Contacts of the helix formed by residues 356 - 373 (chain B) in PDB entry 2XFN
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 THR 356 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B ARG 5.6 0.4 - - - +
355B LEU* 1.3 77.7 - - - +
357B LYS* 1.3 65.0 + - - +
358B GLU* 3.6 15.8 + - - +
359B GLU* 2.9 44.3 + - - +
360B ARG* 3.0 25.3 + - - +
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Residues in contact with LYS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B THR* 1.3 73.3 - - - +
358B GLU* 1.3 72.9 + - - +
360B ARG* 3.3 15.8 + - - +
361B LEU* 2.9 27.0 + - - +
382B HIS* 5.8 1.4 - - - -
383B TYR* 3.3 56.1 + - + -
384B GLU* 4.3 11.3 + - - +
385B GLU* 3.7 20.4 - - + +
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B THR* 3.7 18.8 - - - +
357B LYS* 1.3 95.5 + - - +
359B GLU* 1.3 57.1 + - + +
361B LEU* 3.3 12.5 + - + +
362B LYS* 3.0 27.5 + - - +
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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
----------------------------------------------------------
355B LEU* 3.4 29.4 - - + +
356B THR* 2.9 50.4 + - - +
358B GLU* 1.3 73.0 - - + +
360B ARG* 1.3 66.3 + - - +
362B LYS* 3.4 7.7 + - - +
363B LYS* 3.1 29.1 + - - +
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Residues in contact with ARG 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 4.1 13.1 - - - +
344B ILE* 4.0 24.9 - - + -
352B LEU* 2.8 36.8 + - + +
353B ALA* 3.5 12.0 + - - +
355B LEU* 2.9 32.0 + - + -
356B THR 3.0 10.1 + - - +
357B LYS* 3.5 23.6 - - - +
359B GLU* 1.3 72.7 - - - +
361B LEU* 1.3 66.6 + - - +
363B LYS* 3.2 6.8 + - + -
364B LEU* 2.9 32.8 + - + +
383B TYR* 4.0 10.3 - - - +
385B GLU* 2.8 39.9 + - - -
387B ASN* 6.5 0.4 - - - -
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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
----------------------------------------------------------
299B VAL* 3.9 14.8 - - + -
357B LYS 2.9 14.4 + - - +
358B GLU* 3.6 14.6 - - + +
359B GLU 3.3 0.2 - - - -
360B ARG* 1.3 76.2 - - - +
362B LYS* 1.3 62.3 + - - +
364B LEU* 3.3 2.7 + - - +
365B CYS* 2.9 43.0 + - - -
380B PRO* 4.1 18.2 - - + -
382B HIS 5.5 0.7 - - - +
383B TYR* 3.7 50.6 - - + +
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Residues in contact with LYS 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLU 3.0 16.6 + - - +
359B GLU* 3.8 7.6 - - - +
360B ARG 3.3 0.4 - - - -
361B LEU* 1.3 78.0 - - - +
363B LYS* 1.3 63.3 + - + +
365B CYS* 3.4 4.2 + - - +
366B GLU* 2.9 60.3 + - + +
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Residues in contact with LYS 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PRO* 4.2 19.6 - - + +
352B LEU* 4.7 13.7 - - + -
355B LEU* 3.7 35.4 - - + -
359B GLU* 3.1 16.1 + - - +
360B ARG* 3.2 8.9 + - + +
362B LYS* 1.3 76.5 - - + +
364B LEU* 1.3 63.9 + - + +
366B GLU* 4.0 6.5 - - - +
367B LEU* 3.1 24.1 + - - +
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Residues in contact with LEU 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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297B CYS* 3.5 33.9 - - + -
299B VAL* 4.2 15.0 - - + -
323B PRO* 3.9 19.3 - - + -
324B VAL* 3.7 25.8 - - + -
344B ILE* 4.4 10.3 - - + -
360B ARG* 2.9 22.7 + - + +
361B LEU 3.8 3.8 - - - +
363B LYS* 1.3 75.3 - - + +
365B CYS* 1.3 60.1 + - - +
367B LEU* 3.2 6.3 + - - +
368B TYR* 2.8 57.4 + - + +
383B TYR* 4.0 10.5 - - + +
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Residues in contact with CYS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B VAL* 4.0 4.0 - - - -
301B TYR* 3.8 12.1 - - - -
361B LEU* 2.9 33.3 + - - +
362B LYS* 3.9 5.4 - - - +
364B LEU* 1.3 76.4 - - - +
366B GLU* 1.3 58.9 + - + +
368B TYR* 3.3 1.4 + - - -
369B ALA* 2.9 30.1 + - - +
377B ALA 3.2 27.7 - - - +
378B LEU* 3.7 11.8 - - + +
