Contacts of the helix formed by residues 349 - 369 (chain B) in PDB entry 2XAR
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 PRO 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B ALA 4.9 0.4 - - - +
348B LEU* 1.4 98.4 - - + +
350B LEU* 1.3 65.7 + - - +
351B ASP* 4.2 11.9 - - + +
352B GLU* 3.1 19.7 + - + +
353B SER* 3.1 18.9 + - - -
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Residues in contact with LEU 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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67B HIS* 3.9 20.2 - - + +
324B ASP* 4.2 25.8 - - + +
325B ILE* 5.0 7.0 - - + +
327B ASN* 6.1 1.1 - - - +
348B LEU 3.4 2.5 + - - +
349B PRO* 1.3 70.7 - - - +
351B ASP* 1.3 63.6 + - - +
353B SER* 3.1 8.8 + - - +
354B LEU* 3.0 51.5 + - + +
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Residues in contact with ASP 351 (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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70B ARG* 5.8 2.4 + - - -
71B GLU* 5.7 1.9 - - - +
349B PRO* 4.2 8.0 - - + +
350B LEU* 1.3 81.2 - - - +
352B GLU* 1.3 63.3 + - - +
354B LEU* 3.2 22.5 + - - +
355B LYS* 3.3 12.7 + - - +
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Residues in contact with GLU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU 5.1 3.5 - - - +
202A GLU* 4.5 24.7 - - - +
204A ILE* 4.8 4.3 - - - +
348B LEU* 3.8 25.1 - - + -
349B PRO* 3.1 26.0 + - + +
351B ASP* 1.3 77.5 - - - +
353B SER* 1.3 62.7 + - - +
355B LYS* 3.4 19.0 + - - +
356B ILE* 3.2 36.7 + - + +
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Residues in contact with SER 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B CYS* 4.0 21.7 - - - +
324B ASP* 4.3 12.5 + - - +
325B ILE* 3.6 14.4 - - - -
345B LEU 4.2 12.6 + - - -
348B LEU* 3.9 11.5 + - - +
349B PRO 3.1 13.5 + - - -
350B LEU* 3.1 12.3 + - - -
352B GLU* 1.3 74.1 - - - +
354B LEU* 1.3 64.6 + - - +
356B ILE* 3.3 5.3 + - - +
357B VAL* 3.2 27.9 + - - +
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Residues in contact with LEU 354 (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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67B HIS* 3.9 33.0 - - + +
68B LEU* 3.5 33.3 - - + +
70B ARG* 5.2 11.9 - - - +
325B ILE* 3.6 23.5 - - + +
350B LEU* 3.0 32.8 + - + +
351B ASP* 3.2 20.8 + - - +
353B SER* 1.3 72.6 - - - +
355B LYS* 1.3 56.8 + - - +
357B VAL 3.3 0.5 + - - -
358B LYS* 2.8 39.2 + - - +
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Residues in contact with LYS 355 (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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202A GLU* 4.3 19.3 - - - +
432A ARG* 6.0 2.9 - - - +
433A LYS* 4.8 16.4 - - - +
312B LYS* 5.9 0.2 - - - +
351B ASP 3.3 8.6 + - - +
352B GLU* 3.4 24.7 - - - +
353B SER 3.3 0.2 - - - -
354B LEU* 1.3 78.7 - - - +
356B ILE* 1.3 59.3 + - + +
358B LYS* 3.6 12.0 - - - +
359B GLU* 2.9 63.7 + - + +
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Residues in contact with ILE 356 (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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202A GLU 6.1 0.2 - - - +
204A ILE* 4.3 16.4 - - + -
310B LEU 5.1 1.4 - - - +
312B LYS* 5.8 6.7 - - + -
313B LEU* 3.6 35.9 - - + -
318B ALA* 4.3 15.0 - - + -
321B CYS* 3.9 30.1 - - + -
348B LEU* 4.4 5.4 - - + -
