Contacts of the helix formed by residues 422 - 440 (chain A) in PDB entry 6XYY
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 422 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A GLY* 1.3 70.5 - - - -
423A PRO* 1.3 73.2 - - + +
424A GLY 3.2 3.6 + - - +
425A TYR* 3.7 16.0 + - + +
426A GLN* 3.5 21.1 + - - +
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Residues in contact with PRO 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A SER* 4.9 9.9 - - - +
419A TRP 6.6 0.2 - - - -
420A GLU 5.3 1.1 - - - +
421A GLY 3.7 7.6 - - - +
422A ASN* 1.3 89.4 - - + +
424A GLY* 1.3 63.2 + - - +
426A GLN* 3.4 7.1 + - + +
427A ASN* 3.1 34.2 + - - +
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Residues in contact with GLY 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A THR 3.3 3.1 - - - +
387A ALA* 3.5 18.8 - - - -
388A LEU 3.1 31.5 + - - -
422A ASN* 3.2 2.8 + - - +
423A PRO* 1.3 79.4 - - - +
425A TYR* 1.3 64.8 + - - +
426A GLN 3.2 0.5 + - - -
427A ASN* 3.3 7.4 + - - +
428A GLN 3.6 4.7 + - - -
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Residues in contact with TYR 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ALA* 3.8 33.7 + - + -
386A THR 3.7 7.2 - - - -
387A ALA* 3.6 32.5 - - + -
422A ASN* 3.7 16.9 + - + +
424A GLY* 1.3 73.9 - - - +
426A GLN* 1.3 64.7 + - - +
428A GLN* 3.6 6.4 + - - +
429A GLN* 3.1 30.8 + - + +
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Residues in contact with GLN 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A SER* 3.0 23.8 + - - +
420A GLU* 3.6 19.2 - - - +
421A GLY* 4.7 4.0 - - - -
422A ASN 3.5 18.7 + - - +
423A PRO* 3.4 4.9 + - + +
424A GLY 3.1 1.0 - - - -
425A TYR* 1.3 83.2 - - - +
427A ASN* 1.3 54.8 + - - +
429A GLN* 3.1 19.8 + - - +
430A GLN* 2.7 42.1 + - - +
433A ARG* 4.2 13.7 - - - +
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Residues in contact with ASN 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 2.8 41.1 + - + +
389A PRO 4.0 11.3 - - - -
390A ARG* 4.2 10.2 + - - +
393A TYR* 3.9 26.4 - - + +
416A TYR 5.3 0.2 - - - +
417A THR* 5.6 0.2 - - - -
418A SER* 4.4 15.6 + - - -
423A PRO* 3.1 23.1 + - - +
424A GLY 3.3 2.9 + - - +
426A GLN* 1.3 76.3 - - - +
428A GLN* 1.3 62.9 + - - +
430A GLN* 3.0 6.0 + - - +
431A ILE* 2.9 29.8 + - - +
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Residues in contact with GLN 428 (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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372A LEU* 4.1 3.4 - - + +
380A PHE* 3.4 38.6 - - + +
384A ASP 4.8 0.4 + - - -
385A ALA* 3.6 10.6 - - - +
386A THR* 2.9 42.1 + - - +
388A LEU* 4.2 9.9 - - + +
424A GLY 3.6 2.0 + - - -
425A TYR* 3.6 7.9 + - - +
426A GLN 3.3 0.2 - - - -
427A ASN* 1.3 76.9 - - - +
429A GLN* 1.3 68.9 + - - +
431A ILE* 3.3 6.9 + - - +
432A GLY* 3.1 18.9 + - - -
475A TRP* 3.4 51.8 - - + +
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Residues in contact with GLN 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ASP* 4.9 7.9 + - - -
369A THR* 5.0 7.1 - - - +
425A TYR* 3.1 22.7 + - + +
426A GLN* 3.1 27.3 + - - +
428A GLN* 1.3 78.5 - - - +
430A GLN* 1.3 63.5 + - - +
432A GLY* 3.2 3.5 + - - -
433A ARG* 3.0 48.2 + - - +
475A TRP* 3.0 49.7 + - - +
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Residues in contact with GLN 430 (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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393A TYR* 4.6 2.5 - - + -
415A GLN 4.2 1.9 - - - +
416A TYR* 2.9 68.1 - - + +
417A THR 4.3 4.1 - - - +
418A SER* 3.7 16.8 - - - +
426A GLN* 2.7 26.7 + - - +
427A ASN* 3.7 6.1 - - - +
429A GLN* 1.3 70.2 - - - +
431A ILE* 1.3 65.5 + - - +
433A ARG* 3.3 35.8 + - - +
434A ALA* 2.9 20.4 + - - +
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Residues in contact with ILE 431 (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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372A LEU* 3.5 26.7 - - + -
380A PHE* 5.1 2.2 - - + -
388A LEU* 3.6 28.7 - - + -
393A TYR* 3.5 26.2 - - + +
396A ILE* 3.7 24.7 - - + -
397A MET* 3.8 16.4 - - + -
400A ILE* 3.7 19.3 - - + -
427A ASN 2.9 13.1 + - - +
428A GLN* 3.3 6.0 + - - +
430A GLN* 1.3 75.7 - - - +
432A GLY* 1.3 63.5 + - - +
434A ALA* 3.3 2.0 + - - +
435A VAL* 3.0 22.9 + - - +
