Contacts of the helix formed by residues 487 - 492 (chain C) in PDB entry 5D4D
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 487 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C LEU 5.8 0.4 - - - -
329C GLY* 5.8 1.6 - - - -
437C ARG* 3.1 10.5 + - - +
462C ASP* 3.5 24.5 - - - +
466C PHE* 4.2 19.5 - - + -
467C ILE 4.1 4.5 - - - -
468C ARG* 3.6 23.2 - - + +
486C MET* 1.3 72.6 - - - +
488C ALA* 1.3 59.8 + - - +
489C THR* 3.6 8.8 + - - -
490C GLU* 3.4 22.3 + - + +
491C GLU 2.9 23.0 + - - -
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Residues in contact with ALA 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C HIS* 3.4 21.5 - - + -
328C LEU* 4.0 6.8 + - + -
329C GLY 3.7 15.9 - - - +
433C THR* 4.0 20.6 - - + +
437C ARG* 3.2 21.5 - - - +
467C ILE 4.6 0.4 + - - -
487C THR* 1.3 75.2 - - - +
489C THR* 1.3 58.3 + - - +
491C GLU* 3.3 5.5 + - - +
492C ASP* 3.0 32.4 + - - +
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Residues in contact with THR 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LYS* 5.7 3.8 - - - +
327C HIS* 3.8 10.5 - - + +
329C GLY* 3.7 21.7 + - - -
487C THR* 3.3 6.3 + - - -
488C ALA* 1.3 77.0 - - - +
490C GLU* 1.3 65.2 + - - +
492C ASP* 3.2 19.9 + - + +
493C ARG* 3.9 7.6 - - - +
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Residues in contact with GLU 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468C ARG* 5.8 4.7 - - - +
484C VAL* 5.2 4.0 - - - +
486C MET* 4.1 15.4 - - + +
487C THR* 3.4 25.2 + - + +
488C ALA 3.3 0.2 - - - -
489C THR* 1.3 76.5 - - - +
491C GLU* 1.3 65.1 + - - +
492C ASP 3.1 1.2 + - - -
493C ARG* 3.1 35.0 + - - +
494C TYR* 3.1 48.0 + - - -
531C PHE* 5.9 0.5 - - - -
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Residues in contact with GLU 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432C ARG* 5.6 2.3 + - - +
433C THR* 5.8 2.8 - - - -
435C TYR* 5.0 1.7 - - - +
437C ARG* 2.7 40.2 + - - +
471C TYR* 3.0 21.9 + - + +
486C MET* 4.0 17.4 - - + +
487C THR 2.9 17.2 + - - +
488C ALA* 3.6 5.6 - - - +
490C GLU* 1.3 76.3 - - - +
492C ASP* 1.3 60.2 + - - +
493C ARG 3.0 5.9 + - - -
494C TYR* 3.3 19.0 + - - +
496C ILE* 3.6 19.4 - - + +
516C ARG* 2.8 27.3 + - - -
518C LYS* 5.2 1.7 + - - -
519C GLY* 5.6 2.3 + - - -
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Residues in contact with ASP 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C HIS* 3.2 12.0 + - - -
432C ARG* 2.9 43.9 + - - -
433C THR* 5.0 0.2 - - - +
488C ALA 3.0 16.2 + - - +
489C THR* 3.3 17.2 - - + +
490C GLU 3.0 1.2 - - - -
491C GLU* 1.3 79.0 - - - +
493C ARG* 1.3 58.7 + - + +
494C TYR 3.4 1.7 + - - -
518C LYS* 3.1 54.8 + - + +
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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