Contacts of the helix formed by residues 460 - 480 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D GLU 5.0 2.4 + - - +
459D LEU* 1.3 94.0 - - - +
461D HIS* 1.3 61.2 + - - +
462D GLU* 4.5 2.5 - - + +
463D GLU* 3.9 15.6 - - + +
464D LYS* 2.8 27.7 + - - +
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Residues in contact with HIS 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D LEU 3.8 1.0 + - - -
460D GLN* 1.3 73.6 - - - +
462D GLU* 1.3 66.7 + - + +
464D LYS* 3.7 4.8 - - - +
465D GLN* 2.9 62.9 + - + +
3702D SER 5.3 2.0 - - - -
3703D ARG* 3.4 69.0 + - + +
3706D LEU* 4.5 6.1 + - + -
3707D THR* 5.9 2.2 - - + -
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Residues in contact with GLU 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D GLN* 4.5 2.3 - - + +
461D HIS* 1.3 85.4 - - + +
463D GLU* 1.3 58.0 + - - +
465D GLN* 3.3 6.9 + - - +
466D SER* 2.9 30.4 + - - -
3702D SER* 6.1 1.6 - - - -
3706D LEU* 5.3 15.7 - - + +
3776D GLN* 4.1 18.5 + - - +
3814D TYR* 5.1 5.8 + - - -
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Residues in contact with GLU 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D LEU* 3.7 27.8 - - + -
460D GLN* 3.5 16.5 + - + +
461D HIS 3.3 0.4 - - - -
462D GLU* 1.3 80.1 - - - +
464D LYS* 1.3 56.8 + - - +
466D SER* 2.7 20.7 + - - -
467D LYS* 2.9 27.2 + - - +
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Residues in contact with LYS 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D PRO* 4.5 6.6 - - + +
456D SER 4.9 6.3 - - - +
459D LEU* 4.0 20.7 - - + +
460D GLN 2.8 23.2 + - - +
461D HIS* 3.7 5.4 - - - +
463D GLU* 1.3 72.5 - - - +
465D GLN* 1.3 59.4 + - + +
467D LYS* 3.3 5.3 + - - +
468D LEU* 2.9 39.1 + - + +
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Residues in contact with GLN 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D HIS* 2.9 48.9 + - + +
462D GLU* 3.7 6.5 - - - +
464D LYS* 1.3 78.8 - - + +
466D SER* 1.3 57.9 + - - +
468D LEU* 3.3 18.8 + - - +
469D ARG* 2.9 28.6 + - - +
3706D LEU* 3.5 27.8 + - + +
3707D THR* 3.1 26.2 + - - +
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Residues in contact with SER 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462D GLU 2.9 15.1 + - - -
463D GLU* 2.7 26.3 + - - -
465D GLN* 1.3 74.1 - - - +
467D LYS* 1.3 62.6 + - - +
469D ARG* 3.3 6.7 + - - +
470D SER* 2.9 29.3 + - - -
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Residues in contact with LYS 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D PRO* 3.9 22.2 - - + +
459D LEU* 4.3 17.6 - - + +
463D GLU* 2.9 25.9 + - - +
464D LYS 3.7 4.7 - - - +
465D GLN 3.3 0.2 - - - -
466D SER* 1.3 82.8 + - - +
468D LEU* 1.3 57.6 + - - +
470D SER* 3.3 9.3 + - - +
471D LEU* 2.9 28.5 + - - +
474D ARG* 4.2 8.8 + - - +
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Residues in contact with LEU 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D PRO* 3.8 28.3 - - + -
464D LYS* 2.9 26.4 + - + +
465D GLN* 3.7 21.5 - - - +
467D LYS* 1.3 76.0 - - - +
469D ARG* 1.3 57.8 + - - +
471D LEU* 3.3 7.7 + - + +
472D ARG* 2.9 60.3 + - + +
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Residues in contact with ARG 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D GLN 2.9 16.5 + - - +
466D SER* 3.7 7.4 - - - +
468D LEU* 1.3 77.3 - - - +
470D SER* 1.3 56.6 + - - +
472D ARG* 3.3 6.1 + - - +
473D ASN* 2.9 40.6 + - - +
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Residues in contact with SER 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D SER 2.9 17.2 + - - -
467D LYS* 3.7 11.7 - - - -
469D ARG* 1.3 76.0 - - - +
471D LEU* 1.3 57.8 + - - +
473D ASN* 3.3 8.8 + - - +
474D ARG* 2.9 51.0 + - - +
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Residues in contact with LEU 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452D PHE* 4.4 27.4 - - + -
453D GLU 4.7 4.5 - - - +
454D PRO* 4.6 24.5 - - + -
455D PRO* 4.7 1.8 - - + -
467D LYS 2.9 18.7 + - - +
468D LEU* 3.6 13.7 - - + +
469D ARG 3.3 0.2 - - - -
470D SER* 1.3 76.4 - - - +
472D ARG* 1.3 79.3 + - - +
474D ARG* 3.3 21.9 + - - +
