Contacts of the strand formed by residues 479 - 481 (chain C) in PDB entry 1M7X
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 TYR 479 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ASN 2.8 28.0 + - - -
238C GLN 3.4 6.4 + - - -
239C PHE* 3.3 33.1 - + - -
243C ILE* 3.2 20.4 - - + +
454C VAL* 4.3 12.8 - - + -
455C THR 3.5 2.4 + - - -
456C MET* 3.3 31.8 - - + -
457C ALA* 3.0 23.2 + - - -
467C SER* 4.0 4.9 - - - -
477C PHE* 3.6 7.3 - - - +
478C TRP* 1.3 85.7 - - + +
480C LYS* 1.3 61.5 + - - +
518C ASN* 3.0 24.7 - - + +
519C PHE 4.4 0.7 - - - -
520C VAL* 3.8 20.0 - - + -
563C LYS* 3.9 9.9 - - + -
621C PHE* 3.8 18.6 - + - -
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Residues in contact with LYS 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C ALA 3.6 8.7 - - - +
459C GLU* 3.7 37.1 + - - +
461C THR 3.9 5.3 + - - -
462C ASP* 4.2 11.7 + - - +
463C PHE 3.8 9.3 + - - -
466C VAL* 3.7 40.5 - - + +
467C SER* 4.4 0.2 - - - -
479C TYR* 1.3 76.8 - - - +
481C TRP* 1.3 72.3 + - - +
517C GLU* 3.8 34.5 + - + +
518C ASN 3.0 7.7 + - - -
519C PHE* 2.9 43.4 - - + -
520C VAL* 3.2 3.6 + - - -
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Residues in contact with TRP 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C GLU* 3.7 9.6 - - - -
285C GLU* 3.6 13.3 + - - -
403C ARG* 3.2 51.4 - - + +
456C MET* 5.3 6.8 - - + +
457C ALA 3.1 24.0 + - - +
458C GLU* 4.2 14.6 - - + -
459C GLU 5.3 1.0 + - - +
480C LYS* 1.3 86.6 - - - +
482C ASN* 1.3 60.0 + - - +
483C LEU* 3.0 29.9 + - + +
519C PHE* 4.1 1.6 - - - -
520C VAL* 3.8 21.0 - - + +
522C PRO* 4.1 18.2 - - + -
524C SER* 3.2 38.1 - - - -
525C HIS* 5.1 1.1 - - - -
526C ASP* 5.0 5.6 - - - -
565C LEU* 3.6 26.8 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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