352B GLU* 3.2 32.6 + - + +
353B SER 3.6 5.6 - - - +
354B LEU 3.3 0.2 - - - -
355B LYS* 1.3 82.2 - - + +
357B VAL* 1.3 57.8 + - - +
359B GLU* 3.9 8.5 - - - +
360B TYR* 3.0 25.6 + - - +
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Residues in contact with VAL 357 (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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68B LEU* 4.1 10.3 - - + -
318B ALA* 4.3 5.4 - - - +
321B CYS* 3.6 24.7 - - + -
322B TYR* 3.8 13.5 - - + +
325B ILE* 3.8 10.8 - - + -
353B SER 3.2 16.3 + - - +
354B LEU 4.0 2.2 - - - +
356B ILE* 1.3 75.0 - - + +
358B LYS* 1.3 67.5 + - - +
360B TYR* 3.1 7.0 + - - +
361B LEU* 3.0 23.2 + - + +
413B LEU* 3.7 29.2 - - + -
416B MET* 4.3 18.4 - - + -
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Residues in contact with LYS 358 (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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68B LEU* 3.9 28.4 - - + +
69B TRP* 3.5 39.2 - - + -
71B GLU* 4.1 19.6 - - - +
72B ASN* 3.6 19.7 + - - +
92B VAL* 6.0 1.1 - - - -
354B LEU 2.8 19.3 + - - +
355B LYS* 3.6 11.9 - - - +
357B VAL* 1.3 76.6 - - - +
359B GLU* 1.3 61.5 + - - +
361B LEU* 3.0 8.7 + - - +
362B ILE* 2.9 40.0 + - + +
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Residues in contact with GLU 359 (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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432A ARG* 4.9 5.9 + - - -
310B LEU* 3.6 39.9 - - + +
312B LYS* 3.1 32.1 - - - +
355B LYS* 2.9 54.0 + - + +
356B ILE* 4.0 5.6 - - - +
358B LYS* 1.3 79.6 - - + +
360B TYR* 1.3 56.6 + - - +
362B ILE* 3.7 14.8 - - + +
363B ALA* 2.8 30.5 + - - +
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Residues in contact with TYR 360 (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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192B ARG* 5.9 1.0 + - - -
310B LEU 4.3 4.2 + - - -
311B ASP* 3.3 36.5 + - - +
315B ILE* 3.3 45.4 + - + +
318B ALA* 3.7 17.9 - - + -
356B ILE 3.0 16.0 + - - +
357B VAL* 3.1 12.8 + - - +
359B GLU* 1.3 76.2 - - - +
361B LEU* 1.3 58.9 + - + +
363B ALA* 3.4 6.0 + - - +
364B ALA* 2.8 29.6 + - + +
367B LYS* 4.8 8.3 + - - -
416B MET* 3.4 20.6 - - - -
419B TYR* 3.7 33.4 - + - +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 3.8 28.7 - - + -
69B TRP* 4.5 12.8 - - + +
88B TYR* 3.7 2.3 + - - -
357B VAL* 3.0 14.9 + - + +
358B LYS 3.0 8.1 + - - +
360B TYR* 1.3 74.5 - - + +
362B ILE* 1.3 62.2 + - - +
364B ALA* 3.5 5.6 - - - +
365B THR* 3.2 23.6 + - - -
410B LEU* 5.9 0.4 - - + +
411B LYS* 4.0 28.4 + - + +
412B PRO 4.4 7.2 - - - +
413B LEU* 3.8 26.9 - - + -
416B MET* 3.9 25.6 - - + -
419B TYR* 4.3 17.5 - - + -
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Residues in contact with ILE 362 (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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69B TRP* 3.9 8.5 - - + -
88B TYR* 3.5 13.7 - - - +
92B VAL* 3.6 23.3 - - + -
93B ILE* 3.9 17.9 - - + -
96B LEU* 5.2 11.9 - - + -
307B ILE* 3.7 21.7 - - + +
310B LEU* 5.5 6.7 - - + -
358B LYS* 2.9 39.9 + - + +
359B GLU* 3.7 16.4 - - + +
361B LEU* 1.3 75.6 - - - +
363B ALA* 1.3 66.6 + - - +
365B THR* 2.9 15.4 + - - -
366B ALA* 3.1 11.1 + - - +
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Residues in contact with ALA 363 (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 ILE 3.4 18.0 + - - +