475D GLN* 2.9 57.2 + - + +
531D ARG 5.5 1.1 - - - +
532D GLY* 5.7 0.2 - - - -
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Residues in contact with ARG 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D LEU* 2.9 43.7 + - + +
469D ARG* 3.3 6.9 + - - +
471D LEU* 1.3 107.1 - - - +
473D ASN* 1.3 61.8 + - - +
475D GLN* 3.3 11.4 + - - +
476D SER* 2.9 29.2 + - - -
532D GLY* 2.8 41.9 + - - -
533D ASN* 4.7 6.6 + - - +
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Residues in contact with ASN 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D ARG* 2.9 23.6 + - - +
470D SER* 3.7 7.4 - - - +
472D ARG* 1.3 79.3 - - - +
474D ARG* 1.3 57.7 + - + +
476D SER* 2.6 21.6 + - - -
477D LEU* 2.9 28.5 + - + +
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Residues in contact with ARG 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400D ALA* 5.9 6.7 - - + -
451D TYR* 3.3 63.1 + - + +
452D PHE* 3.6 20.1 - - + -
453D GLU 4.9 7.5 + - - -
467D LYS* 4.2 9.7 + - - +
470D SER* 2.9 33.5 + - - +
471D LEU* 3.5 36.9 - - - +
473D ASN* 1.3 75.9 - - + +
475D GLN* 1.3 57.8 + - - +
477D LEU* 3.4 7.0 + - - +
478D PHE* 2.9 28.1 + - - +
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Residues in contact with GLN 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452D PHE* 5.0 3.5 - - + +
471D LEU* 2.9 46.1 + - + +
472D ARG* 3.7 12.2 - - - +
473D ASN 3.3 0.2 - - - -
474D ARG* 1.3 76.3 - - - +
476D SER* 1.3 58.0 + - - +
478D PHE* 3.1 9.3 + - - +
479D GLN* 2.9 28.8 + - - +
528D SER 3.9 9.5 + - - -
529D LEU* 4.1 19.0 + - + +
531D ARG 2.7 26.5 + - - -
532D GLY* 3.5 4.6 - - - -
533D ASN* 3.1 42.0 + - + +
536D ASN* 4.7 5.3 + - - +
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Residues in contact with SER 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D ARG 2.9 14.9 + - - -
473D ASN* 2.6 27.2 + - - -
475D GLN* 1.3 76.7 - - - +
477D LEU* 1.3 64.0 + - - +
479D GLN* 3.3 7.5 + - - +
480D GLU* 3.3 22.0 + - - +
533D ASN* 4.0 9.1 - - - +
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Residues in contact with LEU 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ARG* 6.0 3.4 - - - +
254D THR 4.1 20.2 - - - +
255D HIS* 5.1 0.9 - - - +
256D ALA* 4.3 32.2 - - + +
394D GLN* 6.0 0.9 - - - +
397D GLU* 4.8 19.7 - - + +
400D ALA* 4.7 22.2 - - + -
404D ILE* 4.8 11.5 - - + +
473D ASN* 2.9 35.5 + - + +
474D ARG* 3.9 5.4 - - - +
476D SER* 1.3 81.2 + - - +
478D PHE* 1.3 61.9 + - - +
480D GLU* 3.6 17.1 + - - +
481D GLU* 4.5 0.7 + - - +
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Residues in contact with PHE 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D MET* 6.0 2.9 - - + -
404D ILE* 4.4 20.6 - - + -
407D THR* 5.0 5.8 - - + -
448D LEU* 6.2 2.5 - - + -
452D PHE* 3.5 36.3 - + - -
474D ARG 2.9 17.0 + - - +
475D GLN* 3.1 10.5 + - - +
477D LEU* 1.3 78.4 - - - +
479D GLN* 1.3 61.8 + - - +
480D GLU 3.4 0.3 + - - -
481D GLU* 3.8 7.4 + - - +
483D MET* 3.5 55.0 - - + +
484D LEU* 4.3 6.5 - - + +
525D ILE* 5.5 8.7 - - + -
529D LEU* 3.5 35.2 - - + -
536D ASN* 6.1 2.2 - - - +
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Residues in contact with GLN 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475D GLN 2.9 15.0 + - - +
476D SER* 3.3 8.4 + - - +
478D PHE* 1.3 73.4 - - - +
480D GLU* 1.3 61.6 + - - +
481D GLU 3.0 11.2 + - - -
482D GLY* 3.5 9.4 + - - -
484D LEU* 3.6 22.4 - - + +
533D ASN* 5.4 0.9 - - - +
535D ALA* 5.3 8.7 - - + +
536D ASN* 3.4 24.9 - - - +
539D LEU* 3.6 25.2 - - + +
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Residues in contact with GLU 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D HIS* 3.7 32.1 - - + +
256D ALA* 4.2 11.8 + - - +
257D ARG* 5.4 4.9 + - - +
476D SER 3.3 15.3 + - - +
477D LEU 3.6 9.2 + - - +
478D PHE 3.3 1.6 - - - -
479D GLN* 1.3 79.7 - - - +
481D GLU* 1.3 57.0 + - - +
482D GLY 3.8 0.9 - - - -
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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
------------------------------------------------------------
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