Contacts of the helix formed by residues 490 - 505 (chain A) in PDB entry 3II5
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 490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488A ALA 3.7 2.8 + - - -
489A PRO* 1.3 73.0 - - - +
491A PRO* 1.3 68.9 - - - +
492A GLN* 2.7 40.2 + - + +
493A GLN* 2.7 54.2 + - + +
494A LEU* 3.0 10.0 + - - +
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Residues in contact with PRO 491 (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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489A PRO 3.8 4.2 - - - +
490A THR* 1.3 88.1 - - - +
492A GLN* 1.3 65.0 + - - +
494A LEU* 4.0 15.1 - - + +
495A GLN* 3.3 23.6 + - - +
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Residues in contact with GLN 492 (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 THR* 2.7 24.7 + - + +
491A PRO* 1.3 84.8 - - - +
493A GLN* 1.3 62.2 + - + +
495A GLN* 3.5 5.1 + - - +
496A ALA* 3.4 19.1 + - - +
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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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467A PHE* 5.8 7.8 - - + -
484A LEU* 4.3 23.9 - - + +
486A VAL* 4.5 17.3 - - - +
488A ALA 4.3 2.8 - - - +
489A PRO* 3.4 10.8 - - + +
490A THR* 2.7 46.4 + - + +
492A GLN* 1.3 72.3 - - + +
494A LEU* 1.3 64.6 + - - +
495A GLN 3.0 1.8 - - - -
496A ALA* 3.2 7.1 + - - +
497A PHE* 3.0 24.8 + - - +
524A LEU* 4.6 2.5 - - - +
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Residues in contact with LEU 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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489A PRO* 4.8 16.5 - - + +
490A THR 3.0 14.5 + - - +
491A PRO* 4.1 11.2 - - + -
493A GLN* 1.3 77.2 - - - +
495A GLN* 1.3 60.4 + - - +
497A PHE* 3.6 9.4 - - + +
498A LYS* 3.2 44.1 + - - +
520A THR* 5.7 3.6 - - + -
524A LEU* 4.2 26.8 - - + +
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Residues in contact with GLN 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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491A PRO 3.3 19.2 + - - +
492A GLN* 3.5 6.5 - - - +
493A GLN 3.0 0.2 - - - -
494A LEU* 1.3 76.2 - - - +
496A ALA* 1.3 65.9 + - - +
497A PHE 3.0 1.6 - - - -
498A LYS* 2.9 32.8 + - - +
499A ASN* 2.9 42.2 + - - +
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Residues in contact with ALA 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 GLN 3.4 9.6 + - - +
493A GLN* 3.2 9.7 + - - +
495A GLN* 1.3 78.7 - - - +
497A PHE* 1.3 56.4 + - - +
499A ASN* 3.8 11.2 - - - +
500A GLU* 3.0 30.9 + - - +
599A VAL* 5.3 13.7 - - + -
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Residues in contact with PHE 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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484A LEU* 5.1 7.6 - - + -
493A GLN 3.0 17.1 + - - +
494A LEU* 3.6 11.4 - - + +
496A ALA* 1.3 76.2 - - - +
498A LYS* 1.3 75.4 + - + +
500A GLU* 3.3 6.2 + - - +
501A VAL* 3.0 32.6 + - + +
518A TYR* 3.9 17.3 - + + -
519A SER 3.7 12.6 - - - -
520A THR* 4.1 17.7 - - + -
524A LEU* 3.7 30.5 - - + -
525A ALA 3.5 33.2 - - - -
526A ILE* 3.6 24.0 - - + -
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Residues in contact with LYS 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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494A LEU* 3.2 45.3 + - - +
495A GLN* 2.9 25.1 + - - +
497A PHE* 1.3 84.6 - - + +
499A ASN* 1.3 54.7 + - - +
501A VAL* 3.7 5.3 - - - +
502A GLY* 2.8 33.4 + - - -
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Residues in contact with ASN 499 (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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495A GLN* 2.9 47.3 + - - +
496A ALA* 3.8 11.2 - - - +
498A LYS* 1.3 76.7 - - - +
500A GLU* 1.3 59.0 + - - +
502A GLY* 3.4 2.6 + - - -
503A VAL* 2.8 33.1 + - + +
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Residues in contact with GLU 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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1A 831 3.1 44.3 + - + -
482A LYS* 3.0 30.8 + - - +
496A ALA 3.0 18.5 + - - +
497A PHE* 3.8 5.1 - - - +
499A ASN* 1.3 73.1 - - - +
501A VAL* 1.3 66.5 + - - +
503A VAL* 3.0 9.6 + - - +
504A LEU* 2.9 25.8 + - + +
526A ILE* 3.6 19.2 - - + +
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Residues in contact with VAL 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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497A PHE* 3.0 27.6 + - + +
498A LYS* 3.7 5.6 - - - +
500A GLU* 1.3 77.9 - - - +
502A GLY* 1.3 59.8 + - - +
504A LEU* 3.2 8.0 + - - +
505A ARG* 2.9 42.8 + - - +
515A PHE* 4.5 10.7 - - + -
518A TYR* 4.0 37.7 - - + -
526A ILE* 3.8 26.9 - - + -
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Residues in contact with GLY 502 (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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498A LYS 2.8 20.8 + - - -
499A ASN* 3.7 3.1 - - - -
500A GLU 3.2 0.2 - - - -
501A VAL* 1.3 74.5 - - - +
503A VAL* 1.3 59.5 + - - +
505A ARG* 3.5 18.1 - - - +
506A LYS* 3.4 23.3 - - - +
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Residues in contact with VAL 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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1A 831 4.7 20.6 - - + -
499A ASN* 2.8 27.1 - - + +
500A GLU* 3.0 8.4 + - - +
502A GLY* 1.3 75.5 - - - +
504A LEU* 1.3 65.7 + - - +
506A LYS* 3.1 24.4 + - + +
507A THR* 3.6 7.8 - - - +
571A ILE* 3.9 35.7 - - + -
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Residues in contact with LEU 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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1A 831 3.7 62.4 - - + +
500A GLU* 2.9 26.0 + - + +
501A VAL* 3.7 4.5 - - - +
503A VAL* 1.3 78.0 - - - +
505A ARG* 1.3 58.4 + - - +
507A THR* 2.4 36.9 + - - +
512A ILE* 5.5 0.2 - - + -
513A LEU* 4.7 10.3 - - + +
515A PHE* 3.8 29.2 - - + +
526A ILE* 4.0 25.8 - - + -
528A THR* 4.9 3.8 - - + -
508B ARG* 3.7 3.6 + - - -
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Residues in contact with ARG 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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447A ASP 4.1 14.5 + - - +
449A TRP* 4.2 14.8 - - + +
501A VAL* 2.9 32.2 + - - +
502A GLY* 3.5 18.4 - - - +
504A LEU* 1.3 74.8 - - - +
506A LYS* 1.3 56.0 + - + +
507A THR 3.1 1.8 - - - -
515A PHE* 4.0 19.2 - - + -
518A TYR* 5.7 6.0 + - - -
726A PO4 3.3 46.3 + - - +
449B TRP* 3.3 14.9 - - - -
508B ARG* 3.0 21.6 + - - +
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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