Contacts of the helix formed by residues 337 - 350 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A HIS* 4.0 3.1 - - - -
335A LYS 3.2 3.0 + - - +
336A MET* 1.3 75.5 - - - +
338A LYS* 1.3 65.3 + - - +
339A THR* 2.9 7.4 + - - -
340A GLU* 2.8 39.8 + - - +
341A LEU* 2.9 21.5 + - - +
377A TYR* 2.8 24.4 + - - -
382A TYR* 2.6 33.1 + - - +
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Residues in contact with LYS 338 (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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218A LEU* 3.7 17.6 - - + +
221A GLU* 3.9 14.6 - - + +
222A LEU* 3.6 25.8 - - + -
225A ASP* 3.2 24.4 + - - +
289A HIS* 3.9 24.7 + - + +
290A ARG* 6.3 0.6 - - - +
337A ASP* 1.3 75.0 - - - +
339A THR* 1.3 56.5 + - - +
341A LEU* 3.7 9.7 - - + +
342A GLY* 2.9 25.8 + - - -
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Residues in contact with THR 339 (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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214A VAL* 3.9 28.5 - - + +
217A ILE* 5.2 0.7 - - + +
218A LEU* 3.2 33.2 - - - +
337A ASP* 2.9 9.4 + - - -
338A LYS* 1.3 78.5 - - - +
340A GLU* 1.3 63.2 + - - +
342A GLY* 3.2 2.3 + - - -
343A CYS* 3.0 29.8 + - - -
377A TYR* 3.6 43.9 + - + -
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Residues in contact with GLU 340 (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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336A MET* 3.5 10.6 - - + -
337A ASP* 2.8 44.9 + - - +
339A THR* 1.3 74.6 - - - +
341A LEU* 1.3 64.7 + - - +
343A CYS* 3.3 1.6 + - - +
344A LEU* 2.8 28.5 + - - +
374A LEU* 4.0 10.0 - - + +
377A TYR* 3.6 14.8 - - + -
378A THR* 3.1 15.9 + - - -
382A TYR* 3.6 4.6 - - - -
388A ARG* 2.6 40.7 + - - -
392A LEU* 3.7 24.0 - - + +
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Residues in contact with LEU 341 (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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221A GLU* 3.5 23.8 - - + +
285A ALA* 3.8 17.3 - - + +
286A GLY* 5.0 5.2 - - - +
289A HIS* 3.5 43.5 - - + +
331A MET* 4.2 13.5 - - + -
336A MET* 4.1 14.2 - - - -
337A ASP 2.9 15.2 + - - +
338A LYS* 3.7 7.4 - - + +
340A GLU* 1.3 77.4 - - - +
342A GLY* 1.3 56.2 + - - +
344A LEU* 3.1 7.3 + - + +
345A ARG* 2.8 46.0 + - + +
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Residues in contact with GLY 342 (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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217A ILE* 3.5 18.6 - - - +
221A GLU* 3.6 29.4 - - - -
256A TRP* 4.2 2.3 - - - -
338A LYS 2.9 11.8 + - - -
339A THR 3.2 2.4 + - - -
341A LEU* 1.3 77.3 - - - +
343A CYS* 1.3 56.9 + - - +
345A ARG* 3.2 3.0 + - - +
346A ALA* 2.8 28.9 + - - +
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Residues in contact with CYS 343 (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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214A VAL* 4.0 26.7 - - - -
217A ILE* 4.0 18.8 - - - -
339A THR* 3.0 21.4 + - - +
340A GLU 3.6 0.7 - - - +
342A GLY* 1.3 72.5 - - - +
344A LEU* 1.4 61.1 + - - +
346A ALA* 2.9 4.8 + - - +
347A VAL* 2.8 33.8 + - - +
370A VAL* 3.4 11.6 - - + +
374A LEU* 3.5 41.5 - - + -
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Residues in contact with LEU 344 (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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285A ALA* 6.4 0.9 - - + -
331A MET* 5.9 1.6 - - + -
336A MET* 3.8 32.3 - - + -
340A GLU 2.8 24.6 + - - +
341A LEU* 3.6 7.0 - - + +
343A CYS* 1.4 71.2 - - - +
345A ARG* 1.3 65.0 + - + +
347A VAL* 3.2 7.0 + - + +
348A VAL* 3.0 26.3 + - - +
