Contacts of the helix formed by residues 460 - 480 (chain B) in PDB entry 6X34
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 GLN 460 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B GLU 5.0 2.6 + - - +
459B LEU* 1.3 94.1 - - - +
461B HIS* 1.3 61.5 + - - +
462B GLU* 3.5 2.2 - - + +
463B GLU* 4.1 15.4 - - + +
464B LYS* 2.8 27.5 + - - +
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Residues in contact with HIS 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B LEU 3.8 0.6 + - - -
460B GLN* 1.3 74.6 - - - +
462B GLU* 1.3 65.8 + - + +
464B LYS* 3.7 4.9 - - - +
465B GLN* 2.9 63.3 + - + +
3702B SER 5.3 1.3 - - - -
3703B ARG* 3.4 70.3 + - + +
3706B LEU* 4.5 5.9 + - + -
3707B THR* 5.5 2.9 - - + -
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Residues in contact with GLU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B GLN* 3.5 2.3 - - + +
461B HIS* 1.3 85.8 - - + +
463B GLU* 1.3 58.3 + - - +
465B GLN* 3.3 7.5 + - - +
466B SER* 2.9 30.2 + - - -
3702B SER* 6.1 1.4 - - - -
3706B LEU* 5.3 15.8 - - + +
3776B GLN* 4.1 19.3 + - - -
3814B TYR* 5.1 5.9 + - - -
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Residues in contact with GLU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B LEU* 3.7 28.3 - - + -
460B GLN* 3.5 15.4 + - + +
461B HIS 3.3 0.6 - - - -
462B GLU* 1.3 79.0 - - - +
464B LYS* 1.3 57.2 + - - +
466B SER* 2.7 21.0 + - - -
467B LYS* 2.9 26.8 + - - +
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Residues in contact with LYS 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B PRO* 4.5 6.6 - - + +
456B SER 4.9 6.5 - - - +
459B LEU* 4.0 18.5 - - + +
460B GLN 2.8 23.9 + - - +
461B HIS* 3.7 5.2 - - - +
463B GLU* 1.3 74.1 - - - +
465B GLN* 1.3 59.9 + - + +
467B LYS* 3.3 5.0 + - - +
468B LEU* 2.9 39.0 + - + +
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Residues in contact with GLN 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B HIS* 2.9 48.4 + - + +
462B GLU* 3.7 6.5 - - - +
464B LYS* 1.3 78.1 - - + +
466B SER* 1.3 57.2 + - - +
468B LEU* 3.3 18.7 + - - +
469B ARG* 2.9 29.2 + - - +
3706B LEU* 3.5 26.3 + - + +
3707B THR* 3.1 27.0 + - - +
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Residues in contact with SER 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B GLU 2.9 16.4 + - - -
463B GLU* 2.7 25.6 + - - -
465B GLN* 1.3 74.9 - - - +
467B LYS* 1.3 63.4 + - - +
469B ARG* 3.3 6.9 + - - +
470B SER* 2.9 28.9 + - - -
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Residues in contact with LYS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B PRO* 3.9 23.0 - - + +
459B LEU* 4.3 17.8 - - + +
463B GLU* 2.9 25.8 + - - +
464B LYS 3.7 4.0 - - - +
466B SER* 1.3 84.2 + - - +
468B LEU* 1.3 57.5 + - - +
470B SER* 3.3 8.9 + - - -
471B LEU* 2.9 29.3 + - - +
474B ARG* 4.2 8.2 + - - +
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Residues in contact with LEU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B PRO* 6.2 0.2 - - + -
455B PRO* 3.8 27.8 - - + -
464B LYS* 2.9 26.8 + - + +
465B GLN* 3.7 22.4 - - - +
466B SER 3.3 0.2 - - - -
467B LYS* 1.3 75.5 - - - +
469B ARG* 1.3 58.9 + - - +
471B LEU* 3.3 7.2 + - + +
472B ARG* 2.9 58.7 + - + +
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Residues in contact with ARG 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B GLN 2.9 16.9 + - - +
466B SER* 3.7 7.9 - - - +
467B LYS 3.3 0.2 - - - -
468B LEU* 1.3 77.9 - - - +
470B SER* 1.3 57.0 + - - +
472B ARG* 3.3 6.4 + - - +
473B ASN* 2.9 40.8 + - - +
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Residues in contact with SER 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B SER 2.9 17.4 + - - -
467B LYS* 3.7 11.1 - - - +
469B ARG* 1.3 75.7 - - - +
471B LEU* 1.3 58.7 + - - +
473B ASN* 3.3 8.3 + - - +
474B ARG* 2.9 51.7 + - - +
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Residues in contact with LEU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B PHE* 4.4 27.1 - - + -
453B GLU 4.7 4.3 - - - +
454B PRO* 4.6 23.3 - - + -
455B PRO* 4.7 2.0 - - + -
467B LYS 2.9 17.0 + - - +
468B LEU* 3.6 14.1 - - + +
470B SER* 1.3 77.9 + - - +
472B ARG* 1.3 78.7 + - - +
474B ARG* 3.3 21.0 + - - +
475B GLN* 2.9 58.1 + - + +
531B ARG 5.5 0.7 - - - +
