Contacts of the helix formed by residues 545 - 556 (chain B) in PDB entry 5ODS
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 ASP 545 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515B ILE* 4.8 0.6 - - - +
544B ALA* 1.3 75.0 - - - +
546B ILE* 1.3 72.2 + - - +
547B THR* 3.1 35.8 + - - -
548B GLN* 3.2 33.0 + - + +
549B ILE* 3.1 25.8 + - - +
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Residues in contact with ILE 546 (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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537B VAL* 4.2 22.0 - - + -
542B PRO* 5.0 14.1 - - + -
544B ALA 3.6 4.2 + - - +
545B ASP* 1.3 77.1 - - - +
547B THR* 1.3 69.1 + - - +
549B ILE* 3.0 35.1 - - + +
550B VAL* 3.1 14.4 + - + +
565B PHE* 4.2 13.0 - - + -
566B LEU* 4.5 15.9 - - + -
569B ALA* 5.9 3.4 - - + -
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Residues in contact with THR 547 (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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545B ASP* 3.1 15.5 + - - -
546B ILE* 1.3 80.5 - - - +
548B GLN* 1.3 60.4 + - - +
550B VAL* 3.1 25.9 - - + +
551B ASP* 2.8 21.8 - - - +
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Residues in contact with GLN 548 (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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515B ILE* 4.1 35.0 - - + +
545B ASP* 3.2 33.3 + - + +
546B ILE 3.2 0.6 - - - -
547B THR* 1.3 80.5 - - - +
549B ILE* 1.3 60.1 + - - +
551B ASP* 2.7 26.7 - - - +
552B VAL* 3.3 13.4 - - - +
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Residues in contact with ILE 549 (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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515B ILE* 4.3 12.1 - - + -
518B LEU* 3.9 29.1 - - + +
533B ALA* 4.7 7.9 - - + +
536B LEU* 4.3 16.8 - - + -
537B VAL* 4.1 12.6 - - + -
544B ALA* 5.1 2.2 - - + +
545B ASP 3.1 10.0 + - - +
546B ILE* 3.0 37.2 - - + +
548B GLN* 1.3 77.6 - - - +
550B VAL* 1.3 65.1 + - - +
552B VAL* 3.1 18.3 + - - +
553B PHE* 3.1 20.4 + - + -
565B PHE* 3.5 33.4 - - + -
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Residues in contact with VAL 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ILE* 3.1 14.5 + - + +
547B THR* 3.1 29.4 - - + +
549B ILE* 1.3 77.5 - - - +
551B ASP* 1.3 58.9 + - + +
553B PHE* 3.1 11.4 + - - +
554B MET* 2.9 32.1 + - + +
562B CYS* 3.7 14.8 - - - -
565B PHE* 3.9 13.7 - - + -
566B LEU* 3.7 31.6 - - + -
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Residues in contact with ASP 551 (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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519B ARG* 5.6 0.3 + - - -
547B THR* 2.8 24.8 - - - +
548B GLN* 2.7 28.6 - - - +
550B VAL* 1.3 79.0 - - + +
552B VAL* 1.3 62.5 + - - +
554B MET* 3.7 13.4 - - + +
555B GLU* 3.0 35.2 + - - +
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Residues in contact with VAL 552 (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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515B ILE* 3.8 23.6 - - + +
518B LEU* 4.0 22.7 - - + -
519B ARG* 4.1 29.2 - - + +
522B MET* 4.4 6.1 - - + -
548B GLN 3.3 16.6 - - - +
549B ILE* 3.1 10.9 + - - +
550B VAL 3.1 0.6 - - - -
551B ASP* 1.3 80.3 + - - +
553B PHE* 1.3 66.2 + - - +
555B GLU* 3.2 22.9 + - - +
556B TYR* 3.4 24.7 - - + -
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Residues in contact with PHE 553 (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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518B LEU* 4.9 6.7 - - + -
522B MET* 4.3 20.6 - - + -
526B PRO 5.5 1.3 - - - -
529B GLY 4.2 2.7 - - - -
530B GLN* 3.8 35.0 - - + -
533B ALA* 3.9 21.8 - - + -
549B ILE* 3.1 26.0 + - + -
550B VAL* 3.1 14.9 + - - +
552B VAL* 1.3 77.2 - - - +
554B MET* 1.3 62.4 + - - +
556B TYR* 3.2 9.7 + - - +
558B LEU* 3.1 47.7 + - + +
561B GLN* 4.6 11.0 - - + -
562B CYS* 3.9 24.5 - - + -
565B PHE* 4.0 21.8 - + - -
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Residues in contact with MET 554 (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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550B VAL* 2.9 21.9 + - + +
551B ASP* 3.7 14.6 - - + +
553B PHE* 1.3 74.9 - - - +
555B GLU* 1.3 64.5 + - - +
557B ASN* 3.0 21.9 + - - +
559B ILE* 4.5 35.0 - - + -
562B CYS* 4.7 11.4 - - - -
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Residues in contact with GLU 555 (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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519B ARG* 2.5 41.6 + - - -
551B ASP* 3.0 28.8 + - - +
552B VAL* 3.3 15.7 - - - +
553B PHE 3.2 0.2 - - - -
554B MET* 1.3 78.1 - - - +
556B TYR* 1.3 70.3 + - + +
557B ASN* 3.5 2.3 + - - +
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Residues in contact with TYR 556 (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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519B ARG* 3.6 11.3 + - + +
522B MET* 3.5 37.9 - - + -
523B ARG* 3.0 43.5 + - + +
552B VAL* 3.4 28.9 + - + -
553B PHE 3.2 5.1 + - - +
555B GLU* 1.3 86.1 - - + +
557B ASN* 1.3 71.5 + - - +
558B LEU* 3.5 25.4 - - + +
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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
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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