Contacts of the helix formed by residues 480 - 499 (chain D) in PDB entry 3SRF
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 ALA 480 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D GLN* 4.0 2.1 - - - +
479D GLU* 1.3 76.6 - - - +
481D TRP* 1.3 61.1 + - - +
482D ALA* 3.3 2.9 - - + +
483D GLU* 3.2 28.6 + - + +
484D ASP* 2.9 28.2 + - - +
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Residues in contact with TRP 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D LEU* 6.2 0.2 - - + -
432D GLU* 4.6 14.1 - - - -
479D GLU 3.5 5.1 + - - +
480D ALA* 1.3 71.4 - - - +
482D ALA* 1.3 55.2 + - + +
484D ASP* 3.1 14.6 + - + +
485D VAL* 2.8 50.0 + - + +
488D ARG* 3.5 25.6 - - - -
513D GLY* 2.9 34.7 + - - -
514D TRP 3.6 17.9 + - - -
515D ARG* 3.6 17.4 - - - -
516D PRO* 3.7 50.7 - - + -
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Residues in contact with ALA 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480D ALA* 3.3 3.0 - - + +
481D TRP* 1.3 81.9 - - + +
483D GLU* 1.3 62.4 + - + +
485D VAL* 3.8 6.4 - - - +
486D ASP* 3.2 33.6 + - - +
514H TRP* 6.1 6.7 - - + -
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Residues in contact with GLU 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478D GLN* 4.3 16.2 - - + +
480D ALA* 3.2 27.9 + - + +
482D ALA* 1.3 78.6 - - + +
484D ASP* 1.3 56.4 + - - +
486D ASP* 3.6 5.9 + - - +
487D LEU* 3.2 28.6 + - - +
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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
----------------------------------------------------------
454D ARG* 2.7 42.4 + - - -
477D VAL* 3.7 12.3 - - - +
478D GLN* 3.7 32.8 + - + +
480D ALA 2.9 15.1 + - - +
481D TRP* 3.1 17.7 + - + +
483D GLU* 1.3 73.6 - - - +
485D VAL* 1.3 65.1 + - - +
487D LEU* 3.7 3.8 + - - +
488D ARG* 3.3 31.9 + - - +
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Residues in contact with VAL 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D LEU* 3.6 13.3 - - + +
481D TRP* 2.8 58.3 + - + +
482D ALA* 3.8 7.4 - - - +
484D ASP* 1.3 72.7 - - - +
486D ASP* 1.3 72.0 - - - +
488D ARG* 3.2 8.9 + - - +
489D VAL* 3.1 27.2 + - + +
512D THR* 3.7 30.3 - - + +
513D GLY 4.1 6.7 - - - +
525D ARG* 4.4 8.3 - - - +
514H TRP* 5.9 2.0 - - + -
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Residues in contact with ASP 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ALA* 3.2 19.6 + - - +
483D GLU* 3.6 6.4 + - - +
484D ASP 3.5 0.2 - - - -
485D VAL* 1.3 82.6 - - - +
487D LEU* 1.3 57.9 + - - +
489D VAL* 3.8 5.5 - - - +
490D ASN* 2.8 45.9 + - - +
525D ARG* 4.1 18.4 + - - -
514H TRP* 4.8 13.7 + - - -
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Residues in contact with LEU 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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454D ARG* 4.6 9.0 - - - +
473D CYS* 4.3 8.7 - - - -
475D ASP* 3.2 40.8 - - + +
478D GLN* 3.7 33.7 - - + +
483D GLU 3.2 16.0 + - - +
484D ASP* 3.9 7.2 - - - +
485D VAL 3.2 0.2 - - - -
486D ASP* 1.3 77.2 - - - +
488D ARG* 1.3 59.6 + - + +
490D ASN* 4.0 4.3 - - - +
491D PHE* 3.0 27.9 + - - +
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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
----------------------------------------------------------
430D LEU* 3.7 50.0 + - + +
431D THR 5.0 1.0 + - - +
432D GLU* 4.9 14.3 + - - +
452D VAL* 3.6 32.3 + - + +
453D THR* 5.8 1.8 - - - +
454D ARG* 3.2 32.5 - - - +
473D CYS* 4.2 15.3 - - - -
481D TRP* 3.5 38.6 - - - -
484D ASP* 3.3 22.2 + - - +
485D VAL* 3.2 10.5 + - - +
487D LEU* 1.3 78.5 - - + +
489D VAL* 1.3 59.8 + - - +
491D PHE* 3.5 8.1 - - - +
492D ALA* 3.1 25.8 + - - +
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Residues in contact with VAL 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428D ILE* 4.4 5.6 - - + +
430D LEU* 4.0 17.0 - - + -
485D VAL 3.1 20.2 + - - +
486D ASP* 3.8 7.6 - - - +
488D ARG* 1.3 75.2 - - - +
490D ASN* 1.3 63.8 + - - +
492D ALA* 3.0 8.0 + - - +
493D MET* 2.8 40.5 + - + +
510D VAL* 4.1 26.0 - - + -
512D THR* 4.1 10.1 - - + -
525D ARG* 3.9 21.8 - - - +
527D VAL* 5.6 2.7 - - + -
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Residues in contact with ASN 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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486D ASP* 2.8 33.8 + - - +
