
321A LEU 2.8 13.3 + - - +
322A GLU* 3.1 12.3 + - - +
324A SER* 1.3 75.4 - - - +
326A LEU* 1.3 53.6 + - - +
328A ILE* 4.0 2.2 - - - -
329A ASN* 2.6 29.6 + - - -
330A HIS* 2.9 27.7 + - + +
331A LYS 5.0 0.7 - - - +
332A LEU* 4.2 21.1 - - + -
544A LEU* 3.7 12.7 - - + +
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Residues in contact with LEU 326 (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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288A MET* 4.4 20.0 - - + +
291A ARG* 3.7 39.5 + - + +
292A TYR* 3.5 47.1 - - + +
295A LEU* 5.0 5.8 - - + -
322A GLU 2.8 16.5 + - - +
323A HIS* 3.7 5.8 - - - +
325A ALA* 1.3 74.8 - - - +
327A ALA* 1.3 67.0 + - - +
329A ASN* 2.8 26.9 + - - +
533A PRO* 5.1 14.8 - - + +
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Residues in contact with ALA 327 (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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323A HIS 3.1 11.9 + - - +
324A SER* 3.0 11.2 + - - +
326A LEU* 1.3 80.1 - - - +
328A ILE* 1.3 60.9 + - - +
329A ASN* 3.3 10.9 + - - -
533A PRO 6.0 0.9 - - - +
536A PRO* 4.7 11.9 - - + -
541A PHE* 3.9 21.1 - - + -
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Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A SER 3.0 7.7 + - - +
325A ALA* 3.4 9.9 - - - +
327A ALA* 1.3 74.4 - - - +
329A ASN* 1.3 74.8 + - - +
330A HIS* 3.4 51.0 + - + +
541A PHE* 4.5 6.5 - - + -
544A LEU* 3.5 27.8 - - + -
545A LEU* 3.8 28.0 - - + -
548A VAL* 4.0 16.8 - - + -
550A ARG* 4.6 8.1 - - + +
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Residues in contact with ASN 329 (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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291A ARG* 3.8 35.7 + - - +
294A ARG 5.2 9.4 - - - +
295A LEU* 4.0 15.8 - - - +
296A LEU* 3.2 13.5 + - - +
325A ALA 2.6 12.4 + - - -
326A LEU* 2.8 22.2 + - - +
327A ALA 3.3 16.0 + - - -
328A ILE* 1.3 81.2 + - - +
330A HIS* 1.3 65.5 + - - +
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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