Contacts of the helix formed by residues 482 - 498 (chain D) in PDB entry 3B60
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 SER 482 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379C GLY* 4.9 1.6 - - - -
5003C ANP 2.5 64.6 + - - -
481D LEU* 1.3 73.8 - - - +
483D GLY* 1.3 52.1 + - - +
484D GLY 2.9 5.5 + - - -
485D GLN* 2.8 33.5 + - - +
486D ARG* 2.7 32.6 + - - +
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Residues in contact with GLY 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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424C GLN* 6.3 5.2 - - - +
425C ASN* 6.3 0.4 - - - -
5003C ANP 3.7 6.7 + - - -
481D LEU 3.6 1.4 + - - -
482D SER* 1.3 70.5 + - - +
484D GLY* 1.3 56.5 + - - +
486D ARG* 3.3 19.6 - - - +
487D GLN* 2.5 39.2 + - - +
510D ALA* 4.8 6.1 - - - -
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Residues in contact with GLY 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C SER* 3.7 9.9 - - - -
5003C ANP 3.6 5.2 + - - -
482D SER* 2.9 8.1 + - - -
483D GLY* 1.3 77.2 - - - +
485D GLN* 1.3 62.6 + - - +
487D GLN* 3.1 3.5 + - - +
488D ARG* 2.8 33.8 + - - +
510D ALA* 3.4 25.3 + - - +
511D LEU* 4.1 4.5 - - - -
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Residues in contact with GLN 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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378C SER* 4.2 2.0 + - - +
379C GLY* 4.9 6.5 - - - -
5003C ANP 3.7 24.4 + - - -
462D PHE* 3.2 52.9 - - + +
481D LEU* 3.4 15.3 - - + +
482D SER* 2.8 43.7 + - - +
484D GLY* 1.3 74.0 - - - +
486D ARG* 1.3 63.7 + - - +
488D ARG* 3.3 24.2 + - - +
489D ILE* 2.9 28.1 + - - +
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Residues in contact with ARG 486 (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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425C ASN* 3.6 29.9 - - - +
425D ASN* 6.1 0.4 - - - +
426D VAL* 2.5 38.8 + - + +
428D LEU* 3.9 15.4 - - + +
477D ASN* 3.8 22.6 + - - +
478D GLY* 2.8 46.4 + - - +
481D LEU* 3.7 16.6 - - + -
482D SER 2.7 17.2 + - - +
483D GLY* 3.3 16.4 - - - +
485D GLN* 1.3 71.5 - - - +
487D GLN* 1.3 57.5 + - - +
489D ILE* 2.6 34.0 + - - +
490D ALA* 2.8 13.0 + - - +
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Residues in contact with GLN 487 (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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422D VAL* 4.8 2.0 - - + +
424D GLN 4.4 5.2 - - - +
426D VAL* 4.5 16.6 - - + +
483D GLY 2.5 19.9 + - - +
484D GLY 3.5 3.4 - - - +
486D ARG* 1.3 71.4 - - - +
488D ARG* 1.3 58.4 + - + +
490D ALA* 3.0 10.2 + - - +
491D ILE* 2.8 33.3 + - + +
506D GLU 3.2 1.4 - - - +
507D ALA* 2.5 40.1 + - - +
508D THR 3.2 6.7 + - - -
509D SER* 3.0 20.5 + - - -
510D ALA* 3.2 36.6 + - - +
511D LEU* 4.0 4.5 - - + +
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Residues in contact with ARG 488 (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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378C SER* 2.6 43.3 + - - -
457D ALA* 3.8 16.5 - - - +
458D TYR* 2.9 43.4 + - - +
459D ALA* 3.9 6.5 - - + +
461D ASP* 4.0 4.2 + - - -
462D PHE* 3.0 32.5 - - - +
484D GLY 2.8 25.2 + - - +
485D GLN* 3.4 18.6 - - - +
487D GLN* 1.3 70.7 - - - +
489D ILE* 1.3 51.1 + - - +
491D ILE* 2.9 16.9 + - - +
492D ALA* 2.5 33.4 + - - +
511D LEU* 3.9 19.6 - - + +
515D SER* 5.1 4.7 + - - -
519D ILE* 4.4 8.3 - - + -
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Residues in contact with ILE 489 (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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428D LEU* 4.6 10.1 - - + -
433D VAL* 4.5 10.3 - - + -
436D ASN* 4.4 17.9 - - + -
437D ILE* 4.0 21.1 - - + -
459D ALA* 5.2 2.7 - - + -
462D PHE* 4.1 18.2 - - + -
463D ILE* 4.4 12.3 - - + -
474D ILE* 4.5 9.6 - - + -
481D LEU* 3.8 26.9 - - + -
485D GLN 2.9 20.3 + - - +
486D ARG* 2.6 17.8 + - - +
488D ARG* 1.3 68.9 - - + +
490D ALA* 1.3 57.5 + - - +
492D ALA* 2.9 9.4 - - + +
493D ARG* 2.8 29.5 + - - +
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Residues in contact with ALA 490 (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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421D LEU 4.4 0.7 - - - +
422D VAL* 3.7 8.4 - - + +
426D VAL* 3.0 47.3 - - + -
428D LEU* 4.9 2.9 - - + +
486D ARG 2.8 13.4 + - - +
487D GLN 3.3 9.2 - - - +
489D ILE* 1.3 73.8 - - - +
491D ILE* 1.3 61.0 + - - +
493D ARG* 3.7 17.9 - - - +
494D ALA* 3.1 24.3 + - - +
