Contacts of the helix formed by residues 491 - 506 (chain A) in PDB entry 3PRF
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 THR 491 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A ALA 3.7 2.8 + - - -
490A PRO* 1.3 74.3 - - - +
492A PRO* 1.3 72.8 - - + +
493A GLN* 3.5 20.0 - - + +
494A GLN* 2.7 38.6 + - + +
495A LEU* 2.9 28.1 + - - +
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Residues in contact with PRO 492 (chain A).
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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490A PRO 3.6 5.1 - - - +
491A THR* 1.3 93.5 - - + +
493A GLN* 1.3 59.0 + - - +
495A LEU* 3.3 10.6 - - + +
496A GLN* 3.2 19.6 + - - +
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Residues in contact with GLN 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A THR* 3.2 13.4 - - + +
492A PRO* 1.3 77.3 - - - +
494A GLN* 1.3 60.9 + - + +
496A GLN* 3.1 11.1 + - + +
497A ALA* 2.9 24.4 + - - +
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Residues in contact with GLN 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A PHE* 4.3 25.6 - - + +
485A LEU* 3.3 50.4 - - + +
487A VAL* 5.0 5.2 - - - +
491A THR* 2.7 37.8 + - + +
493A GLN* 1.3 74.1 - - + +
495A LEU* 1.3 56.4 + - - +
497A ALA* 3.4 7.2 - - + +
498A PHE* 2.7 38.1 + - - +
525A LEU* 5.5 0.7 - - - -
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A PRO* 3.8 32.7 - - + +
491A THR 2.9 15.6 + - - +
492A PRO* 3.3 13.0 - - + +
494A GLN* 1.3 74.6 - - - +
496A GLN* 1.3 55.6 + - - +
498A PHE* 3.9 5.9 - - + +
499A LYS* 3.1 42.6 + - + +
525A LEU* 4.3 14.3 - - + +
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Residues in contact with GLN 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A PRO 3.2 8.8 + - - +
493A GLN* 3.1 13.5 + - + +
495A LEU* 1.3 77.5 - - - +
497A ALA* 1.3 64.0 - - - +
499A LYS* 3.6 7.4 + - - +
500A ASN* 2.8 47.2 + - - +
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Residues in contact with ALA 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A PHE* 3.5 41.9 - - + -
493A GLN 2.9 13.2 + - - +
494A GLN* 3.0 14.1 + - + +
496A GLN* 1.3 73.4 - - - +
498A PHE* 1.3 65.9 + - - +
500A ASN* 3.2 14.9 + - - +
501A GLU* 3.3 14.4 + - - +
595A PHE 5.4 0.3 - - - +
596A GLY* 5.6 2.3 - - - -
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Residues in contact with PHE 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A PHE* 5.4 0.2 - - - -
483A LYS 5.9 0.2 - - - -
485A LEU* 5.8 4.9 - - + -
494A GLN 2.7 19.3 + - - +
495A LEU* 3.9 4.3 - - + +
497A ALA* 1.3 73.8 - - - +
499A LYS* 1.3 79.9 + - + +
500A ASN 3.1 1.6 + - - -
501A GLU* 3.3 5.9 + - - +
502A VAL* 3.2 36.2 + - + +
519A TYR* 4.1 11.2 - + + -
520A SER 3.7 19.3 - - - -
521A THR* 4.3 16.2 - - + -
525A LEU* 3.7 33.4 - - + -
526A ALA* 3.5 33.2 - - - -
527A ILE* 3.8 19.7 - - + -
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Residues in contact with LYS 499 (chain A).
