Contacts of the helix formed by residues 480 - 500 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478E GLN* 3.9 2.3 - - - +
479E GLU* 1.3 77.5 - - - +
481E TRP* 1.3 65.7 + - - +
482E ALA* 3.2 4.3 - - + +
483E GLU* 3.2 26.1 + - + +
484E ASP* 3.0 20.6 + - - +
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Residues in contact with TRP 481 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432E GLU* 4.6 13.2 - - - -
454E ARG* 5.6 0.2 - - - -
478E GLN 5.6 0.2 - - - -
479E GLU 3.6 4.1 + - - -
480E ALA* 1.3 71.6 - - - +
482E ALA* 1.3 58.7 + - - +
484E ASP* 3.3 26.3 + - + -
485E VAL* 2.8 42.8 + - + +
488E ARG* 3.5 18.8 - - - -
513E GLY* 2.8 35.1 + - - -
514E TRP 3.4 17.5 - - - -
515E ARG* 3.4 21.1 - - + -
516E PRO* 3.6 46.0 - - + -
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Residues in contact with ALA 482 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480E ALA* 3.2 4.3 - - + +
481E TRP* 1.3 81.9 - - - +
483E GLU* 1.3 53.1 + - + +
485E VAL* 3.3 6.2 + - - +
486E ASP* 2.7 45.6 + - - +
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Residues in contact with GLU 483 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478E GLN* 4.0 20.1 - - + +
480E ALA* 3.2 25.2 + - + +
482E ALA* 1.3 77.0 - - + +
484E ASP* 1.3 57.0 + - - +
486E ASP* 3.8 9.7 - - - +
487E LEU* 2.9 33.8 + - - +
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Residues in contact with ASP 484 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454E ARG* 2.9 43.0 + - - -
476E PRO 4.5 0.2 - - - +
477E VAL* 4.1 8.4 - - - +
478E GLN* 3.4 34.2 + - + +
480E ALA 3.0 13.0 + - - +
481E TRP* 3.6 33.2 - - + +
482E ALA 3.3 0.2 - - - -
483E GLU* 1.3 73.6 - - - +
485E VAL* 1.3 62.7 + - - +
487E LEU* 4.6 2.9 - - - +
488E ARG* 3.3 27.1 + - - +
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Residues in contact with VAL 485 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430E LEU* 3.8 15.2 - - + +
481E TRP* 2.8 54.0 + - + +
482E ALA* 3.6 6.7 - - - +
484E ASP* 1.3 78.3 - - - +
486E ASP* 1.3 65.2 + - - +
487E LEU 3.3 0.4 + - - -
488E ARG* 3.4 2.6 + - - +
489E VAL* 3.1 33.6 + - - +
512E THR* 3.7 31.4 - - + +
513E GLY 4.1 7.2 - - - +
525E ARG* 4.3 12.1 - - - +
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Residues in contact with ASP 486 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482E ALA* 2.7 31.8 + - - +
483E GLU* 3.4 12.8 + - - +
485E VAL* 1.3 79.8 - - - +
487E LEU* 1.3 60.7 + - - +
489E VAL* 4.1 5.2 - - - +
490E ASN* 3.1 36.7 + - - +
525E ARG* 5.2 5.6 + - - +
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Residues in contact with LEU 487 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454E ARG* 5.4 2.9 - - - +
473E CYS* 4.9 6.3 - - - -
475E ASP* 3.7 37.5 - - + +
476E PRO* 4.9 7.9 - - + +
478E GLN* 4.0 27.8 - - + +
483E GLU 2.9 17.8 + - - +
484E ASP* 4.6 2.5 - - - +
485E VAL 3.3 0.2 - - - -
486E ASP* 1.3 73.9 - - - +
488E ARG* 1.3 66.8 + - + +
490E ASN* 4.0 3.8 + - - +
491E PHE* 3.4 21.8 + - + +
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Residues in contact with ARG 488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430E LEU* 3.9 48.4 + - + +
431E THR 4.8 1.6 + - - +
432E GLU* 4.4 21.6 + - - +
452E VAL* 3.7 29.8 + - + +
453E THR* 5.5 2.9 - - - +
454E ARG* 3.6 40.4 - - - +
473E CYS* 4.3 15.3 - - - -
481E TRP* 3.5 36.2 - - - -
484E ASP* 3.3 21.9 + - - +
485E VAL* 3.4 6.3 + - - +
487E LEU* 1.3 76.7 - - + +
489E VAL* 1.3 65.1 + - - +
491E PHE* 3.4 7.5 - - - +
492E ALA 3.2 15.9 + - - -
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Residues in contact with VAL 489 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428E ILE* 4.8 3.8 - - + -
430E LEU* 4.0 20.0 - - + -
485E VAL 3.1 18.4 + - - +
486E ASP* 3.7 6.0 + - - +
487E LEU 3.3 0.2 - - - -
488E ARG* 1.3 72.9 - - - +
490E ASN* 1.3 58.8 + - - +
491E PHE 3.1 1.1 - - - -
492E ALA* 2.9 9.8 + - - +
493E MET* 2.8 49.6 + - + +
510E VAL* 3.9 29.6 - - + -
512E THR* 4.2 1.3 - - + -
525E ARG* 3.8 24.0 - - - +
527E VAL* 5.8 2.0 - - + -
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Residues in contact with ASN 490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486E ASP* 3.1 23.2 + - - +
487E LEU* 4.4 4.1 - - - +
489E VAL* 1.3 81.4 - - - +
