Contacts of the helix formed by residues 356 - 371 (chain A) in PDB entry 2XFR
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 ALA 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A HIS* 3.1 12.5 + - - -
301A TYR* 3.6 27.0 - - + -
302A LYS* 4.0 18.4 - - + -
346A ASP* 3.5 5.8 - - - -
354A MET 4.1 0.4 + - - -
355A SER* 1.3 75.3 - - - +
357A PRO* 1.4 67.9 - - - +
358A GLU 3.2 2.8 + - - -
359A GLU* 3.3 18.2 + - + +
360A LEU* 3.0 21.2 + - - +
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Residues in contact with PRO 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A HIS* 3.8 15.2 - - + -
341A CYS* 4.2 8.7 - - + +
344A MET* 3.7 42.8 - - + +
345A ARG 4.2 4.0 - - - +
346A ASP* 3.2 10.5 - - - +
349A GLN* 3.9 18.4 - - + +
355A SER* 3.3 17.9 - - - +
356A ALA* 1.4 89.2 - - - +
358A GLU* 1.3 63.7 + - - +
360A LEU* 3.7 3.7 - - + +
361A VAL* 2.9 30.4 + - - +
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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
----------------------------------------------------------
344A MET 3.4 20.0 - - - +
345A ARG* 3.2 28.4 + - - +
346A ASP* 2.8 40.2 + - - +
347A SER 4.7 0.3 + - - -
357A PRO* 1.3 76.7 - - - +
359A GLU* 1.3 68.7 + - - +
361A VAL* 3.4 5.6 + - - +
362A GLN* 3.0 39.0 + - - +
394A ARG* 2.8 33.8 + - - +
395A ASN* 5.5 2.4 - - - +
482A GLU* 4.7 4.3 - - - +
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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
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301A TYR* 3.6 23.5 + - + +
346A ASP* 2.5 32.7 - - - +
356A ALA* 3.3 13.7 + - + +
358A GLU* 1.3 82.0 - - - +
360A LEU* 1.3 60.6 + - - +
362A GLN* 3.3 15.3 + - - +
363A GLN* 2.9 29.6 + - - +
477A PRO* 6.0 0.3 - - - +
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Residues in contact with LEU 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 SER 6.0 0.2 - - - +
296A GLY* 4.1 1.8 - - - -
297A ILE 3.7 39.9 - - - +
298A HIS* 3.8 11.2 - - + +
301A TYR* 3.8 26.1 - - + -
309A GLU* 3.9 2.0 - - - +
323A TYR* 3.6 39.0 - - + +
339A PHE* 3.7 18.2 - - + -
341A CYS* 5.0 4.3 - - - -
356A ALA 3.0 17.1 + - - +
357A PRO* 3.7 3.6 - - + +
359A GLU* 1.3 74.0 - - - +
361A VAL* 1.3 65.7 + - - +
363A GLN* 3.1 3.4 + - - +
364A VAL* 2.9 32.7 + - + +
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 3.9 11.7 - - + -
340A THR 3.4 24.9 - - - +
341A CYS* 3.7 22.0 - - + +
342A ALA 4.5 0.2 - - - +
357A PRO 2.9 21.7 + - - +
358A GLU* 3.6 5.8 - - - +
360A LEU* 1.3 75.6 - - + +
362A GLN* 1.3 64.1 + - - +
364A VAL 3.3 0.2 + - - -
365A LEU* 2.9 46.4 + - + +
377A CYS* 5.1 4.7 - - - -
395A ASN* 3.9 32.3 - - + +
480A PHE* 4.9 0.2 - - + -
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Residues in contact with GLN 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* 3.0 30.0 + - - +
359A GLU* 3.7 13.8 + - - +
360A LEU 3.3 0.2 - - - -
361A VAL* 1.3 75.2 - - - +
363A GLN* 1.3 62.0 + - - +
365A LEU* 4.2 0.3 - - - +
366A SER* 2.8 31.8 + - - -
394A ARG* 3.9 21.8 - - - +
395A ASN* 5.1 1.3 - - - +
477A PRO* 4.1 22.8 - - + +
478A PHE 4.8 0.9 - - - +
480A PHE* 3.6 57.8 + - + +
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Residues in contact with GLN 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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301A TYR* 2.7 28.5 + - - +
316A ASN* 2.8 39.1 + - - -
321A ASP* 2.9 34.2 + - - +
323A TYR* 3.6 14.1 - - + -
359A GLU 2.9 18.3 + - - +
360A LEU 3.1 5.1 + - - +
362A GLN* 1.3 78.2 - - - +
364A VAL* 1.3 56.5 + - + +
366A SER* 3.9 3.5 - - - -
367A ALA* 2.9 27.9 + - - +
474A LYS* 3.9 20.7 + - - +
477A PRO* 4.7 5.6 - - + +
