Contacts of the helix formed by residues 383 - 400 (chain B) in PDB entry 2XI4
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 ASN 383 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ASP* 3.0 44.6 + - - +
381B ASP 3.4 0.6 - - - -
382B ASN* 1.3 74.0 - - - +
384B GLY* 1.3 59.5 + - - +
385B ILE* 3.0 31.4 + - - +
386B LYS* 3.2 29.8 + - + +
387B ASN* 2.8 35.8 + - - +
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Residues in contact with GLY 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LYS* 3.6 15.7 - - - -
347B ILE 2.9 41.1 + - - +
382B ASN 3.2 6.8 + - - -
383B ASN* 1.3 74.0 + - - +
385B ILE* 1.3 56.5 + - - +
387B ASN 3.6 0.2 + - - -
388B ARG* 3.0 19.2 + - - +
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Residues in contact with ILE 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLU* 3.4 27.8 - - - +
346B LYS* 3.8 32.3 - - + -
383B ASN* 3.0 10.4 + - - +
384B GLY* 1.3 73.1 - - - +
386B LYS* 1.3 62.7 + - + +
388B ARG* 3.2 29.2 + - - +
389B ASP* 2.9 37.5 + - - +
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Residues in contact with LYS 386 (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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352B PHE* 5.3 0.2 - - - -
375B TYR 5.3 2.3 - - - +
377B ASP* 3.3 33.3 + - + +
380B ASP* 2.7 34.7 + - + +
383B ASN* 3.2 24.3 + - + +
385B ILE* 1.3 81.3 - - + +
387B ASN* 1.3 60.7 + - - +
389B ASP* 4.2 4.8 - - - +
390B GLY* 2.9 25.6 + - - -
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Residues in contact with ASN 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ILE* 3.1 37.1 + - + +
348B SER* 3.9 13.5 - - - +
349B ARG* 3.4 25.1 + - - +
352B PHE* 3.4 24.7 - - + -
376B THR* 5.5 0.3 - - - +
380B ASP 5.1 0.5 - - - +
381B ASP* 3.2 22.4 + - - +
382B ASN 4.2 3.2 - - - -
383B ASN 2.8 26.4 + - - +
386B LYS* 1.3 73.8 - - - +
388B ARG* 1.3 64.2 + - - +
391B LEU* 3.2 20.1 + - - +
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Residues in contact with ARG 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B PHE* 3.7 19.4 - - + -
344B GLU* 2.7 56.2 + - - +
345B SER* 3.2 27.8 - - - +
347B ILE* 3.8 10.0 - - + +
384B GLY 3.0 16.5 + - - +
385B ILE* 3.2 32.7 + - - +
387B ASN* 1.3 78.5 - - - +
389B ASP* 1.3 84.5 + - - +
391B LEU* 3.4 3.6 + - - +
392B ASP* 3.1 21.0 + - + +
435B TRP* 3.4 39.2 + - + +
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Residues in contact with ASP 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ILE* 2.9 25.9 + - - +
386B LYS* 4.2 4.9 - - - +
388B ARG* 1.3 104.8 + - - +
390B GLY* 1.3 55.6 + - - +
392B ASP* 3.3 10.2 + - - +
393B ASP* 2.8 45.1 + - - +
435B TRP 4.8 4.9 - - - +
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Residues in contact with GLY 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B PHE* 4.2 6.7 - - - -
375B TYR* 3.8 16.1 - - - -
386B LYS 2.9 18.8 + - - -
387B ASN 4.0 1.1 - - - -
389B ASP* 1.3 75.0 - - - +
391B LEU* 1.3 55.2 + - - +
393B ASP* 3.3 10.0 + - - +
394B ILE* 2.8 38.2 + - - +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 3.8 14.4 - - + -
339B PHE* 3.7 29.8 - - + -
347B ILE* 4.5 3.1 - - + -
351B ASP 4.1 9.9 - - - +
352B PHE* 3.9 15.9 - - + +
355B GLY* 3.8 39.7 - - - +
356B VAL* 3.9 10.1 - - + +
359B SER* 4.3 5.6 - - - +
387B ASN 3.2 15.5 + - - +
388B ARG 3.5 4.9 - - - +
390B GLY* 1.3 71.6 - - - +
392B ASP* 1.3 60.0 + - - +
394B ILE* 3.1 19.3 + - + +
395B VAL* 2.9 34.5 + - - +
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Residues in contact with ASP 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ASP* 3.6 25.3 - - - +
328B GLY* 3.4 4.5 + - - -
329B SER* 3.0 44.5 + - - -
332B LEU* 3.5 12.0 - - + +
388B ARG* 3.1 12.6 + - + +
389B ASP* 3.3 15.7 - - - +
391B LEU* 1.3 78.4 - - - +
393B ASP* 1.3 65.4 + - - +
395B VAL* 3.3 1.6 + - - +
