Contacts of the helix formed by residues 553 - 558 (chain B) in PDB entry 3ODX
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 GLN 553 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544B GLU* 3.3 29.3 + - + +
551B ARG 3.9 1.9 + - - +
552B LEU* 1.3 74.6 - - - +
554B LEU* 1.3 58.6 + - - +
555B LYS* 3.1 38.1 - - + -
556B ASP* 2.6 39.0 + - - +
557B MET* 3.1 13.6 + - - +
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Residues in contact with LEU 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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438B LEU* 3.5 29.8 - - + -
442B PHE* 3.7 33.0 - - + -
446B MET* 4.3 15.0 - - + -
461B PHE* 4.3 6.1 - - + -
526B LEU* 4.0 25.4 - - + -
530B GLN* 5.0 5.4 - - - +
540B VAL* 4.5 12.3 - - + -
544B GLU* 2.8 19.0 + - - +
553B GLN* 1.3 71.8 - - - +
555B LYS* 1.3 63.2 + - - +
557B MET* 3.1 17.7 + - - +
558B ILE* 3.3 25.6 + - + +
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Residues in contact with LYS 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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523B LEU* 4.0 22.9 - - + +
544B GLU* 4.4 1.0 + - - +
553B GLN* 3.1 33.0 - - + +
554B LEU* 1.3 79.6 - - - +
556B ASP* 1.3 70.8 + - - +
559B PRO* 2.8 25.6 - - - +
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Residues in contact with ASP 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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551B ARG 4.9 1.6 - - - +
552B LEU* 4.1 20.4 - - + +
553B GLN* 2.6 45.9 + - - +
555B LYS* 1.3 89.7 - - - +
557B MET* 1.3 56.3 + - - -
559B PRO* 3.5 12.4 - - - +
560B THR* 3.2 13.9 + - - -
563B GLN* 5.0 3.1 + - - +
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Residues in contact with MET 557 (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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434B MET* 3.5 27.6 - - + +
435B LEU* 6.0 0.3 - - - +
437B VAL* 4.3 12.8 - - + -
438B LEU* 4.2 24.5 - - + +
442B PHE* 4.2 19.5 - - + -
515B PHE* 5.7 0.3 - - - -
549B CYS* 3.8 29.2 - - + +
552B LEU* 3.2 40.8 - - + +
553B GLN 3.3 12.6 - - - +
554B LEU* 3.1 8.5 + - - +
556B ASP* 1.3 79.3 - - - +
558B ILE* 1.3 62.8 + - - +
559B PRO 3.3 0.4 - - - -
560B THR* 2.8 29.9 - - - +
561B GLU 4.3 0.3 + - - -
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Residues in contact with ILE 558 (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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438B LEU* 4.6 8.3 - - + -
460B ILE 5.5 0.9 - - - +
461B PHE* 3.9 22.0 - - + -
515B PHE* 3.9 25.6 - - + -
518B ARG 4.9 0.9 - - - +
519B GLN* 4.0 23.4 - - + +
522B ALA* 4.1 20.9 - - + -
523B LEU* 4.1 13.7 - - + -
526B LEU* 3.6 30.7 - - + -
554B LEU* 3.3 23.2 + - + +
557B MET* 1.3 78.2 - - - +
559B PRO* 1.3 68.4 - - + +
560B THR 3.3 0.3 + - - -
561B GLU* 3.7 6.9 + - - +
562B MET 4.8 0.2 + - - -
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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
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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