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Residues in contact with ILE 491 (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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422D VAL* 3.8 26.0 - - + -
457D ALA* 4.2 16.4 - - + +
487D GLN* 2.8 15.6 + - + +
488D ARG* 3.0 17.3 - - - +
490D ALA* 1.3 76.2 - - - +
492D ALA* 1.3 69.8 + - - +
494D ALA* 3.3 1.2 + - - +
495D LEU* 2.7 36.7 + - + +
504D LEU* 4.7 6.3 - - + -
507D ALA* 3.4 33.9 - - + +
511D LEU* 5.0 0.9 - - + -
519D ILE* 4.4 31.2 - - + -
523D LEU* 5.5 3.6 - - + -
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Residues in contact with ALA 492 (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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437D ILE* 3.9 25.8 - - + -
453D ALA* 4.1 14.8 - - - +
454D ALA* 4.4 6.5 - - - -
457D ALA* 4.0 13.9 - - + -
459D ALA* 6.0 1.1 - - + -
488D ARG 2.5 16.2 + - - +
489D ILE* 2.9 17.5 - - + +
491D ILE* 1.3 69.2 - - - +
493D ARG* 1.3 57.1 + - - +
495D LEU* 2.5 29.7 + - - +
496D LEU 2.9 9.5 + - - -
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Residues in contact with ARG 493 (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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216C GLU* 4.0 24.4 + - - +
219C ILE* 5.8 2.6 - - - +
220C PHE* 5.4 6.9 - - - -
421D LEU 4.8 6.4 + - - -
422D VAL* 6.1 0.6 - - - +
423D SER* 5.5 0.8 + - - -
426D VAL* 4.0 14.3 - - - +
427D HIS 2.8 27.9 + - - -
428D LEU* 3.1 24.0 - - - +
429D PHE* 5.7 3.6 - - - -
436D ASN* 3.6 24.3 + - - +
437D ILE* 3.4 17.7 - - - +
439D TYR 5.6 0.4 - - - -
440D ALA* 3.4 17.4 - - + +
489D ILE 2.8 15.8 + - - +
490D ALA* 3.7 9.5 + - - +
492D ALA* 1.3 74.9 - - - +
494D ALA* 1.3 63.6 + - - +
495D LEU 3.1 0.2 + - - -
496D LEU* 3.2 10.2 + - - +
497D ARG* 3.0 49.2 + - - +
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Residues in contact with ALA 494 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420D ALA* 3.1 25.1 - - + +
421D LEU 3.4 31.9 - - - +
422D VAL* 3.4 14.6 - - + -
490D ALA 3.1 17.2 + - - +
491D ILE 3.7 1.1 - - - +
492D ALA 2.9 1.2 + - - -
493D ARG* 1.3 79.2 - - - +
495D LEU* 1.3 61.6 + - - +
497D ARG* 4.0 13.7 - - - +
498D ASP* 4.1 6.1 + - - -
502D LEU* 4.6 6.3 - - + +
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Residues in contact with LEU 495 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452D GLU* 5.7 1.3 - - - +
453D ALA* 4.5 9.4 - - + +
456D MET* 3.0 39.0 - - + +
457D ALA* 4.5 5.2 - - + -
491D ILE* 2.7 25.0 + - + +
492D ALA* 2.5 14.4 + - - +
494D ALA* 1.3 72.0 - - - +
496D LEU* 1.3 63.9 + - - +
498D ASP* 3.2 17.0 + - - +
502D LEU* 4.2 24.9 - - + -
504D LEU* 6.2 1.3 - - + -
519D ILE* 6.3 0.9 - - + -
522D ALA* 5.8 1.6 - - + -
523D LEU* 4.5 18.8 - - + +
526D LEU* 4.2 32.0 - - + +
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Residues in contact with LEU 496 (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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437D ILE* 3.8 23.1 - - + +
438D ALA* 4.6 2.7 - - - -
440D ALA 5.0 1.8 - - - +
445D TYR* 3.2 38.6 - - + -
449D GLN* 3.3 28.7 - - + +
450D ILE* 3.5 29.8 - - + -
452D GLU* 5.9 2.0 - - - +
453D ALA* 3.6 20.5 - - + +
492D ALA 2.9 6.7 + - - +
493D ARG 3.7 6.5 - - - +
495D LEU* 1.3 73.3 - - - +
497D ARG* 1.3 69.9 + - - +
498D ASP* 2.8 10.6 + - - +
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Residues in contact with ARG 497 (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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216C GLU* 4.8 1.4 + - - +
219C ILE* 4.0 26.0 + - - +
220C PHE* 2.9 55.4 + - - +
419D VAL 5.5 2.0 - - - +
420D ALA* 4.8 11.2 - - + +
421D LEU 4.2 6.5 + - - +
440D ALA* 3.0 46.2 - - + +
441D ARG* 4.3 8.1 - - + -
445D TYR* 3.8 16.1 + - - -
493D ARG* 3.0 44.6 + - - +
494D ALA* 4.0 16.9 - - - +
496D LEU* 1.3 79.4 - - - +
498D ASP* 1.3 68.3 + - - +
499D SER* 5.1 2.7 - - - +
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Residues in contact with ASP 498 (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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494D ALA 4.1 2.7 + - - -
495D LEU 3.2 13.4 + - - +
496D LEU 2.8 10.1 + - - +
497D ARG* 1.3 84.7 - - - +
499D SER* 1.3 60.8 + - - +
500D PRO* 4.5 1.6 - - - +
526D LEU* 4.7 14.0 - - - +
530D ARG* 2.8 42.2 + - - +
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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
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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