374A LEU* 4.2 10.8 - - + -
392A LEU* 3.6 33.2 - - + +
393A LEU* 4.0 23.8 - - + -
395A ARG* 5.4 2.7 - - + -
396A LEU* 4.3 22.7 - - + -
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Residues in contact with ARG 345 (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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221A GLU* 2.5 43.8 + - - -
224A VAL* 5.0 4.4 - - - +
253A LEU* 3.6 25.4 - - - +
256A TRP* 3.3 42.7 - - + +
282A LEU* 3.2 45.4 + - + +
283A LEU* 5.0 3.4 - - - +
285A ALA* 4.1 17.5 - - + -
286A GLY* 4.1 11.3 - - - +
341A LEU* 2.8 37.4 + - + +
342A GLY 3.7 0.7 - - - +
344A LEU* 1.3 77.0 - - + +
346A ALA* 1.3 58.2 + - - +
348A VAL* 3.2 3.3 + - - +
349A LEU* 2.8 26.2 + - - +
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Residues in contact with ALA 346 (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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217A ILE* 4.7 6.5 - - + -
256A TRP* 3.9 9.6 - - + -
260A ILE* 4.4 20.0 - - + -
342A GLY 2.8 13.6 + - - +
343A CYS* 2.9 8.0 + - - +
345A ARG* 1.3 78.2 - - - +
347A VAL* 1.3 57.9 + - - +
349A LEU* 2.9 4.3 + - - +
350A PHE* 2.8 37.2 + - + -
370A VAL* 3.7 24.0 - - + -
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Residues in contact with VAL 347 (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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343A CYS 2.8 19.2 + - - +
344A LEU* 3.4 10.5 - - + +
346A ALA* 1.3 76.1 - - - +
348A VAL* 1.3 57.2 + - - +
350A PHE* 3.2 10.4 + - - +
367A ARG* 2.7 56.4 + - + +
370A VAL* 3.6 21.5 - - + +
371A TYR* 4.5 18.4 - - + +
374A LEU* 5.3 2.7 - - + -
393A LEU* 5.2 6.5 - - + -
396A LEU* 3.9 24.0 - - + -
394B LEU* 4.2 11.0 - - + -
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Residues in contact with VAL 348 (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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274A LEU 5.5 0.2 - - - +
278A GLY* 4.4 13.4 - - - +
281A GLU* 4.1 31.2 - - + +
282A LEU* 3.6 19.5 - - + -
344A LEU 3.0 17.2 + - - +
345A ARG* 3.5 6.5 - - - +
346A ALA 3.1 0.2 - - - -
347A VAL* 1.3 79.8 - - - +
349A LEU* 1.3 65.1 + - - +
350A PHE 3.3 0.3 + - - -
351A ASN* 3.5 16.8 - - - +
367A ARG* 4.0 5.2 - - - +
396A LEU* 3.8 27.6 - - + -
399A LEU* 4.3 13.5 - - + -
400A ARG* 5.8 2.2 - - - +
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Residues in contact with LEU 349 (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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256A TRP* 3.9 22.2 - - + -
257A ALA* 4.2 7.6 - - + -
260A ILE* 4.3 19.7 - - + -
263A PHE* 3.6 41.7 - - + -
274A LEU* 3.6 27.8 - - + +
275A LEU* 4.2 25.6 - - + -
278A GLY* 5.8 0.2 - - - -
282A LEU* 4.3 14.8 - - + -
345A ARG 2.8 14.9 + - - +
346A ALA* 3.4 7.4 - - - +
348A VAL* 1.3 77.1 - - - +
350A PHE* 1.3 63.0 + - + +
351A ASN* 3.1 7.1 + - - +
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Residues in contact with PHE 350 (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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212A MET* 4.2 5.2 - - + -
260A ILE* 3.8 30.3 - - + -
261A PRO 4.0 12.1 - - - -
263A PHE* 4.1 24.9 - + + -
266A LEU* 4.1 4.7 - - + -
274A LEU* 4.4 9.0 - - + -
346A ALA* 2.8 22.4 + - + +
347A VAL 3.4 2.9 - - - -
349A LEU* 1.3 79.2 - - + +
351A ASN* 1.3 59.7 + - - +
352A PRO* 2.9 6.4 - - - +
363A VAL* 3.5 13.6 - - + +
366A LEU* 3.8 41.1 - - + -
367A ARG* 2.8 42.7 + - + +
370A VAL* 3.9 24.5 - - + -
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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
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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