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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495A LEU* 3.1 28.7 + - + +
496A GLN* 4.0 10.3 - - - +
497A ALA 3.4 0.2 - - - -
498A PHE* 1.3 97.5 - - + +
500A ASN* 1.3 57.8 + - - +
502A VAL* 4.3 13.5 - - - +
503A GLY* 3.2 21.2 + - - -
519A TYR* 4.4 27.3 + - - -
521A THR* 5.6 5.4 - - - -
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Residues in contact with ASN 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A GLN* 2.8 38.2 + - - +
497A ALA* 3.2 12.5 + - - +
498A PHE 3.0 0.8 - - - -
499A LYS* 1.3 78.5 - - - +
501A GLU* 1.3 66.1 + - - +
503A GLY* 3.2 1.8 + - - -
504A VAL* 2.9 33.4 + - - +
595A PHE 4.7 1.3 - - - +
596A GLY* 6.2 0.9 - - - -
597A LEU 3.5 24.7 + - - +
598A ALA* 5.2 2.6 - - - +
599A THR* 5.8 4.2 - - - +
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Residues in contact with GLU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A SER* 4.8 1.0 - - - +
468A PHE* 6.0 1.7 - - - -
483A LYS* 2.8 38.9 + - - -
497A ALA 3.3 8.9 + - - +
498A PHE* 3.3 4.4 + - - +
500A ASN* 1.3 77.6 - - - +
502A VAL* 1.3 52.6 + - - +
504A VAL* 3.1 3.6 + - - +
505A LEU* 2.7 51.6 + - + +
527A ILE* 3.2 19.2 - - + +
594A ASP* 4.3 0.2 - - - -
595A PHE* 3.3 49.4 + - + +
596A GLY* 4.5 1.8 + - - -
727A FP3 3.3 18.2 + - - +
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Residues in contact with VAL 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A PHE* 3.2 27.0 + - + +
499A LYS* 4.3 14.8 - - - +
501A GLU* 1.3 77.4 - - - +
503A GLY* 1.3 63.0 + - - +
505A LEU* 4.0 5.3 - - - +
506A ARG* 2.9 39.0 + - - +
516A PHE* 4.4 10.5 - - + -
519A TYR* 3.9 41.5 - - + -
527A ILE* 3.9 23.8 - - + -
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Residues in contact with GLY 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A LYS 3.2 15.3 + - - -
500A ASN* 3.2 4.4 + - - -
502A VAL* 1.3 81.1 - - - +
504A VAL* 1.3 60.3 + - - +
506A ARG* 3.8 11.6 - - - +
507A LYS* 3.4 23.6 + - - +
448B ASP* 5.5 0.3 - - - +
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Residues in contact with VAL 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A ASN* 2.9 23.1 + - - +
501A GLU* 3.6 6.1 - - - +
503A GLY* 1.3 76.7 - - - +
505A LEU* 1.3 60.9 + - - +
507A LYS* 3.0 27.8 + - - +
508A THR* 3.6 8.8 + - + +
572A ILE* 4.0 23.8 - - + -
595A PHE* 3.7 31.4 - - + +
597A LEU* 4.0 25.4 - - + +
599A THR* 4.7 21.3 - - + -
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Residues in contact with LEU 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A GLU* 2.7 47.1 + - + +
502A VAL 4.0 1.6 - - - +
504A VAL* 1.3 69.7 - - - +
506A ARG* 1.3 56.2 + - - +
507A LYS 2.9 4.5 - - - -
508A THR* 2.7 39.1 + - - +
513A ILE* 5.0 0.2 - - + -
514A LEU* 4.1 21.8 - - + +
516A PHE* 3.6 40.3 - - + +
527A ILE* 3.8 17.7 - - + -
529A THR* 4.7 7.0 - - + -
595A PHE* 3.7 30.7 - - + -
727A FP3 4.7 0.7 - - + -
509B ARG* 3.6 2.1 + - - -
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Residues in contact with ARG 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A ASP* 5.1 12.3 + - - +
449A ASP* 5.3 6.1 + - - +
450A TRP* 3.7 35.4 - - - +
502A VAL* 2.9 35.6 + - - +
503A GLY* 3.8 11.4 - - - +
505A LEU* 1.3 74.5 - - - +
507A LYS* 1.3 56.0 + - - +
508A THR 3.4 0.7 - - - -
516A PHE* 4.2 18.3 - - + -
519A TYR* 5.8 3.4 - - - -
448B ASP* 4.1 26.1 + - - +
450B TRP* 3.4 23.8 - - - +
509B ARG* 3.7 9.8 + - - +
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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