Contacts of the helix formed by residues 314 - 329 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLU* 3.3 5.6 - - - -
303B LEU* 3.6 30.3 - - + -
305B GLY* 4.7 0.7 - - - -
306B LYS 4.5 1.6 + - - -
307B TYR* 3.4 35.2 + - + +
308B THR* 3.0 38.1 + - - -
309B LYS 5.7 0.2 - - - -
310B PHE* 6.5 0.2 - - - -
311B SER* 4.6 6.7 - - - +
312B ASP* 2.9 1.4 - - - +
313B SER* 1.3 88.6 - - - +
315B ALA* 1.3 53.0 + - - -
316B SER 3.3 0.2 - - - -
317B VAL* 3.0 22.4 + - + -
318B ILE* 2.8 45.9 + - + +
336B TYR* 5.4 2.7 - + + -
370B PRO* 3.6 29.7 - - + +
371B GLY 4.9 5.8 + - - -
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 3.1 5.6 + - - +
69B LEU* 4.3 10.5 - - + -
312B ASP* 3.0 30.5 + - + +
314B TYR* 1.3 75.9 - - - +
316B SER* 1.3 57.7 + - - +
318B ILE* 3.7 7.2 + - - +
319B LYS* 3.0 28.4 + - - +
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Residues in contact with SER 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 2.6 34.2 + - - +
69B LEU* 3.9 23.7 - - - +
76B ARG* 4.2 13.9 + - - +
315B ALA* 1.3 73.5 - - - +
317B VAL* 1.3 58.5 + - - +
319B LYS* 3.6 7.5 - - - +
320B ALA* 2.8 28.4 + - - +
323B HIS* 5.7 0.3 - - - -
528B GLU* 4.0 25.2 - - - +
529B PHE* 4.5 5.3 - - - -
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Residues in contact with VAL 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 4.4 4.7 - - + +
303B LEU* 5.6 1.1 - - + -
313B SER 5.3 0.2 - - - +
314B TYR* 3.0 33.4 + - + +
316B SER* 1.3 77.0 + - - +
318B ILE* 1.3 67.5 + - + +
320B ALA* 3.1 5.7 + - - +
321B LEU* 3.0 25.8 + - + +
368B LEU* 3.8 28.7 - - + -
370B PRO* 6.0 3.8 - - + -
528B GLU* 4.0 30.3 - - + +
540B TYR* 4.2 14.1 - - + +
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 5.6 0.9 - - + -
314B TYR* 2.8 34.4 + - + +
315B ALA* 4.1 5.4 - - - +
317B VAL* 1.3 73.4 - - + +
319B LYS* 1.3 58.2 + - - +
321B LEU* 2.9 13.4 + - + +
322B GLU* 2.8 45.9 + - + +
332B LEU* 4.7 2.0 - - + -
334B ILE* 3.9 37.9 - - + -
336B TYR* 3.2 31.9 - - + +
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Residues in contact with LYS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG* 3.6 28.0 - - - +
249B SER* 4.7 10.5 + - - -
250B ILE* 5.4 12.1 - - - +
292B TYR* 6.0 0.8 + - - +
315B ALA 3.0 21.2 + - - +
316B SER* 3.6 8.7 - - - +
317B VAL 3.2 0.2 - - - -
318B ILE* 1.3 76.7 - - - +
320B ALA* 1.3 61.4 + - - +
322B GLU* 2.8 36.2 + - + +
323B HIS* 2.9 50.3 + - + +
533B PRO* 6.1 0.2 - - + -
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B SER 2.8 15.2 + - - +
317B VAL 3.1 9.6 + - - +
319B LYS* 1.3 75.2 - - - +
321B LEU* 1.3 63.1 + - - +
323B HIS* 3.0 30.5 + - - +
324B SER* 3.3 9.6 + - - -
528B GLU* 4.0 8.7 - - + +
531B SER* 4.0 15.4 + - - +
540B TYR* 3.7 32.4 - - + +
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Residues in contact with LEU 321 (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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301B ILE* 4.1 29.8 - - + -
317B VAL* 3.0 24.8 + - + +
318B ILE* 2.9 14.7 + - + +
320B ALA* 1.3 74.2 - - - +
322B GLU* 1.3 55.4 + - - +
324B SER* 3.0 9.4 + - - +
325B ALA* 2.8 26.9 + - - +
332B LEU* 3.6 18.1 - - + +
334B ILE* 3.7 26.5 - - + -
368B LEU* 5.0 3.6 - - + -
540B TYR* 3.7 38.8 - - + +
543B LEU* 5.0 2.2 - - + -
544B LEU* 4.9 3.9 - - + +
