Contacts of the helix formed by residues 337 - 350 (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 ASP 337 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B HIS* 4.2 4.7 - - - -
335B LYS 3.3 2.4 + - - +
336B MET* 1.3 75.6 - - - +
338B LYS* 1.3 59.3 + - - +
339B THR* 2.8 19.1 + - - -
340B GLU* 2.7 31.4 + - - +
341B LEU* 2.9 28.2 + - - +
377B TYR* 3.1 19.6 + - - -
381B ARG* 4.8 1.8 + - - +
382B TYR* 2.4 31.6 + - - +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 4.1 19.7 - - + +
221B GLU* 3.7 34.9 + - + +
222B LEU* 4.5 14.6 - - + -
225B ASP* 3.9 23.3 + - - +
286B GLY 5.1 3.0 + - - -
289B HIS* 3.6 30.1 + - + +
290B ARG* 5.0 8.2 - - - +
337B ASP* 1.3 75.4 - - - +
339B THR* 1.3 62.2 + - - +
341B LEU* 3.4 19.6 + - + +
342B GLY* 2.9 24.8 + - - -
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Residues in contact with THR 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B VAL* 4.0 30.5 - - + +
217B ILE* 4.2 1.4 - - - +
218B LEU* 2.9 37.2 - - + +
337B ASP* 2.8 11.4 + - - -
338B LYS* 1.3 83.6 - - - +
340B GLU* 1.3 54.2 + - - +
342B GLY* 3.4 1.7 + - - -
343B CYS* 3.0 29.1 + - - -
377B TYR* 3.7 38.9 + - + -
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Residues in contact with GLU 340 (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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336B MET* 3.4 10.2 - - + -
337B ASP* 2.7 47.7 + - - +
339B THR* 1.3 75.2 - - - +
341B LEU* 1.3 63.8 + - - +
343B CYS* 3.7 0.9 - - - +
344B LEU* 2.8 36.2 + - - +
374B LEU* 4.3 17.2 - - + +
377B TYR* 3.9 11.9 - - + -
378B THR* 3.6 7.8 + - - -
382B TYR* 3.3 7.5 - - - -
388B ARG* 2.7 43.9 + - - -
392B LEU* 3.8 16.1 - - + +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLU* 3.5 20.9 - - - +
285B ALA* 3.9 27.4 - - + +
286B GLY* 5.0 4.7 - - - -
289B HIS* 3.7 26.5 - - + +
331B MET* 4.4 4.3 - - + -
336B MET* 4.3 18.8 - - - -
337B ASP 2.9 16.1 + - - +
338B LYS* 3.6 27.1 - - + +
340B GLU* 1.3 79.9 - - - +
342B GLY* 1.3 57.0 + - - +
344B LEU* 3.1 7.4 + - + +
345B ARG* 2.9 44.0 + - + +
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Residues in contact with GLY 342 (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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217B ILE* 3.4 21.3 - - - +
221B GLU* 3.6 25.5 - - - +
256B TRP* 4.0 3.5 - - - -
338B LYS 2.9 13.0 + - - -
340B GLU 3.3 0.2 - - - -
341B LEU* 1.3 77.2 - - - +
343B CYS* 1.3 51.6 + - - +
345B ARG* 3.2 3.4 + - - +
346B ALA* 2.7 35.2 + - - +
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Residues in contact with CYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B VAL* 4.1 20.2 - - - -
217B ILE* 3.6 23.8 - - - +
339B THR* 3.0 23.0 + - - +
340B GLU 3.7 4.9 - - - +
341B LEU 3.3 0.2 - - - -
342B GLY* 1.3 70.6 - - - +
344B LEU* 1.3 57.4 + - - +
346B ALA* 2.9 1.8 + - - -
347B VAL* 2.7 39.1 + - - +
370B VAL* 3.5 13.0 - - + +
374B LEU* 3.9 37.5 - - + -
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ALA* 6.3 1.3 - - + -
331B MET* 6.2 1.1 - - + -
336B MET* 4.0 29.6 - - + -
340B GLU 2.8 20.2 + - - +
341B LEU* 3.6 8.1 - - + +
343B CYS* 1.3 76.1 - - - +
345B ARG* 1.3 64.5 + - + +
