Contacts of the helix formed by residues 319 - 336 (chain B) in PDB entry 2UVL
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 CYS 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B CYS* 3.9 1.6 - - - -
294B CYS* 3.9 3.6 - - - -
295B CYS* 3.7 19.0 - - + +
312B HIS* 3.5 6.3 - - - +
316B PHE* 3.1 16.8 + - - +
317B PRO 3.4 0.8 - - - -
318B ARG* 1.3 75.7 - - - +
320B GLU* 1.3 60.8 + - - +
321B TYR* 3.5 20.2 - - - -
322B LEU* 3.5 12.2 - - + +
323B ILE* 3.0 30.0 + - - +
1338B ZN 2.4 36.8 - - - -
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B CYS* 4.1 13.6 - - - -
318B ARG 3.2 10.0 + - - +
319B CYS* 1.3 71.0 - - - +
321B TYR* 1.3 61.8 + - - +
323B ILE* 3.5 20.6 + - - +
324B ARG* 2.9 30.7 + - - +
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Residues in contact with TYR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLN 6.0 0.2 - - - -
258B ARG* 3.5 15.8 + - - -
278B SER* 2.7 19.1 + - - -
279B ALA 3.6 9.0 - - - -
280B GLY* 3.6 19.1 - - - -
292B CYS* 4.9 0.2 - - - -
293B PHE* 3.6 26.2 - + + -
294B CYS* 3.5 27.6 - - + -
309B TRP* 3.6 21.7 - + - -
312B HIS* 4.5 4.7 - + - -
319B CYS* 3.3 3.8 - - - -
320B GLU* 1.3 75.6 - - - +
322B LEU* 1.3 68.3 + - - +
324B ARG* 3.1 30.2 + - - +
325B ILE* 3.0 45.7 + - + +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TRP* 3.6 41.5 - - + +
312B HIS* 3.6 20.4 - - + +
313B ALA* 3.5 31.9 - - + +
316B PHE 3.6 20.6 - - - +
317B PRO* 4.3 0.7 - - + +
319B CYS* 3.4 18.0 + - + +
321B TYR* 1.3 79.6 - - - +
323B ILE* 1.3 56.7 + - - +
326B LYS* 2.9 46.0 + - + +
327B GLY 3.6 0.3 + - - -
330B PHE* 4.7 2.0 - - + -
331B ILE* 3.8 19.2 - - + +
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Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PRO 4.1 4.0 - - - +
318B ARG* 3.7 20.4 - - - +
319B CYS 3.0 21.4 + - - +
320B GLU* 3.7 25.1 - - - +
322B LEU* 1.3 75.3 - - - +
324B ARG* 1.3 63.0 + - - +
327B GLY* 2.9 28.9 + - - +
328B GLN* 3.9 35.2 - - + +
331B ILE* 3.7 23.8 - - + -
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Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B PHE* 5.3 3.2 - - - -
320B GLU 2.9 21.3 + - - +
321B TYR* 3.6 34.1 - - - +
323B ILE* 1.3 75.6 - - - +
325B ILE* 1.3 77.2 + - + +
327B GLY 5.0 0.2 + - - -
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TRP* 3.7 28.0 - - + -
321B TYR* 3.0 43.7 + - + +
322B LEU 4.2 0.7 - - - +
324B ARG* 1.3 107.7 - - - +
326B LYS* 1.3 69.0 + - + +
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Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TRP* 3.6 56.0 - - + +
322B LEU* 2.9 15.2 + - + +
325B ILE* 1.3 85.9 - - + +
327B GLY* 1.3 63.7 + - - +
330B PHE* 3.4 58.5 + - + +
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Residues in contact with GLY 327 (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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322B LEU 3.6 1.4 + - - -
323B ILE* 2.9 21.6 + - - -
325B ILE 3.7 0.4 - - - -
326B LYS* 1.3 81.7 - - - +
328B GLN* 1.3 65.4 + - - -
329B GLU* 3.3 4.0 - - - -
330B PHE* 3.4 1.0 + - - +
331B ILE* 3.2 26.0 + - - +
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Residues in contact with GLN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PRO 5.6 0.4 - - - +
323B ILE* 3.9 39.0 - - + +
327B GLY* 1.3 69.8 - - - -
329B GLU* 1.3 60.5 + - - +
331B ILE* 3.7 9.4 - - + +
332B ARG* 2.8 68.8 + - + +
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLY* 3.3 1.5 - - - -
328B GLN* 1.3 77.0 - - - +
330B PHE* 1.3 62.4 + - - +
332B ARG* 3.7 18.4 - - - +
333B GLN* 3.1 37.1 + - - +
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Residues in contact with PHE 330 (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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307B ASP* 5.7 0.4 - - - -
309B TRP* 3.8 23.6 - - + -
310B VAL* 4.0 19.1 - - + -
313B ALA* 3.8 13.0 - - + -
322B LEU* 4.7 1.3 - - + -
326B LYS* 3.4 62.7 + - + +
327B GLY 3.4 2.3 + - - +
328B GLN 3.3 0.4 - - - -
329B GLU* 1.3 79.1 - - - +
331B ILE* 1.3 71.7 + - + +
333B GLN* 3.2 10.7 + - + +
334B VAL* 3.0 38.6 + - + +
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ALA* 4.3 9.0 - - + +
317B PRO* 3.5 50.3 - - + +
322B LEU* 3.8 27.6 - - + -
323B ILE* 3.7 26.5 - - + -
327B GLY 3.2 17.0 + - - +
328B GLN* 3.2 13.0 + - + +
330B PHE* 1.3 83.7 - - + +
332B ARG* 1.3 59.8 + - + +
334B VAL* 3.1 4.2 + - - +
335B GLN* 2.9 32.0 + - + +
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLN* 2.8 55.0 + - + +
329B GLU* 3.7 25.6 - - - +
331B ILE* 1.3 74.0 - - + +
333B GLN* 1.3 62.2 + - - +
335B GLN* 3.3 8.0 + - - +
336B ALA* 3.2 25.3 + - - +
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Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLU* 3.1 29.9 + - - +
330B PHE* 3.2 15.9 - - + +
332B ARG* 1.3 77.9 - - - +
334B VAL* 1.3 61.9 + - + +
336B ALA* 3.5 17.1 + - - +
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL* 3.6 28.9 - - + +
313B ALA* 3.7 6.1 - - + -
314B LYS* 3.6 35.4 - - + +
330B PHE* 3.0 46.6 + - + +
331B ILE 3.5 6.7 - - - +
333B GLN* 1.3 76.2 - - + +
335B GLN* 1.3 64.3 + - - +
336B ALA 3.2 8.7 + - - +
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Residues in contact with GLN 335 (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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313B ALA 2.7 28.0 + - - +
314B LYS* 2.8 24.4 + - - +
317B PRO* 3.6 26.5 - - + +
331B ILE* 2.9 21.7 + - + +
332B ARG* 3.3 8.9 + - - +
334B VAL* 1.3 75.6 - - - +
336B ALA* 1.3 57.0 + - + +
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Residues in contact with ALA 336 (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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332B ARG 3.2 13.2 + - - +
333B GLN* 3.5 12.3 - - - +
334B VAL 3.2 11.0 - - - +
335B GLN* 1.3 79.3 - - + +
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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
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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