Contacts of the helix formed by residues 468 - 485 (chain D) in PDB entry 3G4K
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 468 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D LEU 3.5 0.2 - - - -
467D ASP* 1.3 92.8 - - + +
469D TYR* 1.3 68.0 + - - +
470D SER* 3.2 14.5 + - - +
471D ASP* 2.9 51.4 + - - +
472D ARG* 3.0 27.6 + - - +
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Residues in contact with TYR 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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355D GLU* 5.8 2.9 - - - -
425D SER* 5.9 1.1 - - - -
428D LYS* 3.7 25.5 - - + +
429D MET* 3.5 38.4 - - + +
432D ASP* 2.5 30.6 + - - -
468D ASN* 1.3 72.2 - - - +
470D SER* 1.3 58.3 - - - +
472D ARG* 3.6 11.3 - - + +
473D ILE* 2.7 64.2 + - + +
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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
----------------------------------------------------------
468D ASN* 3.2 11.6 - - - +
469D TYR* 1.3 82.3 - - - +
471D ASP* 1.3 60.7 + - - +
473D ILE* 3.5 9.1 - - - +
474D GLN* 3.1 40.2 + - - +
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Residues in contact with ASP 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452D MET* 3.5 27.6 - - + +
465D LEU 5.3 1.0 - - - +
466D LEU* 4.0 14.7 - - + +
467D ASP* 4.5 3.3 + - - +
468D ASN* 2.9 38.1 + - - +
470D SER* 1.3 75.5 + - - +
472D ARG* 1.3 64.6 + - - +
474D GLN* 3.4 11.5 + - - +
475D VAL* 3.1 29.7 + - - +
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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
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350D VAL* 2.8 29.6 + - - +
351D PHE* 3.9 10.8 - - + +
352D THR* 4.1 10.5 - - - +
355D GLU* 2.8 44.6 + - - +
466D LEU* 3.1 48.0 + - + +
467D ASP 5.0 2.0 - - - -
468D ASN 3.0 24.0 + - - +
469D TYR* 3.6 10.5 - - + +
471D ASP* 1.3 77.2 - - - +
473D ILE* 1.3 60.5 + - - +
475D VAL* 3.3 5.0 + - - +
476D LEU* 3.1 30.1 + - + +
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Residues in contact with ILE 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D MET* 3.8 33.2 - - + +
432D ASP* 3.6 16.6 - - + +
433D ILE* 4.0 14.6 - - + -
469D TYR* 2.7 63.5 + - + +
470D SER* 3.5 10.1 - - - +
472D ARG* 1.3 70.8 - - - +
474D GLN* 1.3 64.6 + - + +
476D LEU* 3.3 8.6 + - + +
477D GLN* 2.8 47.3 + - - +
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Residues in contact with GLN 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D LEU* 5.3 2.7 - - + -
448D ASP* 3.2 48.7 + - + +
449D LEU* 5.8 1.1 - - + +
452D MET* 4.1 12.9 - - + +
470D SER* 3.1 22.4 + - - +
471D ASP* 3.6 22.6 + - - +
473D ILE* 1.3 83.6 - - + +
475D VAL* 1.3 57.4 + - + +
477D GLN* 3.4 14.8 + - - +
478D ASN* 2.9 43.0 + - - +
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Residues in contact with VAL 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D LEU* 4.7 6.1 - - + -
351D PHE* 3.6 23.3 - - + -
449D LEU* 5.4 2.7 - - + -
452D MET* 3.4 28.3 - - - -
464D LEU* 4.1 5.2 - - + -
466D LEU* 3.8 17.7 - - + -
471D ASP 3.1 15.4 + - - +
472D ARG 3.6 7.2 - - - +
474D GLN* 1.3 75.1 - - - +
476D LEU* 1.3 57.7 + - - +
478D ASN* 3.4 3.7 + - - +
479D MET* 2.8 30.0 + - + +
550D TRP* 3.8 22.2 - - + -
553D LEU* 4.3 8.7 - - + -
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Residues in contact with LEU 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D LEU* 4.3 8.3 - - + -
351D PHE* 3.7 36.6 - - + -
355D GLU* 4.2 34.8 - - + +
358D ALA* 5.5 0.2 - - + -
359D ALA* 4.2 18.6 - - + -
429D MET* 4.6 4.5 - - - -
433D ILE* 4.0 21.5 - - + -
472D ARG 3.1 19.4 + - - +
473D ILE* 3.8 18.8 - - + +
475D VAL* 1.3 74.1 - - - +
477D GLN* 1.3 63.5 - - - +
479D MET* 3.5 7.9 - - + +
480D VAL* 3.0 29.8 + - - +
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Residues in contact with GLN 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D ASP* 2.9 42.7 + - - +
433D ILE* 4.0 13.6 - - - +
436D ALA* 3.6 23.7 - - + +
437D THR* 5.8 0.7 - - - +
445D LEU* 3.8 18.1 - - + +
473D ILE* 2.8 35.2 + - + +
474D GLN* 3.4 19.4 + - - +
476D LEU* 1.3 72.5 - - - +
478D ASN* 1.3 59.2 + - - +
480D VAL* 3.9 1.6 - - - +
481D HIS* 2.9 30.5 + - - +