347B VAL* 3.2 6.4 + - + +
348B VAL* 2.9 27.1 + - - +
374B LEU* 4.1 17.9 - - + -
392B LEU* 3.8 40.2 - - + +
393B LEU* 4.2 12.6 - - + -
395B ARG* 5.1 3.1 - - + -
396B LEU* 4.3 22.3 - - + +
399B LEU* 6.2 2.2 - - + -
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Residues in contact with ARG 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLU* 2.7 39.5 + - - -
224B VAL* 5.0 4.4 - - - +
253B LEU* 3.6 23.5 - - - +
256B TRP* 3.1 44.1 - - + +
282B LEU* 3.1 45.6 + - + +
283B LEU* 4.6 4.9 - - - +
285B ALA* 4.1 17.9 - - + -
286B GLY* 4.2 12.7 - - - +
341B LEU* 2.9 31.6 + - + +
342B GLY 3.5 4.3 - - - +
344B LEU* 1.3 77.7 - - + +
346B ALA* 1.3 56.3 + - - +
348B VAL* 3.1 2.7 + - - -
349B LEU* 2.8 26.3 + - - +
399B LEU* 6.2 0.4 - - + -
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE* 4.6 7.9 - - + -
256B TRP* 3.8 10.9 - - + -
260B ILE* 4.3 19.5 - - + -
342B GLY 2.7 19.8 + - - +
343B CYS* 3.5 5.4 - - - +
345B ARG* 1.3 69.3 - - - +
347B VAL* 1.3 66.5 + - - +
349B LEU* 3.1 3.8 + - - +
350B PHE* 2.9 31.6 + - + -
370B VAL* 3.9 22.4 - - + -
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 4.6 8.5 - - + -
343B CYS 2.7 20.9 + - - +
344B LEU* 3.5 11.2 - - + +
346B ALA* 1.3 73.9 - - - +
348B VAL* 1.3 63.4 + - - +
349B LEU 3.3 0.2 + - - -
350B PHE* 3.4 10.7 - - - +
367B ARG* 2.7 50.4 + - + +
370B VAL* 3.6 22.0 - - + -
371B TYR* 4.4 19.1 - - + -
374B LEU* 5.4 2.5 - - + -
393B LEU* 5.1 7.0 - - + -
396B LEU* 3.9 25.4 - - + -
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLY* 4.5 11.6 - - - +
281B GLU* 3.7 30.7 - - + +
282B LEU* 3.4 23.1 - - + +
344B LEU 2.9 16.3 + - - +
345B ARG* 3.1 8.3 + - - +
347B VAL* 1.3 77.7 - - - +
349B LEU* 1.3 63.0 + - - +
351B ASN* 3.2 21.3 + - - +
367B ARG* 4.1 5.4 - - - +
396B LEU* 3.9 27.4 - - + -
399B LEU* 4.0 15.3 - - + -
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Residues in contact with LEU 349 (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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256B TRP* 3.8 22.9 - - + -
257B ALA* 4.4 3.4 - - + -
260B ILE* 4.1 18.8 - - + -
263B PHE* 3.9 35.2 - - + -
274B LEU* 3.6 32.6 - - + +
275B LEU* 3.9 28.0 - - + -
278B GLY* 5.7 0.9 - - - -
282B LEU* 4.1 14.6 - - + -
345B ARG 2.8 13.2 + - - +
346B ALA* 3.1 7.6 + - - +
348B VAL* 1.3 79.9 - - - +
350B PHE* 1.3 62.6 + - + +
351B ASN* 2.8 14.2 + - - +
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Residues in contact with PHE 350 (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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212B MET* 4.1 7.4 - - + -
260B ILE* 3.6 26.2 - - + -
261B PRO 3.7 19.7 - - - -
263B PHE* 4.1 25.1 - + + -
266B LEU* 4.5 2.9 - - + -
274B LEU* 4.5 10.8 - - + -
346B ALA* 2.9 23.5 + - + +
347B VAL 3.6 2.5 - - - +
349B LEU* 1.3 77.0 - - + +
351B ASN* 1.3 59.6 + - - +
352B PRO* 3.2 4.9 - - - +
363B VAL* 3.6 13.4 - - + +
366B LEU* 3.2 36.6 - - + -
367B ARG* 2.9 41.0 + - + +
370B VAL* 3.9 24.7 - - + -
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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
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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