Contacts of the helix formed by residues 498 - 511 (chain B) in PDB entry 2DB3
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 498 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496B VAL* 3.5 7.5 - - - +
497B GLU* 1.3 95.0 - - + +
499B LYS* 1.3 60.0 + - - +
500B ARG* 3.7 6.6 + - - +
501B GLY* 2.8 23.3 + - - -
502B ALA* 2.9 24.3 + - - +
546B THR* 3.7 4.5 - - - -
2F U 3.9 18.2 - - - +
3F U 3.5 9.6 - - - -
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Residues in contact with LYS 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B THR* 1.3 70.8 - - - +
500B ARG* 1.3 58.7 + - - +
502B ALA* 3.2 3.1 + - - +
503B ASP* 3.0 28.5 + - - +
520B HIS* 3.6 18.2 + - + -
521B GLY* 3.9 2.6 - - - -
522B ASP* 3.0 49.4 + - - +
546B THR* 3.7 9.1 - - - +
3F U 2.9 35.9 + - - +
4F U 3.3 36.5 + - - +
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Residues in contact with ARG 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B THR* 3.2 6.8 - - - +
499B LYS* 1.3 77.5 - - - +
501B GLY* 1.3 65.8 + - - +
503B ASP* 3.3 6.9 + - + +
504B PHE* 2.9 27.0 + - + +
522B ASP* 5.0 2.1 + - - +
3F U 4.6 0.4 + - - -
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Residues in contact with GLY 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B VAL* 4.0 10.4 - - - +
498B THR* 2.8 21.8 + - - -
500B ARG* 1.3 76.6 - - - +
502B ALA* 1.3 55.9 + - - +
504B PHE* 3.4 8.6 + - - +
505B LEU* 3.0 31.9 + - - +
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Residues in contact with ALA 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B VAL* 3.4 23.2 - - + +
498B THR 2.9 8.3 + - - +
499B LYS 3.4 8.7 - - - +
500B ARG 3.1 0.2 - - - -
501B GLY* 1.3 75.3 - - - +
503B ASP* 1.3 66.1 + - - +
506B ALA* 3.2 22.0 + - - +
518B SER* 4.4 1.2 - - - -
520B HIS* 3.7 17.5 - - + +
544B ILE* 3.5 22.0 - - + +
545B ALA 4.8 0.9 - - - -
546B THR* 4.0 13.0 - - + +
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Residues in contact with ASP 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B LYS 3.0 15.4 + - - +
500B ARG* 3.3 6.9 + - + +
502B ALA* 1.3 76.6 - - - +
504B PHE* 1.3 64.7 + - - +
506B ALA* 3.7 4.9 + - - +
507B SER* 3.4 21.3 + - - -
518B SER* 5.1 2.4 + - - -
520B HIS* 4.0 20.4 + - + +
523B ARG* 5.7 1.9 + - - +
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Residues in contact with PHE 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B ARG* 5.1 15.7 - - + -
500B ARG* 2.9 20.0 + - + +
501B GLY* 3.5 8.1 - - - +
503B ASP* 1.3 77.0 + - - +
505B LEU* 1.3 88.8 + - + +
506B ALA 3.1 0.2 + - - -
507B SER* 3.1 11.8 + - - -
508B PHE* 3.0 46.6 + + + +
564B TYR* 5.6 0.9 - - - -
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Residues in contact with LEU 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B ARG* 5.3 0.2 - - + -
481B LEU* 3.4 34.3 - - + -
494B VAL* 4.3 6.3 - - + -
496B VAL* 3.9 18.4 - - + -
501B GLY 3.0 14.2 + - - +
502B ALA 4.2 2.5 - - - +
504B PHE* 1.3 90.3 - - + +
506B ALA* 1.3 62.7 + - - +
508B PHE* 3.3 33.5 + - + +
509B LEU* 3.0 29.8 + - + +
544B ILE* 4.2 13.7 - - + -
564B TYR* 3.5 31.6 - - + +
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Residues in contact with ALA 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B ALA 3.2 18.4 + - - +
503B ASP* 3.9 4.7 - - - +
504B PHE 3.1 1.4 - - - -
505B LEU* 1.3 78.4 - - - +
507B SER* 1.3 58.2 + - - +
509B LEU 3.3 0.7 + - - -
510B SER* 3.0 30.6 + - - -
516B THR* 3.8 13.9 - - + +
517B THR* 4.2 2.7 - - - +
518B SER* 3.8 20.2 - - - +
544B ILE* 3.7 20.5 - - + +
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Residues in contact with SER 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B ASP* 3.4 13.0 + - - -
504B PHE* 3.1 15.9 + - - -
506B ALA* 1.3 76.7 - - - +
508B PHE* 1.3 64.8 + - - +
510B SER* 3.8 9.1 - - - -
511B GLU* 3.2 24.7 + - - +
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Residues in contact with PHE 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B ARG* 3.9 39.9 - - + -
481B LEU* 6.1 0.9 - - + -
482B ILE* 4.6 4.9 - - + -
504B PHE* 3.0 34.4 + + + +
505B LEU* 3.3 33.4 - - + +
507B SER* 1.3 78.5 + - - +
509B LEU* 1.3 63.9 + - + +
511B GLU* 3.0 37.9 - - - +
512B LYS* 3.3 43.5 - - - +
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Residues in contact with LEU 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B LEU* 4.6 12.3 - - + -
482B ILE* 3.9 25.1 - - + -
485B LEU* 3.7 32.5 - - + -
505B LEU* 3.0 22.6 + - + +
506B ALA 3.9 2.0 - - - +
508B PHE* 1.3 85.2 - - + +
510B SER* 1.3 62.5 + - - +
512B LYS* 3.2 7.4 + - - -
513B GLU 3.4 0.2 + - - -
514B PHE* 3.0 36.7 + - + -
516B THR* 3.6 19.3 - - + +
542B VAL* 4.1 2.9 - - + -
544B ILE* 3.8 29.4 - - + -
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Residues in contact with SER 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B ALA 3.0 18.4 + - - -
507B SER* 3.3 10.9 + - - -
509B LEU* 1.3 79.1 - - - +
511B GLU* 1.3 59.2 + - - +
512B LYS 3.2 0.4 - - - -
513B GLU* 3.4 13.2 + - - +
514B PHE 3.7 8.6 + - - -
516B THR* 3.5 25.3 + - - -
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Residues in contact with GLU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B SER 3.2 11.3 + - - +
508B PHE* 3.0 39.1 - - - +
510B SER* 1.3 73.4 - - - +
512B LYS* 1.3 63.5 + - + +
513B GLU* 3.0 12.9 + - - +
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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