380B PRO* 3.6 30.3 - - + -
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Residues in contact with GLU 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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362B LYS* 2.9 57.9 + - + +
363B LYS* 4.0 5.9 - - - +
365B CYS* 1.3 73.9 - - + +
367B LEU* 1.3 65.7 + - - +
369B ALA* 3.4 3.2 + - - +
370B LYS* 3.1 43.4 + - - +
378B LEU* 4.0 18.8 - - + -
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Residues in contact with LEU 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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91B HIS* 5.6 2.5 - - + +
317B ILE* 3.9 17.7 - - + -
322B ALA* 4.0 20.6 - - + -
323B PRO* 3.9 21.8 - - + -
324B VAL* 3.6 35.9 - - + +
363B LYS 3.1 18.8 + - - +
364B LEU* 3.5 4.7 - - - +
366B GLU* 1.3 77.5 - - - +
368B TYR* 1.3 69.7 + - + +
370B LYS* 3.1 14.8 + - + +
371B VAL* 3.0 40.6 + - + +
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Residues in contact with TYR 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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297B CYS 5.0 0.2 + - - -
299B VAL* 4.0 21.7 - - + +
301B TYR* 3.9 15.9 - - - +
315B MET* 4.0 15.0 - - + -
317B ILE* 4.8 1.1 - - + -
324B VAL* 3.8 6.2 - - + +
327B THR* 3.5 31.4 - - + +
340B ILE* 3.8 21.2 + - + -
342B GLY* 3.7 18.7 + - - -
364B LEU* 2.8 45.4 + - + +
365B CYS* 3.9 2.9 - - - +
367B LEU* 1.3 92.5 - - + +
369B ALA* 1.3 58.2 + - - +
371B VAL* 4.4 4.0 - - - +
372B LEU* 2.8 46.1 + - + +
377B ALA* 3.8 12.8 - - + -
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Residues in contact with ALA 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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365B CYS 2.9 18.4 + - - +
366B GLU* 3.7 5.2 - - - +
367B LEU 3.2 0.2 - - - -
368B TYR* 1.3 75.9 - - - +
370B LYS* 1.3 57.9 + - + +
373B GLY* 2.9 24.8 + - - -
374B SER 3.0 32.7 + - - +
375B LEU* 4.9 3.1 - - + -
377B ALA* 3.5 5.1 - - + +
378B LEU* 3.7 24.5 - - + -
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Residues in contact with LYS 370 (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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91B HIS* 4.3 13.6 - - + +
96B SER* 4.3 2.8 + - - -
366B GLU* 3.1 30.9 + - - +
367B LEU* 3.1 15.3 + - + +
369B ALA* 1.3 78.9 - - + +
371B VAL* 1.3 65.9 + - + +
373B GLY* 3.3 10.8 + - - -
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Residues in contact with VAL 371 (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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89B ILE* 3.7 18.2 - - + +
91B HIS* 3.7 31.9 - - + +
96B SER* 2.7 35.8 + - - +
311B TYR* 5.0 1.2 + - - -
315B MET* 3.4 37.7 - - + -
317B ILE* 4.0 10.5 - - + -
367B LEU* 3.0 31.4 + - + +
368B TYR 4.2 0.4 - - - +
370B LYS* 1.3 78.0 - - + +
372B LEU* 1.3 61.1 + - - +
373B GLY 3.5 0.5 + - - -
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Residues in contact with LEU 372 (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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89B ILE* 3.9 15.7 - - + -
305B PHE* 3.8 29.2 - - + -
306B TRP* 4.0 29.2 - - + -
309B LYS* 3.9 2.8 - - - +
311B TYR* 3.5 30.7 - - + -
313B GLY* 5.0 3.8 - - - -
315B MET* 3.9 37.0 - - + -
340B ILE* 5.0 3.4 - - + -
368B TYR* 2.8 29.5 + - + +
371B VAL* 1.3 72.3 - - - +
373B GLY* 1.3 64.6 + - - +
374B SER* 3.2 17.6 + - - +
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Residues in contact with GLY 373 (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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309B LYS* 3.0 24.9 + - - -
369B ALA 2.9 10.8 + - - -
370B LYS* 3.3 7.2 + - - -
371B VAL 3.2 3.8 + - - -
372B LEU* 1.3 78.0 - - - +
374B SER* 1.3 57.4 + - - +
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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