487D LEU* 4.2 4.8 - - - +
489D VAL* 1.3 75.0 - - - +
491D PHE* 1.3 56.5 + - - +
493D MET* 3.4 17.7 + - - +
494D ASN* 3.1 36.6 + - - +
530D PRO* 4.7 13.7 - - - +
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Residues in contact with PHE 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D PRO* 4.3 22.0 - - + -
102D ILE* 3.9 25.8 - - + -
452D VAL* 3.7 26.2 - - + -
471D VAL* 3.7 28.3 - - + -
472D LEU 4.0 16.8 - - - -
473D CYS* 4.0 19.3 - - + -
474D LYS 5.7 0.4 - - - -
475D ASP* 5.0 12.8 - - - +
487D LEU 3.0 20.8 + - - +
488D ARG* 3.5 5.2 - - - +
489D VAL 3.1 0.4 - - - -
490D ASN* 1.3 75.2 - - - +
492D ALA* 1.3 57.2 + - - +
494D ASN* 3.2 10.9 + - - +
495D VAL* 3.1 42.3 + - + +
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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
----------------------------------------------------------
428D ILE* 3.7 26.9 - - + -
450D ILE* 3.8 17.0 - - + +
452D VAL* 3.5 20.0 - - + -
488D ARG 3.1 14.6 + - - +
489D VAL 3.0 8.8 + - - +
491D PHE* 1.3 73.8 - - - +
493D MET* 1.3 64.2 + - - +
495D VAL* 3.4 6.1 + - - +
496D GLY 3.2 18.2 + - - -
502D PHE* 3.8 7.3 - - - -
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Residues in contact with MET 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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428D ILE* 3.7 9.9 - - + -
489D VAL* 2.8 27.4 + - + +
490D ASN* 3.4 24.0 - - - +
492D ALA* 1.3 77.8 - - - +
494D ASN* 1.3 63.0 + - - +
497D LYS* 3.2 26.6 + - - +
502D PHE* 3.4 37.1 - - + -
508D VAL* 3.6 28.5 - - + -
527D VAL* 5.5 4.3 - - - -
528D PRO 4.7 1.6 - - - +
529D VAL* 3.7 16.8 - - + -
530D PRO* 3.7 26.9 - - + -
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Residues in contact with ASN 494 (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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102D ILE* 3.5 28.5 - - + +
490D ASN* 3.1 21.1 + - - +
491D PHE* 3.2 11.1 + - - +
493D MET* 1.3 76.9 - - - +
495D VAL* 1.3 64.5 + - - +
497D LYS* 3.4 18.9 + - - +
498D ALA* 3.2 18.9 + - - +
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Residues in contact with VAL 495 (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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102D ILE* 3.8 26.2 - - + +
105D ARG* 5.1 2.5 - - - +
450D ILE* 4.6 9.9 - - + -
469D PHE* 6.4 1.1 - - + -
471D VAL* 3.5 34.8 - - + -
491D PHE* 3.1 35.8 + - + +
492D ALA* 3.7 9.9 - - - +
493D MET 3.3 0.4 - - - -
494D ASN* 1.3 74.5 - - - +
496D GLY* 1.3 61.4 + - - +
498D ALA* 3.4 1.6 + - - +
499D ARG* 3.0 47.7 + - + +
501D PHE* 5.5 2.2 - - + -
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Residues in contact with GLY 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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450D ILE* 4.0 8.7 - - - +
492D ALA 3.2 8.3 + - - -
493D MET 3.7 0.2 + - - -
494D ASN 3.5 0.2 - - - -
495D VAL* 1.3 79.2 - - - +
497D LYS* 1.3 55.3 + - - +
500D GLY* 2.9 6.4 + - - -
501D PHE* 2.7 37.9 + - - -
502D PHE* 3.4 33.6 + - - -
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Residues in contact with LYS 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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493D MET* 3.2 20.6 + - - +
494D ASN* 3.5 21.5 + - - +
495D VAL 3.2 0.6 - - - -
496D GLY* 1.3 77.1 - - - +
498D ALA* 1.3 64.0 + - - +
500D GLY* 3.2 13.5 + - - -
502D PHE* 3.7 19.9 - - + +
503D LYS* 5.2 2.5 - - - -
504D LYS* 5.2 7.5 - - - +
529D VAL* 3.7 15.9 - - + -
530D PRO* 2.8 33.2 + - - -
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Residues in contact with ALA 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ILE* 3.8 18.8 - - + -
103D LEU* 3.8 28.1 - - + +
494D ASN 3.2 13.3 + - - +
495D VAL 4.1 1.3 - - - +
497D LYS* 1.3 79.1 - - - +
499D ARG* 1.3 61.0 + - + +
500D GLY* 4.6 0.2 - - - -
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Residues in contact with ARG 499 (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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40D THR* 4.1 13.5 + - - -
102D ILE 4.7 7.2 - - - +
103D LEU* 3.6 43.3 + - - +
105D ARG* 3.8 34.0 - - - +
469D PHE* 6.4 0.2 - - - -
495D VAL* 3.0 33.5 + - + +
498D ALA* 1.3 75.9 - - - +
500D GLY* 1.3 59.5 + - - +
501D PHE* 3.6 35.4 - - + -
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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