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Residues in contact with ASN 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D LEU* 3.6 49.0 + - - +
449D LEU* 3.9 43.0 - - + +
474D GLN* 2.9 32.8 + - - +
475D VAL 3.9 2.9 - - - +
477D GLN* 1.3 73.7 - - - +
479D MET* 1.3 56.2 + - - +
481D HIS* 3.6 4.7 - - - +
482D CYS* 2.8 39.2 + - - -
546D LEU* 4.0 11.7 - - + +
550D TRP* 4.3 5.6 - - + -
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Residues in contact with MET 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D THR* 4.1 12.3 - - + +
341D LEU* 3.5 27.8 - - + +
342D LEU* 3.6 44.0 - - + -
347D LEU* 3.4 33.4 - - + -
351D PHE* 4.2 9.9 - - + -
359D ALA* 5.1 1.6 - - - -
475D VAL* 2.8 17.5 + - + +
476D LEU* 3.5 12.3 - - + +
477D GLN 3.3 0.2 - - - -
478D ASN* 1.3 75.3 - - - +
480D VAL* 1.3 58.8 + - + +
482D CYS* 3.2 7.3 + - - +
483D ALA* 2.9 24.3 + - - +
550D TRP* 3.6 19.7 - - + -
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Residues in contact with VAL 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D VAL* 4.3 8.9 - - + +
338D THR* 3.9 15.9 - - + +
359D ALA* 3.9 16.2 - - + +
362D ALA 5.2 0.9 - - - -
363D SER* 3.5 31.2 - - - +
366D HIS* 5.4 2.5 - - + -
433D ILE* 3.6 31.9 - - + -
437D THR* 4.2 15.7 - - + -
476D LEU 3.0 17.8 + - - +
477D GLN 4.1 1.1 - - - +
479D MET* 1.3 75.6 - - + +
481D HIS* 1.3 57.2 + - - +
483D ALA* 3.2 2.4 + - - +
484D ASP* 2.8 27.5 + - + +
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Residues in contact with HIS 481 (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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436D ALA 4.3 12.0 + - - +
437D THR* 4.6 14.5 + - + +
439D MET* 3.7 18.8 - - - -
442D HIS* 2.7 36.4 + - + +
445D LEU* 4.0 24.2 - - + -
477D GLN 2.9 19.3 + - - +
478D ASN* 3.6 5.4 - - - +
480D VAL* 1.3 76.2 - - - +
482D CYS* 1.3 56.7 + - - +
484D ASP* 3.3 9.5 + - - +
485D LEU* 2.9 57.0 + - + +
546D LEU* 3.5 26.0 - - + -
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Residues in contact with CYS 482 (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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341D LEU* 4.1 4.5 - - + -
478D ASN 2.8 27.6 + - - +
479D MET* 3.5 6.5 - - - +
481D HIS* 1.3 71.8 - - - +
483D ALA* 1.3 57.2 + - - +
485D LEU 3.2 3.8 - - - -
486D SER* 3.0 28.4 + - - -
546D LEU* 3.6 35.4 - - - -
547D TRP* 3.3 28.1 - - + +
550D TRP* 3.8 33.4 - - - -
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Residues in contact with ALA 483 (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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333D ASP* 5.0 1.0 - - - +
334D VAL* 3.7 24.6 - - + +
337D SER* 3.8 14.8 - - - -
338D THR* 3.4 28.9 - - - +
341D LEU* 4.1 4.0 - - + +
479D MET 2.9 11.2 + - - +
480D VAL 3.2 6.9 + - - +
482D CYS* 1.3 76.2 - - - +
484D ASP* 1.3 62.1 + - - +
486D SER* 2.6 28.7 + - - -
487D ASN* 5.3 0.9 + - - -
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Residues in contact with ASP 484 (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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325D TYR* 4.0 15.6 + - - -
330D HIS* 3.0 11.3 + - - -
334D VAL* 3.9 9.3 - - + +
366D HIS* 3.0 9.3 + - + +
437D THR* 4.2 23.1 - - + +
439D MET* 5.9 1.4 - - - +
480D VAL* 2.8 14.3 + - + +
481D HIS* 3.4 15.6 + - - +
483D ALA* 1.3 76.6 - - - +
485D LEU* 1.3 67.0 + - + +
486D SER 3.4 2.4 + - - -
487D ASN* 4.8 3.8 + - - +
807D ZN 2.1 35.7 - - - -
904D ROL 5.2 4.9 - - - -
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Residues in contact with LEU 485 (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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439D MET* 4.2 9.0 - - - -
481D HIS* 2.9 49.5 + - + +
482D CYS 3.2 5.4 - - - +
483D ALA 3.2 0.2 - - - -
484D ASP* 1.3 86.3 - - + +
486D SER* 1.3 57.8 + - - +
487D ASN 3.5 2.7 - - - -
488D PRO* 3.7 3.9 - - - +
538D PHE* 4.0 13.9 - - + -
542D ILE* 3.8 23.3 - - + -
543D VAL* 3.4 23.1 - - + +
546D LEU* 3.6 18.4 - - + -
547D TRP* 3.3 11.1 + - - +
904D ROL 4.0 29.2 - - + -
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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