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Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ILE* 4.7 6.1 - - + -
323A TYR* 3.7 34.1 - - + -
337A ILE* 4.0 26.3 - - + +
339A PHE* 3.7 50.9 - - + -
360A LEU* 2.9 22.3 + - + +
361A VAL 4.1 0.2 - - - +
363A GLN* 1.3 72.1 - - - +
365A LEU* 1.3 69.7 + - + +
367A ALA* 3.3 6.7 + - - +
368A GLY* 3.0 21.1 + - - -
375A VAL* 5.0 0.7 - - + +
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Residues in contact with LEU 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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339A PHE* 4.5 17.3 - - + -
361A VAL* 2.9 42.6 + - + +
362A GLN 4.2 1.8 - - - +
364A VAL* 1.3 76.5 - - - +
366A SER* 1.3 57.9 + - - +
368A GLY* 3.3 1.4 + - - -
369A TRP* 2.9 66.3 + - + -
375A VAL* 3.7 29.2 - - + +
377A CYS* 4.7 4.5 - - - -
395A ASN* 3.9 19.1 - - + +
411A LEU* 3.9 13.5 - - + -
480A PHE* 3.9 11.0 - - + -
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Residues in contact with SER 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLN 2.8 23.3 + - - -
363A GLN* 3.9 3.4 - - - -
365A LEU* 1.3 76.5 - - - +
367A ALA* 1.3 58.5 + - - +
369A TRP* 3.4 1.2 + - - -
370A ARG* 2.9 50.8 + - - +
477A PRO* 3.4 6.7 - - - +
478A PHE* 3.1 45.1 + - - +
480A PHE* 4.4 5.0 - - - -
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Residues in contact with ALA 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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321A ASP* 4.5 5.6 - - - +
323A TYR* 4.1 8.1 - - + +
324A ARG* 3.7 41.2 - - + +
327A ALA* 4.1 2.2 - - + -
337A ILE* 5.8 0.7 - - + -
363A GLN 2.9 17.9 + - - +
364A VAL* 3.3 7.4 + - - +
366A SER* 1.3 76.2 - - - +
368A GLY* 1.3 62.8 + - - +
370A ARG* 3.3 5.3 + - - +
371A GLU* 3.2 27.7 + - - +
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Residues in contact with GLY 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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327A ALA* 4.1 6.4 - - - +
337A ILE* 4.1 14.3 - - - +
364A VAL 3.0 14.6 + - - -
365A LEU 3.8 2.5 - - - -
367A ALA* 1.3 76.0 - - - +
369A TRP* 1.3 62.7 + - - +
371A GLU 3.1 7.3 + - - -
373A LEU* 2.9 32.9 + - - +
375A VAL* 3.9 14.4 - - - -
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Residues in contact with TRP 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 LEU* 2.9 53.9 + - + +
366A SER 3.9 4.0 - - - +
368A GLY* 1.3 76.4 - - - +
370A ARG* 1.3 61.1 + - - +
372A GLY* 3.0 14.3 + - - -
373A LEU 3.6 18.5 + - - -
375A VAL* 3.7 18.0 - - + +
395A ASN 4.7 0.7 - - - -
398A PRO* 3.7 31.2 - - + -
409A HIS* 3.6 50.9 + + + +
410A LYS 3.5 33.4 + - - +
411A LEU* 4.1 5.8 - - + -
478A PHE* 4.1 12.8 - + + -
480A PHE* 4.2 9.6 - + - -
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Residues in contact with ARG 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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324A ARG* 4.1 25.5 + - - +
366A SER* 2.9 37.5 + - - +
367A ALA* 3.9 5.6 - - - +
369A TRP* 1.3 76.1 - - - +
371A GLU* 1.3 63.6 + - - +
372A GLY 3.3 0.6 + - - -
475A LEU* 3.7 41.4 + - - +
476A GLN 2.9 31.1 + - - -
477A PRO 4.4 0.8 + - - -
478A PHE* 3.7 41.6 - - + +
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Residues in contact with GLU 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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324A ARG* 2.8 36.6 + - + -
327A ALA* 3.7 30.1 - - + +
328A ARG* 2.9 50.7 + - - +
331A LYS* 3.0 43.4 + - + +
367A ALA 3.2 15.8 + - - +
368A GLY 3.1 5.3 + - - +
370A ARG* 1.3 77.5 - - - +
372A GLY* 1.3 61.2 + - - +
373A LEU* 3.4 7.9 + - + +
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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