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Residues in contact with GLY 432 (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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366A ASP* 6.5 0.9 - - - -
368A GLY* 3.9 12.0 + - - -
369A THR* 4.7 18.4 - - - -
372A LEU* 4.0 13.3 - - - +
428A GLN 3.1 14.4 + - - -
429A GLN* 3.2 4.5 + - - -
431A ILE* 1.3 76.3 - - - +
433A ARG* 1.3 60.6 + - - +
435A VAL* 3.2 6.8 + - - +
436A GLY* 3.0 19.9 + - - -
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Residues in contact with ARG 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ARG* 6.4 0.2 - - - +
366A ASP* 4.5 12.6 + - - +
416A TYR* 4.0 12.1 - - + -
426A GLN* 4.2 19.8 - - - +
429A GLN* 3.0 36.5 + - - +
430A GLN* 3.3 28.4 + - - +
432A GLY* 1.3 74.4 - - - +
434A ALA* 1.3 54.0 + - - +
436A GLY* 4.6 0.9 - - - +
437A ASP* 2.6 41.6 + - - -
559A ARG* 3.9 31.2 - - - +
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Residues in contact with ALA 434 (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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397A MET* 4.1 26.2 - - + -
401A PHE* 4.2 12.9 - - + -
416A TYR* 3.7 27.9 - - + -
430A GLN 2.9 13.5 + - - +
431A ILE 3.3 8.7 + - - +
433A ARG* 1.3 75.7 - - - +
435A VAL* 1.3 62.6 + - - +
437A ASP* 3.9 0.3 - - - +
438A HIS* 3.0 28.4 + - - +
563A TRP* 4.0 2.1 - - + -
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Residues in contact with VAL 435 (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 ILE* 4.5 16.2 - - + -
328A LEU* 4.1 14.8 - - + -
368A GLY* 3.7 23.3 - - - +
371A PHE* 4.6 1.1 - - + -
372A LEU* 4.6 6.7 - - + -
400A ILE* 3.8 34.5 - - + -
401A PHE* 5.2 0.4 - - - -
431A ILE* 3.0 19.8 + - + +
432A GLY 3.6 7.0 - - - +
434A ALA* 1.3 75.8 - - + +
436A GLY* 1.3 64.0 + - - +
439A PHE* 3.0 48.1 + - + +
440A PHE* 5.6 0.2 - - + -
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Residues in contact with GLY 436 (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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367A GLU* 3.9 9.9 - - - -
368A GLY* 3.6 22.4 - - - -
432A GLY 3.0 12.0 + - - -
433A ARG* 3.8 1.6 - - - -
435A VAL* 1.3 77.0 - - - +
437A ASP* 1.3 65.0 + - - +
440A PHE* 2.9 24.8 + - - +
441A THR* 3.1 14.6 + - - -
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Residues in contact with ASP 437 (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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416A TYR* 2.9 21.8 + - - +
433A ARG 2.6 25.1 + - - +
434A ALA 3.9 0.9 - - - +
436A GLY* 1.3 74.1 - - - +
438A HIS* 1.3 61.2 + - - +
441A THR* 4.4 14.0 + - - +
442A CYS* 3.0 36.2 + - - +
559A ARG* 2.7 53.7 + - - +
563A TRP* 3.6 19.2 + - + +
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Residues in contact with HIS 438 (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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270A PRO* 4.0 18.2 - - + +
401A PHE* 3.9 14.4 - + + -
434A ALA 3.0 18.1 + - - +
435A VAL 4.2 0.4 - - - +
437A ASP* 1.3 78.0 - - - +
439A PHE* 1.3 98.4 + + - +
443A PRO* 3.2 20.2 - - - +
563A TRP* 3.3 48.4 - + + -
571A ARG* 6.2 2.2 - - - -
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Residues in contact with PHE 439 (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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269A ALA* 3.6 9.5 - - - +
270A PRO* 4.2 21.1 - - + -
271A TRP* 2.9 33.8 + + + -
327A ILE* 4.4 15.9 - - + -
328A LEU* 3.4 46.0 - - + -
400A ILE* 4.3 23.3 - - + -
401A PHE* 5.0 0.9 - + - -
435A VAL* 3.0 35.6 + - + +
438A HIS* 1.3 107.3 - + - +
440A PHE* 1.3 72.0 + - + +
443A PRO* 3.8 3.6 - - - -
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Residues in contact with PHE 440 (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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238A SER* 4.2 9.6 - - - -
264A SER* 3.5 23.3 - - - +
266A THR* 5.2 0.2 + - - -
269A ALA* 5.5 0.9 - - - -
271A TRP* 3.5 31.0 - + - -
328A LEU* 3.7 26.5 - - + -
363A ASN* 3.7 4.9 - - - +
367A GLU* 3.9 38.1 - - + -
368A GLY* 5.5 0.4 - - - -
371A PHE* 3.5 38.8 - + - -
435A VAL 5.3 0.2 - - - -
436A GLY* 2.9 15.2 + - - +
438A HIS 3.6 0.8 - - - -
439A PHE* 1.3 86.5 - - + +
441A THR* 1.3 66.4 + - - +
442A CYS 3.4 1.8 - - - -
443A PRO* 3.3 4.6 - - - +
444A THR* 2.9 26.1 + - - -
480A HIS* 5.7 2.9 - - + -
601A PPI 4.3 1.3 - - + -
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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