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B SER* 5.2 3.1 + - - -
292B TYR* 5.4 14.2 + - + +
318B ILE* 2.8 35.1 + - + +
319B LYS* 2.8 46.2 + - + +
321B LEU* 1.3 74.0 - - - +
323B HIS* 1.3 67.8 + - + +
325B ALA* 3.5 9.2 - - + +
326B LEU* 2.8 26.4 + - - +
332B LEU* 4.4 8.5 - - + -
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Residues in contact with HIS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG* 3.7 14.0 + - - -
292B TYR* 5.7 4.0 - - - -
319B LYS* 2.9 46.6 + - + +
320B ALA* 3.0 11.5 + - - +
322B GLU* 1.3 78.9 - - + +
324B SER* 1.3 61.0 + - - +
326B LEU* 3.4 7.1 + - - +
327B ALA* 3.1 20.1 + - - +
528B GLU 5.8 0.7 - - - -
531B SER* 3.0 38.9 + - - -
532B ARG* 3.3 21.3 - - - +
533B PRO* 3.4 40.8 - - + +
536B PRO* 3.9 13.5 - - + +
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Residues in contact with SER 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ALA 3.3 7.5 + - - -
321B LEU* 3.0 10.8 + - - -
323B HIS* 1.3 76.4 - - - +
325B ALA* 1.3 65.0 + - - +
327B ALA* 3.0 13.4 + - - +
328B ILE* 3.0 12.1 + - - +
536B PRO* 4.2 7.0 - - - +
537B SER 4.3 0.3 + - - -
540B TYR* 3.6 8.2 - - - +
541B PHE* 3.1 45.8 + - - +
544B LEU* 3.4 22.4 - - - +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 5.3 0.6 - - - +
321B LEU 2.8 13.3 + - - +
322B GLU* 3.5 12.6 - - + +
324B SER* 1.3 76.4 - - - +
326B LEU* 1.3 52.0 + - - +
328B ILE* 4.0 2.2 - - - -
329B ASN* 2.6 30.0 + - - -
330B HIS* 2.9 27.4 + - - +
331B LYS 5.0 0.7 - - - +
332B LEU* 4.2 20.9 - - + -
544B LEU* 3.7 12.1 - - + +
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Residues in contact with LEU 326 (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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288B MET* 4.4 20.4 - - + +
291B ARG* 3.7 40.1 - - + +
292B TYR* 3.5 48.0 - - + +
295B LEU* 5.0 6.3 - - + -
322B GLU 2.8 16.1 + - - +
323B HIS* 3.7 6.1 - - - +
325B ALA* 1.3 75.4 - - - +
327B ALA* 1.3 67.2 + - - +
329B ASN* 2.8 26.1 + - - +
533B PRO* 5.1 15.3 - - + +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B HIS 3.1 12.7 + - - +
324B SER* 3.0 11.4 + - - +
326B LEU* 1.3 79.2 - - - +
328B ILE* 1.3 60.1 + - - +
329B ASN* 3.3 11.1 + - - -
533B PRO 6.0 1.1 - - - +
536B PRO* 4.7 11.7 - - + -
541B PHE* 3.9 21.3 - - + -
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Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B SER 3.0 7.5 + - - +
325B ALA* 3.4 9.9 - - - +
327B ALA* 1.3 74.9 - - - +
329B ASN* 1.3 71.8 + - - +
330B HIS* 3.4 52.0 + - + +
541B PHE* 4.5 7.4 - - + -
544B LEU* 3.5 26.9 - - + -
545B LEU* 3.8 28.7 - - + -
548B VAL* 4.0 16.4 - - + -
550B ARG* 4.6 8.1 - - + +
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Residues in contact with ASN 329 (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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291B ARG* 3.8 36.1 + - - +
294B ARG 5.2 9.6 - - - +
295B LEU* 4.0 14.5 - - - -
296B LEU* 3.2 13.9 + - - +
325B ALA 2.6 12.0 + - - -
326B LEU* 2.8 21.9 + - - +
327B ALA 3.3 15.2 + - - -
328B ILE* 1.3 80.1 + - - +
330B HIS* 1.3 66.7 + - - +
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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
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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