491E PHE* 1.3 53.0 + - - +
493E MET* 3.3 10.7 + - - +
494E ASN* 2.8 45.0 + - - +
530E PRO* 4.3 22.4 - - - +
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Residues in contact with PHE 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E PRO* 3.9 22.9 - - + -
102E ILE* 3.7 28.9 - - + -
452E VAL* 3.8 19.1 - - + -
471E VAL* 3.8 28.7 - - + -
472E LEU 3.7 17.0 - - - -
473E CYS* 4.1 25.8 - - + -
475E ASP* 5.1 10.8 - - - -
487E LEU* 3.4 15.3 + - + +
488E ARG* 3.4 9.4 - - - +
490E ASN* 1.3 78.3 - - - +
492E ALA* 1.3 58.4 + - - +
494E ASN* 3.0 10.0 + - - +
495E VAL* 3.0 36.2 + - + +
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Residues in contact with ALA 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428E ILE* 3.6 24.5 - - + -
450E ILE* 3.7 25.3 - - + +
452E VAL* 3.3 29.2 - - + -
488E ARG 3.2 2.5 + - - +
489E VAL 2.9 9.2 + - - +
491E PHE* 1.3 77.4 - - - +
493E MET* 1.3 63.9 + - - +
495E VAL* 3.5 7.4 + - - +
496E GLY 3.3 17.3 + - - -
502E PHE* 3.9 0.7 - - - -
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Residues in contact with MET 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428E ILE* 3.7 10.1 - - + -
489E VAL* 2.8 33.2 + - + +
490E ASN* 3.3 15.9 - - - +
492E ALA* 1.3 78.1 - - - +
494E ASN* 1.3 57.2 + - - +
497E LYS* 3.0 32.5 + - + +
502E PHE* 3.2 34.9 - - + -
508E VAL* 3.6 26.7 - - + -
527E VAL* 5.6 4.9 - - - -
528E PRO 4.7 2.0 - - - +
529E VAL* 3.8 16.6 - - + -
530E PRO* 3.3 33.9 - - + -
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Residues in contact with ASN 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ILE* 3.8 20.2 - - + +
490E ASN* 2.8 26.9 + - - +
491E PHE* 3.0 11.9 + - - +
493E MET* 1.3 76.4 - - - +
495E VAL* 1.3 58.9 + - - +
497E LYS* 3.6 16.3 + - - +
498E ALA* 2.9 31.7 + - - +
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Residues in contact with VAL 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ILE* 3.9 22.7 - - + +
105E ARG* 3.5 27.6 - - - +
450E ILE* 4.8 7.4 - - + -
469E PHE* 6.4 1.1 - - + -
471E VAL* 3.6 27.4 - - + -
491E PHE* 3.0 31.6 + - + +
492E ALA* 3.7 10.5 - - - +
493E MET 3.3 0.4 - - - -
494E ASN* 1.3 74.3 - - - +
496E GLY* 1.3 60.6 + - - +
498E ALA* 3.9 0.2 - - - +
499E ARG* 2.8 42.0 + - + +
501E PHE* 5.0 7.0 - - + -
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Residues in contact with GLY 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E ILE* 4.0 1.0 - - - +
492E ALA 3.3 8.7 + - - -
495E VAL* 1.3 78.8 - - - +
497E LYS* 1.3 56.5 + - - +
500E GLY* 2.8 9.4 + - - -
501E PHE* 2.7 48.6 + - - -
502E PHE* 3.4 26.7 + - - -
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Residues in contact with LYS 497 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493E MET* 3.0 23.5 + - + +
494E ASN* 3.6 20.2 + - - +
496E GLY* 1.3 78.4 - - - +
498E ALA* 1.3 62.9 + - - +
500E GLY* 3.5 8.3 + - - -
502E PHE* 3.5 18.4 - - + +
503E LYS* 4.7 2.5 - - - +
504E LYS* 4.1 14.1 - - - +
529E VAL* 3.8 22.0 - - + -
530E PRO* 2.7 34.3 + - + +
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Residues in contact with ALA 498 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ILE* 3.8 19.5 - - + -
103E LEU* 4.6 16.8 - - + +
494E ASN 2.9 19.0 + - - +
495E VAL 3.9 0.9 - - - +
497E LYS* 1.3 73.7 - - - +
499E ARG* 1.3 62.9 + - + +
500E GLY* 3.1 5.6 + - - -
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Residues in contact with ARG 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E THR* 4.3 11.1 + - - -
102E ILE 4.7 0.7 - - - +
103E LEU* 3.0 51.8 + - - +
105E ARG* 3.5 55.7 - - - +
469E PHE* 6.2 1.6 - - - -
495E VAL* 2.8 28.5 + - + +
498E ALA* 1.3 71.7 - - + +
500E GLY* 1.3 59.7 + - - +
501E PHE* 3.6 27.3 - - + -
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Residues in contact with GLY 500 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E THR* 3.1 18.1 - - - +
496E GLY 2.8 6.8 + - - -
497E LYS 3.8 8.5 - - - -
498E ALA 3.1 4.3 - - - -
499E ARG* 1.3 80.3 - - - +
501E PHE* 1.3 64.8 + - - +
502E PHE* 3.3 6.2 - - - +
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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
------------------------------------------------------------
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