532B GLY* 5.7 0.7 - - - -
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Residues in contact with ARG 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B LEU* 2.9 43.1 + - + +
469B ARG* 3.7 6.7 - - - +
471B LEU* 1.3 106.4 - - - +
473B ASN* 1.3 60.4 + - - +
475B GLN* 3.3 10.8 + - - +
476B SER* 2.9 29.6 + - - -
532B GLY* 2.8 43.3 + - - -
533B ASN* 4.7 7.0 + - - +
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Residues in contact with ASN 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B ARG* 2.9 23.7 + - - +
470B SER* 3.7 8.0 - - - +
471B LEU 3.3 0.2 - - - -
472B ARG* 1.3 80.3 - - - +
474B ARG* 1.3 58.5 + - + +
476B SER* 2.6 21.0 + - - -
477B LEU* 2.9 29.9 + - + +
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Residues in contact with ARG 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ALA* 5.9 7.0 - - + -
451B TYR* 3.3 63.5 + - + +
452B PHE* 3.6 19.1 - - + -
453B GLU 4.9 7.1 + - - -
467B LYS* 4.2 9.7 + - - +
470B SER* 2.9 32.6 + - - +
471B LEU* 3.5 38.3 - - - +
473B ASN* 1.3 76.1 - - + +
475B GLN* 1.3 58.1 + - - +
477B LEU* 3.4 6.3 + - - +
478B PHE* 2.9 28.8 + - - +
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Residues in contact with GLN 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B PHE* 5.0 3.3 - - + +
471B LEU* 2.9 47.8 + - + +
472B ARG* 3.7 12.2 - - - +
474B ARG* 1.3 76.7 - - - +
476B SER* 1.3 58.2 + - - +
478B PHE* 3.1 8.9 + - - +
479B GLN* 2.9 28.8 + - - +
528B SER 3.9 10.7 + - - -
529B LEU* 4.1 18.5 + - + +
531B ARG 2.7 25.5 + - - -
532B GLY* 3.5 4.6 - - - -
533B ASN* 3.1 41.9 + - + +
536B ASN* 4.7 5.2 + - - +
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Residues in contact with SER 476 (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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255B HIS* 6.0 0.2 - - - -
472B ARG 2.9 14.8 + - - -
473B ASN* 2.6 27.2 + - - -
475B GLN* 1.3 75.8 - - - +
477B LEU* 1.3 63.9 + - - +
479B GLN* 3.3 7.8 + - - +
480B GLU* 3.3 21.8 + - - +
533B ASN* 4.0 9.6 - - - +
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Residues in contact with LEU 477 (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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221B ARG* 6.0 3.4 - - - +
254B THR* 4.1 20.9 - - - +
255B HIS* 5.1 0.9 - - - +
256B ALA* 4.3 32.1 - - + +
394B GLN* 6.0 0.9 - - - +
397B GLU* 4.8 19.5 - - + +
400B ALA* 4.7 21.3 - - + -
404B ILE* 4.8 11.0 - - + +
473B ASN* 2.9 36.5 + - + +
474B ARG* 3.9 6.1 - - - +
476B SER* 1.3 79.7 + - - +
478B PHE* 1.3 61.3 + - - +
480B GLU* 3.6 17.6 + - - +
481B GLU* 4.5 0.3 + - - +
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Residues in contact with PHE 478 (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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403B MET* 6.0 2.9 - - + -
404B ILE* 4.4 19.5 - - + -
407B THR* 5.0 5.8 - - + -
448B LEU* 6.2 2.9 - - + -
452B PHE* 3.5 35.7 - + + -
474B ARG 2.9 15.5 + - - +
475B GLN* 3.1 11.2 + - - +
477B LEU* 1.3 77.8 - - - +
479B GLN* 1.3 61.7 + - - +
480B GLU 3.4 0.5 + - - -
481B GLU* 3.8 7.3 + - - +
483B MET* 3.5 54.4 - - + +
484B LEU* 4.3 7.2 - - + +
525B ILE* 5.5 8.5 - - + -
529B LEU* 3.5 34.3 - - + -
536B ASN* 6.1 1.8 - - - +
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Residues in contact with GLN 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B GLN 2.9 15.2 + - - +
476B SER* 3.3 7.5 + - - +
478B PHE* 1.3 72.3 - - - +
480B GLU* 1.3 61.5 + - - +
481B GLU 3.0 11.4 + - - -
482B GLY* 3.5 10.4 + - - -
484B LEU* 3.6 23.9 - - + +
533B ASN* 5.4 0.7 - - - +
535B ALA* 5.3 8.0 - - + +
536B ASN* 3.4 26.2 - - - +
539B LEU* 3.6 23.9 - - + +
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Residues in contact with GLU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B HIS* 3.7 31.5 - - + +
256B ALA* 4.2 12.8 + - + +
257B ARG* 5.4 4.3 + - - +
476B SER 3.3 14.6 + - - +
477B LEU* 3.6 8.5 + - - +
478B PHE 3.3 2.2 - - - -
479B GLN* 1.3 79.3 - - - +
481B GLU* 1.3 57.0 + - - +
482B GLY 3.8 0.7 - - - -
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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
------------------------------------------------------------
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