308B GLN 3.2 24.9 - - - +
311B ASP* 3.4 21.1 - - + +
359B GLU 2.8 20.4 + - - +
360B TYR 3.5 4.9 - - - +
362B ILE* 1.3 71.2 - - - +
364B ALA* 1.3 63.2 + - - +
366B ALA* 2.9 4.9 + - - +
367B LYS* 2.8 30.1 + - - +
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Residues in contact with ALA 364 (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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360B TYR* 2.8 26.2 + - + +
361B LEU* 3.5 12.1 - - - +
363B ALA* 1.3 70.9 - - - +
365B THR* 1.3 64.5 + - - +
367B LYS* 3.1 22.4 + - - +
368B ASP* 3.3 13.3 + - - +
411B LYS* 3.7 19.3 - - + -
419B TYR* 4.0 20.6 - - + +
500B IHP 4.5 2.7 + - - +
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Residues in contact with THR 365 (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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88B TYR* 2.7 32.4 + - + -
93B ILE* 4.2 11.7 - - + -
361B LEU 3.2 6.7 + - - -
362B ILE 2.9 12.5 + - - -
364B ALA* 1.3 74.0 - - - +
366B ALA* 1.3 64.3 + - - +
368B ASP* 3.0 13.9 + - - +
369B CYS* 3.1 12.5 + - - +
407B ASP 5.0 0.7 - - - +
408B LEU* 4.0 16.4 - - + -
409B SER 2.8 40.5 + - - +
411B LYS* 3.8 9.8 + - - +
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Residues in contact with ALA 366 (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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93B ILE* 5.9 0.4 - - + +
97B LEU* 5.8 1.1 - - + -
169B PRO* 5.7 0.3 - - - +
304B LEU* 3.7 14.7 - - + +
307B ILE* 3.5 37.9 - - + -
308B GLN* 3.1 27.8 + - + +
362B ILE 3.1 1.2 + - - -
363B ALA 2.9 9.0 + - - +
365B THR* 1.3 80.1 - - - +
367B LYS* 1.3 61.5 + - - +
369B CYS* 3.3 21.2 - - - +
408B LEU* 5.4 1.6 - - - -
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Residues in contact with LYS 367 (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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169B PRO* 6.5 0.2 - - - -
170B LYS* 3.2 36.0 + - - +
171B CYS* 3.8 32.7 - - + -
173B PHE* 4.9 1.5 - - - -
308B GLN* 3.5 28.7 - - + +
311B ASP* 2.9 40.2 + - - +
360B TYR* 4.8 10.9 + - - -
363B ALA* 2.8 22.0 + - - +
364B ALA* 3.1 12.5 + - - +
366B ALA* 1.3 77.6 - - - +
368B ASP* 1.3 57.1 + - + +
369B CYS 3.6 0.7 - - - -
500B IHP 6.0 2.0 - - - +
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Residues in contact with ASP 368 (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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168B LYS* 3.3 24.5 + - - +
170B LYS* 3.2 23.8 + - - +
364B ALA 3.3 7.5 + - - +
365B THR 3.0 5.5 + - - +
367B LYS* 1.3 77.4 - - - +
369B CYS* 1.3 66.4 + - - +
370B SER* 4.3 1.9 + - - -
407B ASP* 4.3 7.2 - - - +
411B LYS* 3.5 15.9 + - - +
500B IHP 2.5 62.9 + - - +
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Residues in contact with CYS 369 (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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168B LYS* 4.0 2.9 - - - +
169B PRO* 3.5 17.2 - - - +
304B LEU* 3.4 31.9 - - - -
365B THR 3.1 7.6 + - - +
366B ALA 3.3 22.3 - - - +
367B LYS 3.6 1.9 - - - +
368B ASP* 1.3 84.3 - - - +
370B SER* 1.3 61.8 + - - +
405B PHE* 4.3 10.1 - - - -
406B ILE 3.5 5.4 - - - +
407B ASP 3.4 11.4 - - - +
408B LEU* 3.4 31.2 - - + -
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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