396B GLY* 3.0 20.6 + - - -
435B TRP* 4.1 14.9 - - + +
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Residues in contact with ASP 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LYS 5.1 4.5 - - - +
326B ASP* 5.0 7.4 - - - +
375B TYR* 3.7 17.7 - - + -
389B ASP* 2.8 31.5 + - - +
390B GLY* 3.6 6.0 - - - +
392B ASP* 1.3 74.0 - - - +
394B ILE* 1.3 53.6 + - - +
396B GLY* 5.2 0.4 - - - -
397B ASP* 2.7 43.1 + - - -
517B ARG* 3.8 22.9 + - - +
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Residues in contact with ILE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B PHE* 4.1 13.0 - - + -
356B VAL* 4.1 4.5 - - + -
359B SER* 3.9 25.4 - - - +
360B VAL* 4.5 2.5 - - + -
371B VAL* 4.0 18.4 - - + -
375B TYR* 3.5 44.6 - - + -
390B GLY 2.8 23.8 + - - +
391B LEU* 3.1 23.3 + - + +
393B ASP* 1.3 72.3 - - - +
395B VAL* 1.3 64.0 + - - +
398B HIS* 2.9 26.9 + - + +
524B TRP* 4.0 17.4 - - + -
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Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ILE* 4.1 13.5 - - + -
288B PHE* 3.9 13.5 - - + -
328B GLY* 3.4 29.8 - - - +
331B PHE* 4.3 0.9 - - + -
332B LEU* 3.7 18.6 - - + -
359B SER* 3.1 30.5 - - - +
391B LEU* 2.9 18.8 + - + +
392B ASP 3.9 0.2 - - - +
394B ILE* 1.3 75.9 - - - +
396B GLY* 1.3 57.9 + - - +
399B ASN* 3.0 51.0 + - - +
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Residues in contact with GLY 396 (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 PHE* 5.9 0.2 - - - -
327B GLU* 3.9 12.8 - - - -
328B GLY* 3.8 18.5 - - - -
392B ASP 3.0 11.6 + - - -
393B ASP* 3.8 1.6 - - - -
395B VAL* 1.3 76.6 - - - +
397B ASP* 1.3 62.8 + - - +
399B ASN* 5.2 0.2 - - - -
400B VAL* 3.1 9.3 + - - +
401B ILE* 2.9 32.7 + - - +
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Residues in contact with ASP 397 (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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375B TYR* 2.4 31.3 + - - +
393B ASP* 2.7 26.8 + - - +
394B ILE 4.1 0.2 - - - +
396B GLY* 1.3 71.7 - - - +
398B HIS* 1.3 61.2 + - - +
401B ILE* 4.0 13.5 - - - +
402B CYS* 2.9 38.4 + - - +
403B PRO* 3.4 0.3 - - - +
517B ARG* 2.6 49.3 + - - -
520B MET* 3.7 5.8 - - - +
524B TRP* 3.5 10.8 - - + +
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Residues in contact with HIS 398 (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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232B PRO* 3.7 20.4 - - + +
289B ARG* 2.9 23.5 + - - -
359B SER* 3.6 21.2 + - - -
360B VAL* 4.6 1.1 - - + -
362B HIS* 3.4 27.1 - + - -
394B ILE* 2.9 20.4 + - + +
395B VAL* 4.4 1.1 - - - +
397B ASP* 1.3 78.5 - - - +
399B ASN* 1.3 79.0 + - - +
403B PRO* 3.2 20.1 - - - +
524B TRP* 3.4 45.7 - + + +
528B LEU* 5.8 0.7 - - + -
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Residues in contact with ASN 399 (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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231B CYS* 3.3 13.3 - - - +
232B PRO* 3.7 2.9 - - - +
233B TRP* 2.8 32.2 + - + +
287B ILE* 4.8 1.0 + - - +
288B PHE* 3.5 43.6 - - + +
289B ARG* 2.6 29.7 + - - +
359B SER 4.5 5.1 + - - -
395B VAL* 3.0 35.1 + - - +
398B HIS* 1.3 94.9 - - - +
400B VAL* 1.3 59.8 + - - +
403B PRO* 3.8 2.8 - - - +
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Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B SER* 3.8 40.2 - - - +
227B GLY* 4.3 2.0 - - - +
231B CYS* 4.5 4.5 - - - -
233B TRP* 4.6 3.8 - - + +
288B PHE* 3.8 25.6 - - + -
323B VAL* 3.9 9.0 - - + -
327B GLU* 3.8 34.8 - - + +
396B GLY 3.1 6.2 + - - +
398B HIS 3.6 0.2 - - - -
399B ASN* 1.3 84.2 - - + +
401B ILE* 1.3 68.9 + - - +
402B CYS 3.5 0.9 - - - -
403B PRO* 3.4 3.8 - - - +
404B LEU* 3.0 25.5 + - + +
440B HIS* 4.7 2.0 - - + -
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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