Contacts of the helix formed by residues 356 - 373 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A ARG 5.6 0.4 - - - +
355A LEU* 1.3 76.0 - - - +
357A LYS* 1.3 65.3 + - - +
358A GLU* 3.5 16.3 + - - +
359A GLU* 2.9 41.1 + - - +
360A ARG* 3.0 24.4 + - - +
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Residues in contact with LYS 357 (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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356A THR* 1.3 73.4 - - - +
358A GLU* 1.3 72.7 + - - +
360A ARG* 3.3 15.6 + - - +
361A LEU* 2.9 28.8 + - - +
382A HIS* 5.7 1.6 - - - -
383A TYR* 3.1 57.1 + - + -
384A GLU* 3.9 14.0 + - - +
385A GLU* 3.6 20.8 - - + +
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Residues in contact with GLU 358 (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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356A THR* 3.2 18.4 - - - +
357A LYS* 1.3 93.6 + - - +
359A GLU* 1.3 61.8 + - + +
361A LEU* 3.4 12.6 + - + +
362A LYS* 3.1 22.9 + - - +
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LEU* 3.4 30.9 - - + +
356A THR* 2.9 45.9 + - - +
358A GLU* 1.3 75.3 - - + +
360A ARG* 1.3 64.1 + - - +
362A LYS* 3.4 10.3 + - - +
363A LYS* 3.1 29.1 + - + +
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Residues in contact with ARG 360 (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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295A ILE* 4.1 13.6 - - - +
344A ILE* 4.1 23.6 - - + -
352A LEU* 2.9 33.4 + - + +
353A ALA* 3.5 12.4 + - - +
355A LEU* 2.9 34.7 + - + -
356A THR* 3.0 11.8 + - - +
357A LYS* 3.5 22.3 - - - +
359A GLU* 1.3 72.4 - - - +
361A LEU* 1.3 68.9 + - - +
363A LYS* 3.2 5.6 + - + +
364A LEU* 3.0 32.8 + - + +
383A TYR* 4.0 9.9 - - - +
385A GLU* 2.8 40.4 + - - -
387A ASN* 6.3 0.4 - - - -
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Residues in contact with LEU 361 (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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299A VAL* 3.9 14.8 - - + -
357A LYS 2.9 17.6 + - - +
358A GLU* 3.7 11.0 - - + +
359A GLU 3.3 0.2 - - - -
360A ARG* 1.3 78.2 - - - +
362A LYS* 1.3 57.0 + - - +
364A LEU* 3.3 1.8 + - - +
365A CYS* 2.9 48.7 + - - -
380A PRO* 4.2 17.7 - - + -
382A HIS 5.6 0.9 - - - -
383A TYR* 3.7 50.8 - - + +
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Residues in contact with LYS 362 (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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358A GLU 3.1 16.7 + - - +
359A GLU* 3.7 10.5 - - - +
360A ARG 3.2 0.4 - - - -
361A LEU* 1.3 77.4 - - - +
363A LYS* 1.3 65.9 + - - +
365A CYS* 3.3 6.2 + - - +
366A GLU* 2.9 62.5 + - + +
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Residues in contact with LYS 363 (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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323A PRO* 4.1 22.3 - - + +
352A LEU* 4.7 13.7 - - + -
355A LEU* 3.4 36.1 - - + -
359A GLU* 3.1 15.3 + - - +
360A ARG* 3.8 5.2 - - + +
362A LYS* 1.3 79.7 - - + +
364A LEU* 1.3 65.8 + - + +
366A GLU* 3.5 11.9 + - - +
367A LEU* 3.0 23.4 + - - +
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Residues in contact with LEU 364 (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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297A CYS* 3.4 34.8 - - + -
299A VAL* 4.2 16.2 - - + -
323A PRO* 3.9 18.2 - - + -
324A VAL* 3.7 25.6 - - + -
344A ILE* 4.2 11.9 - - + -
360A ARG* 3.0 23.9 + - + +
361A LEU 3.7 3.6 - - - +
363A LYS* 1.3 80.0 - - + +
365A CYS* 1.3 57.9 + - - +
367A LEU* 3.2 8.3 + - - +
368A TYR* 2.8 56.6 + - + +
383A TYR* 4.0 7.6 - - + +
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Residues in contact with CYS 365 (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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299A VAL* 4.0 4.7 - - - -
301A TYR* 3.9 11.7 - - - -
361A LEU* 2.9 32.6 + - - +
362A LYS* 3.7 5.8 - - - +
364A LEU* 1.3 75.9 - - - +
366A GLU* 1.3 57.4 + - - +
368A TYR* 3.8 2.4 - - - +
369A ALA* 2.8 31.9 + - - +
