Contacts of the helix formed by residues 553 - 558 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A GLU* 3.3 30.8 + - + +
551A ARG 3.8 3.2 + - - +
552A LEU* 1.3 75.8 - - - +
554A LEU* 1.3 58.7 + - - +
555A LYS* 3.1 38.4 + - + +
556A ASP* 2.7 36.6 + - - +
557A MET* 2.9 15.4 + - - +
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Residues in contact with LEU 554 (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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438A LEU* 3.5 30.1 - - + -
442A PHE* 3.7 38.8 - - + -
446A MET* 4.3 13.5 - - + -
461A PHE* 4.5 3.8 - - + -
526A LEU* 3.7 33.2 - - + -
530A GLN* 4.8 5.2 - - - +
540A VAL* 4.8 9.4 - - + -
544A GLU* 2.7 20.2 + - - +
553A GLN* 1.3 70.3 - - - +
555A LYS* 1.3 64.3 + - - +
557A MET* 3.0 16.4 + - - +
558A ILE* 3.2 22.8 + - + +
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Residues in contact with LYS 555 (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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523A LEU* 4.0 25.9 - - + +
544A GLU* 4.2 0.8 + - - +
553A GLN* 3.1 31.9 + - + +
554A LEU* 1.3 81.0 - - - +
556A ASP* 1.3 70.2 + - - +
559A PRO* 3.0 24.9 - - - +
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Residues in contact with ASP 556 (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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551A ARG 4.6 2.1 - - - +
552A LEU* 4.0 21.7 - - + +
553A GLN* 2.7 47.2 + - - +
555A LYS* 1.3 86.8 - - - +
557A MET* 1.3 57.8 + - - +
559A PRO* 3.0 17.6 - - - +
560A THR* 3.6 12.5 - - - +
563A GLN* 5.6 0.9 + - - -
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Residues in contact with MET 557 (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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434A MET* 4.0 24.0 - - + +
435A LEU* 6.1 0.2 - - - +
437A VAL* 4.1 19.5 - - + -
438A LEU* 3.6 33.9 - - + +
442A PHE* 4.1 12.6 - - + -
549A CYS* 3.9 29.2 - - + +
552A LEU* 3.3 39.9 - - + +
553A GLN 2.9 9.8 + - - +
554A LEU* 3.0 8.9 + - - +
556A ASP* 1.3 75.5 - - - +
558A ILE* 1.3 67.1 + - - +
560A THR* 2.7 31.9 + - - -
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Residues in contact with ILE 558 (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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438A LEU* 4.5 6.3 - - + -
460A ILE 5.7 0.7 - - - +
461A PHE* 3.9 26.2 - - + -
515A PHE* 3.7 31.4 - - + -
519A GLN* 4.0 30.4 - - + +
522A ALA* 4.3 14.4 - - + -
523A LEU* 4.0 17.7 - - + -
526A LEU* 3.5 32.3 - - + -
554A LEU* 3.2 18.0 + - + +
557A MET* 1.3 75.6 - - - +
559A PRO* 1.3 64.6 - - + +
560A THR 3.1 4.7 + - - -
561A GLU* 3.9 3.5 + - - +
562A MET 5.1 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