Contacts of the helix formed by residues 316 - 327 (chain B) in PDB entry 1XIU
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 VAL 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B 9CR 3.7 36.8 - - + -
238B PRO* 5.6 1.8 - - + -
239B VAL* 4.2 16.2 - - + -
242B ILE* 5.8 2.7 - - + -
311B ALA* 3.2 25.1 + - + +
314B ALA* 4.3 6.3 - - + +
315B GLY* 1.3 78.9 - - - +
317B GLY* 1.3 63.8 + - - +
318B THR 3.3 2.9 - - - -
319B ILE* 3.4 7.5 - - + +
320B PHE* 3.2 18.9 + - + +
409B HIS* 4.6 12.1 - - + -
413B PHE* 4.1 23.3 - - + -
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Residues in contact with GLY 317 (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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311B ALA 3.3 5.6 + - - -
312B HIS* 3.4 50.7 - - - +
315B GLY 3.4 3.6 - - - -
316B VAL* 1.3 78.3 - - - +
318B THR* 1.3 57.3 + - - +
320B PHE* 3.2 6.0 + - - +
321B ASP* 2.8 24.9 + - - -
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Residues in contact with THR 318 (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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312B HIS* 4.1 5.2 + - - -
316B VAL 3.3 1.2 - - - -
317B GLY* 1.3 72.7 - - - +
319B ILE* 1.3 66.7 + - - +
321B ASP* 3.1 7.2 + - - +
322B ARG* 3.0 32.7 + - + +
409B HIS* 6.5 0.2 - - - -
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Residues in contact with ILE 319 (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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202B 9CR 4.0 20.4 - - + -
316B VAL* 3.4 14.1 - - + +
318B THR* 1.3 79.9 - - - +
320B PHE* 1.3 67.8 + - - +
322B ARG* 3.1 36.1 + - + +
323B VAL* 3.2 14.2 + - + +
402B ILE* 4.2 16.4 - - + +
405B LYS* 3.7 31.0 - - + -
406B CYS* 3.8 21.8 - - - -
409B HIS* 3.8 28.9 - - + +
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Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B 9CR 4.5 17.3 - - + -
242B ILE* 5.0 3.4 - - + -
296B ASP 4.2 1.8 - - - -
297B GLY* 4.4 1.6 - - - -
298B ILE* 3.6 38.1 - - + -
306B VAL* 3.3 31.6 - - + -
307B HIS 4.1 4.0 - - - -
308B ARG* 3.3 40.8 - - + -
311B ALA* 3.4 19.5 - - + -
312B HIS* 5.8 0.2 - - - -
316B VAL* 3.2 11.4 + - + +
317B GLY* 3.2 9.9 - - - +
319B ILE* 1.3 85.7 - - - +
321B ASP* 1.3 63.0 + - - +
323B VAL* 3.1 17.5 + - + +
324B LEU* 3.2 32.5 + - + +
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Residues in contact with ASP 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LYS* 5.5 0.7 - - - -
308B ARG* 2.6 50.2 + - - +
312B HIS* 2.8 22.9 + - - -
317B GLY 2.8 11.9 + - - +
318B THR* 3.1 7.0 + - + +
320B PHE* 1.3 74.9 - - - +
322B ARG* 1.3 57.6 + - + +
324B LEU* 3.9 12.1 - - - +
325B THR* 3.0 42.1 + - + +
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Residues in contact with ARG 322 (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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355A LYS* 4.0 15.2 - - - +
400A ARG* 5.0 4.6 - - - +
318B THR* 3.0 25.0 + - + +
319B ILE* 3.5 26.5 - - + +
320B PHE 3.1 0.8 - - - -
321B ASP* 1.3 77.7 - - - +
323B VAL* 1.3 63.4 + - - +
325B THR* 4.2 4.9 - - - -
326B GLU* 2.9 68.1 + - - +
398B ALA* 5.0 0.4 - - - +
401B SER* 3.4 42.0 + - - -
402B ILE* 3.6 23.0 - - + +
405B LYS* 4.7 5.4 - - - +
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Residues in contact with VAL 323 (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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202B 9CR 4.9 9.6 - - + -
284B ILE* 5.0 1.3 - - + -
287B PHE* 4.0 24.9 - - + -
288B SER* 3.7 22.0 - - - +
298B ILE* 4.4 9.2 - - + -
319B ILE* 3.2 15.9 + - + +
320B PHE* 3.1 11.8 + - + +
321B ASP 3.1 0.2 - - - -
322B ARG* 1.3 79.4 - - - +
324B LEU* 1.3 58.2 + - - +
327B LEU* 3.3 7.6 + - + +
328B VAL* 3.0 30.7 + - + +
402B ILE* 3.9 29.4 - - + -
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Residues in contact with LEU 324 (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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296B ASP* 4.0 26.2 - - - +
297B GLY 3.9 27.8 - - - +
298B ILE* 4.3 13.5 - - + -
308B ARG* 4.0 11.9 - - + +
320B PHE* 3.2 29.6 + - + +
321B ASP* 3.1 26.9 + - - +
323B VAL* 1.3 78.6 - - - +
325B THR* 1.3 64.0 + - + +
328B VAL* 3.7 14.5 - - + +
329B ALA* 2.7 37.0 + - - +
332B ARG* 5.5 0.2 + - - -
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Residues in contact with THR 325 (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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353A ASP* 5.5 0.2 - - - -
355A LYS* 3.4 23.0 + - - +
321B ASP* 3.0 24.7 + - + +
324B LEU* 1.3 86.5 - - + +
326B GLU* 1.3 63.3 + - - +
327B LEU 3.6 0.2 + - - -
329B ALA* 4.0 11.1 - - - +
330B LYS* 3.8 19.9 - - - +
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ASP* 3.7 30.7 - - + +
355A LYS* 2.8 26.2 + - - +
400A ARG* 5.1 1.4 + - - -
322B ARG* 2.9 59.6 + - - +
325B THR* 1.3 81.9 - - - +
327B LEU* 1.3 62.1 + - - +
330B LYS* 4.1 3.6 - - - +
395B ARG* 2.9 36.1 + - - +
398B ALA* 3.6 16.1 - - + +
402B ILE* 3.9 9.6 - - + +
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ILE* 3.8 29.2 - - + -
288B SER* 3.8 18.2 - - - +
323B VAL* 3.3 12.9 + - + +
325B THR 3.5 0.8 - - - -
326B GLU* 1.3 90.8 - - - +
328B VAL* 1.3 65.8 + - - +
329B ALA 3.4 0.4 - - - -
330B LYS* 3.2 2.7 + - - +
331B MET* 2.8 47.6 + - + +
395B ARG* 4.3 13.2 - - + +
398B ALA* 4.2 18.8 - - + -
399B LEU* 4.2 21.3 - - + +
402B ILE* 3.6 23.3 - - + -
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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