377A ALA 3.3 24.9 - - - +
378A LEU* 3.7 12.8 - - + +
380A PRO* 3.7 29.4 - - + -
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Residues in contact with GLU 366 (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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362A LYS* 2.9 58.4 + - + +
363A LYS* 3.9 12.0 - - - +
365A CYS* 1.3 76.5 - - + +
367A LEU* 1.3 62.7 + - - +
369A ALA* 3.5 1.7 + - - +
370A LYS* 3.2 21.8 + - - +
378A LEU* 3.9 20.2 - - + -
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Residues in contact with LEU 367 (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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91A HIS* 5.4 3.1 - - + +
317A ILE* 3.9 13.2 - - + -
322A ALA* 3.8 21.3 - - + -
323A PRO* 3.9 13.0 - - + -
324A VAL* 3.5 45.3 - - + +
363A LYS 3.0 13.9 + - - +
364A LEU* 3.4 7.4 - - - +
366A GLU* 1.3 78.0 - - - +
368A TYR* 1.3 65.3 + - + +
370A LYS* 3.1 10.9 + - + +
371A VAL* 2.9 48.7 + - + +
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Residues in contact with TYR 368 (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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297A CYS 5.0 0.2 + - - -
299A VAL* 4.0 22.7 - - + -
301A TYR* 3.9 16.6 - - - +
315A MET* 4.0 15.3 - - + -
317A ILE* 4.7 0.9 - - + -
324A VAL* 3.8 18.5 - - + +
327A THR* 3.5 32.0 - - + +
340A ILE* 3.9 22.1 + - + -
342A GLY* 3.7 18.7 + - - -
364A LEU* 2.8 36.9 + - + +
365A CYS* 3.9 3.4 - - - +
367A LEU* 1.3 87.3 - - + +
369A ALA* 1.3 63.3 + - - +
371A VAL* 4.4 3.8 - - - +
372A LEU* 2.9 38.9 + - + +
377A ALA* 3.9 11.9 - - + -
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Residues in contact with ALA 369 (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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365A CYS 2.8 18.9 + - - +
366A GLU* 3.8 4.3 - - - +
367A LEU 3.2 0.2 - - - -
368A TYR* 1.3 77.2 - - - +
370A LYS* 1.3 56.6 + - - +
373A GLY* 2.9 9.2 + - - -
374A SER 2.9 50.1 + - - +
375A LEU* 4.9 1.8 - - + -
377A ALA* 3.5 5.3 - - + +
378A LEU* 3.7 25.4 - - + -
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Residues in contact with LYS 370 (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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91A HIS* 4.3 14.6 + - + +
94A GLY* 3.4 35.6 + - - -
96A SER* 4.5 1.4 + - - -
321A GLU* 5.9 1.4 + - - -
366A GLU 3.2 13.2 + - - +
367A LEU* 3.1 13.9 + - + +
369A ALA* 1.3 75.2 - - - +
371A VAL* 1.3 67.1 + - + +
373A GLY* 3.2 11.9 + - - -
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Residues in contact with VAL 371 (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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89A ILE* 3.8 21.9 - - + +
91A HIS* 3.7 29.4 - - + +
96A SER* 2.7 37.3 + - - +
311A TYR* 5.0 1.6 + - - -
315A MET* 3.5 33.2 - - + -
317A ILE* 4.0 10.8 - - + -
367A LEU* 2.9 39.5 + - + +
368A TYR 4.1 0.4 - - - +
370A LYS* 1.3 78.4 - - + +
372A LEU* 1.3 59.6 + - - +
373A GLY 3.6 0.2 + - - -
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Residues in contact with LEU 372 (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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89A ILE* 3.7 22.4 - - + -
301A TYR* 6.5 0.2 - - + -
305A PHE* 3.9 28.9 - - + -
306A TRP* 4.1 19.5 - - + -
309A LYS* 4.1 2.8 + - - +
311A TYR* 3.5 37.5 + - + -
313A GLY* 5.4 2.9 - - - -
315A MET* 3.9 30.5 - - + -
340A ILE* 5.5 3.1 - - + -
368A TYR* 2.9 26.4 + - + +
371A VAL* 1.3 75.5 - - - +
373A GLY* 1.3 59.7 + - - +
374A SER* 2.8 25.9 + - - +
377A ALA* 4.7 0.2 - - + -
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Residues in contact with GLY 373 (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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309A LYS* 3.0 18.0 + - - -
369A ALA 2.9 9.4 + - - -
370A LYS* 3.2 10.8 + - - -
371A VAL 3.3 0.8 + - - -
372A LEU* 1.3 77.0 - - - +
374A SER* 1.3 57.1 + - - +
375A LEU 4.3 0.6 + - - -
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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